2023

Jähne, J., Le Thi, T., Blumenscheit, C., Schneider, A., Pham, T., Le Thi, P., Blom, J., Vater, J., Schweder, T., Lasch, P., others. (2023). Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds. Multidisciplinary Digital Publishing Institute.Volume 11(1), 168. DOI: 10.3389/fpls.2023.1194887

Riyanti, Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Riviani, R., Meinita, M., Schäberle, T., Harwoko, H.. (2023). Draft Genome Sequence of Sinomicrobium sp. Strain PAP. 21, Isolated from a Coast Sample of Papua, Indonesia. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 12(4), e01268--22 DOI: 10.1128/mra.01268-22.

Schröder, L., Rupp, O., Senkler, M., Rugen, N., Hohnjec, N., Goesmann, A., Küster, H., Braun, H.. (2023). The Viscum album Gene Space database. Frontiers.Volume 14, 1193122 DOI: 10.3389/fpls.2023.1193122.

Kremer, K., Meier, D., Theis, L., Miller, S., Rost-Nasshan, A., Naing, Y., Zarzycki, J., Paczia, N., Serrania, J., Blumenkamp, P., others. (2023). Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway. American Society for Microbiology 1752 N St., NW, Washington, DC DOI: https://doi.org/10.1128/aem.00238-23.

Pulami, D., Schwabe, L., Blom, J., Schwengers, O., Wilharm, G., Kämpfer, P., Glaeser, S.. (2023). Genomic plasticity and adaptive capacity of the quaternary alkyl-ammonium compound and copper tolerant Acinetobacter bohemicus strain QAC-21b isolated from pig manure. Springer International Publishing. DOI: 10.1007/s10482-022-01805-w

2022

Ren, Y., Chakraborty, T., Doijad, S., Falgenhauer, L., Falgenhauer, J., Goesmann, A., Hauschild, A., Schwengers, O., Heider, D.. (2022). Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Oxford University Press.Volume 38(2), 325--334.

Dardić, D., Böhringer, N., Plaza, A., Zubeil, F., Pohl, J., Sommer, S., Padva, L., Becker, J., Patras, M., Bill, M., others. (2022). Antidiabetic profiling of veramycins, polyketides accessible by biosynthesis, chemical synthesis and precursor-directed modification. Royal Society of Chemistry.Volume 9(6), 1604--1615.

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D (2022) Multi-label classification for multi-drug resistance prediction of Escherichia coli. Computational and structural biotechnology journal: 1264-1270, DOI:10.1016/j.csbj.2022.03.007

Dardić D, Böhringer N, Plaza A, Zubeil F, Pohl J, Sommer S, Padva L, Becker J, Patras MA, Bill M, Kurz M, Toti L, Görgens SW, Schuler SMM, Billion A, Schwengers O, Wohlfart P, Goesmann A, Tennagels N, Vilcinskas A, Hammann PE, Schäberle TF, Bauer A (2022) Antidiabetic profiling of veramycins, polyketides accessible by biosynthesis, chemical synthesis and precursor-directed modification. Organic Chemistry Frontiers, DOI:10.1039/D1QO01652K

Breuer J, Barth P, Noe Y, Shalamova L, Goesmann A, Weber F, Rossbach O (2022) What goes around comes around: Artificial circular RNAs bypass cellular antiviral responses. Mol Ther Nucleic Acids, DOI:10.1016/j.omtn.2022.04.017

Djahanschiri, Bardya AND Di Venanzio, Gisela AND Distel, Jesus S. AND Breisch, Jennifer AND Dieckmann, Marius Alfred AND Goesmann, Alexander AND Averhoff, Beate AND Göttig, Stephan AND Wilharm, Gottfried AND Feldman, Mario F. AND Ebersberger, Ingo. (2022). Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. Public Library of Science.Volume 18(6), 1-40. DOI: 10.1371/journal.pgen.1010020

Wittig, A., Miranda, F., Hölzer, M., Altenburg, T., Bartoszewicz, J., Beyvers, S., Dieckmann, M., Genske, U., Giese, S., Nowicka, M., Richard, H., Schiebenhoefer, H., Schmachtenberg, A., Sieben, P., Tang, M., Tembrockhaus, J., Renard, B., Fuchs, S.. (2022). CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Volume 38(17), 4223-4225. DOI: 10.1093/bioinformatics/btac411

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D (2022) Multi-label classification for multi-drug resistance prediction of Escherichia coli. Comput Struct Biotechnol J, DOI:10.1016/j.csbj.2022.03.007

Kuzmich S, Blumenkamp P, Meier D, Szadkowski D, Goesmann A, Becker A, Søgaard-Andersen L (2022) CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3',3'-cGAMP Nucleotide Levels during Development in Myxococcus xanthus. mBio, DOI:10.1128/mbio.00044-22

Berckx, F., Nguyen, T., Bandong, C., Lin, H., Yamanaka, T., Katayama, S., Wibberg, D., Blom, J., Kalinowski, J., Tateno, M., others. (2022). A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world. BioMed Central London.Volume 23(1), 602.  DOI: 10.1186/s12864-022-08838-5

Eisenberg, T., Mühldorfer, K., Erhard, M., Fawzy, A., Kehm, S., Ewers, C., Semmler, T., Blom, J., Lipski, A., Rau, J., others. (2022). Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix. Microbiology Society.Volume 72(7), 005454. DOI: 10.1099/ijsem.0.005454

Entfellner, E., Li, R., Jiang, Y., Ru, J., Blom, J., Deng, L., Kurmayer, R.. (2022). Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix. Frontiers Media SA.Volume 13. DOI: 10.3389/fmicb.2022.901762

Kämpfer, P., Glaeser, S., Blom, J., Wolf, J., Benning, S., Schloter, M., Neumann-Schaal, M.. (2022). Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks. Springer Berlin Heidelberg Berlin/Heidelberg.Volume 204(8), 505. DOI: 10.1007/s00203-022-03079-2

Fatton, M., Filippidou, S., Junier, T., Cailleau, G., Berge, M., Poppleton, D., Blum, T., Kaminek, M., Odriozola, A., Blom, J., others. (2022). Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. John Wiley \& Sons, Inc. Hoboken, USA.Volume 24(12), 6320--6335. DOI: 10.1007/s00203-022-03079-2

Guzman, J., Poehlein, A., Glaeser, S., Schwengers, O., Blom, J., Hollensteiner, J., Kämpfer, P., Vilcinskas, A.. (2022). Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica. Microbiology Society.Volume 72(8), 005497. DOI: 10.1099/ijsem.0.005497

Sulja, A., Pothier, J., Blom, J., Moretti, C., Buonaurio, R., Rezzonico, F., Smits, T.. (2022). Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734. BioMed Central London.Volume 23(1), 742. DOI: 10.1186/s12864-022-08966-y

Maus, I., Wibberg, D., Belmann, P., Hahnke, S., Huang, L., Spröer, C., Bunk, B., Blom, J., Sczyrba, A., Pühler, A., others. (2022). The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses. Frontiers Media SA.Volume 13.  DOI: 10.3389/fmicb.2022.1032515

Zboralski, A., Biessy, A., Ciotola, M., Cadieux, M., Albert, D., Blom, J., Filion, M.. (2022). Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens. Frontiers Media SA.Volume 13. DOI: 10.3389/fmicb.2022.1038888

Volokhov, D., Furtak, V., Blom, J., Zagorodnyaya, T., Gao, Y., Gulland, F.. (2022). Mycoplasma miroungirhinis sp. nov. and Mycoplasma miroungigenitalium sp. nov., isolated from northern elephant seals (Mirounga angustirostris), Mycoplasma phocoenae sp. nov., isolated from harbour porpoise (Phocoena phocoena), and Mycoplasma phocoeninasale sp. nov., isolated from harbour porpoise and California sea lions (Zalophus californianus). Microbiology Society.Volume 72(1), 005224. DOI: 10.1099/ijsem.0.005224

Blumenscheit, C., Jähne, J., Schneider, A., Blom, J., Schweder, T., Lasch, P., Borriss, R.. (2022). Genome sequence data of Bacillus velezensis BP1. 2A and BT2. 4. Elsevier.Volume 41, 107978. DOI: 10.1016/j.dib.2022.107978

Lau Vetter, M., Huang, B., Fenske, L., Blom, J.. (2022). Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. MDPI.Volume 10(4), 724. DOI: 10.3390/microorganisms10040724

Ruinelli, M., Blom, J., Smits, T., Pothier, J.. (2022). Comparative genomics of Prunus-associated members of the Pseudomonas syringae species complex reveals traits supporting co-evolution and host adaptation. Frontiers Research Foundation.Volume 13(804681). DOI: 10.3389/fmicb.2022.804681

Fenske, L., Noll, I., Blom, J., Ewers, C., Semmler, T., Fawzy, A., Eisenberg, T.. (2022). A dominant clonal lineage of Streptococcus uberis in cattle in Germany. Springer International Publishing. DOI: 10.1007/s10482-022-01740-w

Neuzil-Bunesova, V., Ramirez Garcia, A., Modrackova, N., Makovska, M., Sabolova, M., Spröer, C., Bunk, B., Blom, J., Schwab, C.. (2022). Feed Insects as a Reservoir of Granadaene-Producing Lactococci. Frontiers. DOI: 10.3389/fmicb.2022.848490

Dia, N., Cottyn, B., Blom, J., Smits, T., Pothier, J.. (2022). Differentiation of the Xanthomonas hortorum--Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays. Frontiers Research Foundation.Volume 4(898778). DOI: 10.3389/fagro.2022.898778

Wittig, A., Miranda, F., Hölzer, M., Altenburg, T., Bartoszewicz, J., Beyvers, S., Dieckmann, M., Genske, U., Giese, S., Nowicka, M., others. (2022). CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Oxford University Press.Volume 38(17), 4223--4225. DOI: 10.1093/bioinformatics/btac411

Hurka, S., Lüddecke, T., Paas, A., Dersch, L., Schulte, L., Eichberg, J., Hardes, K., Brinkrolf, K., Vilcinskas, A.. (2022). Bioactivity Profiling of In Silico Predicted Linear Toxins from the Ants Myrmica rubra and Myrmica ruginodis. Multidisciplinary Digital Publishing Institute.Volume 14(12), 846. DOI: 10.3390/toxins14120846

Hurka, S., Brinkrolf, K., Özbek, R., Förster, F., Billion, A., Heep, J., Timm, T., Lochnit, G., Vilcinskas, A., Lüddecke, T.. (2022). Venomics of the Central European Myrmicine Ants Myrmica rubra and Myrmica ruginodis. MDPI.Volume 14(5), 358. DOI: 10.3390/toxins14050358

Fenske, L., Noll, I., Blom, J., Ewers, C., Semmler, T., Fawzy, A., Eisenberg, T.. (2022). A dominant clonal lineage of Streptococcus uberis in cattle in Germany. Antonie van Leeuwenhoek. Volume 115, 857–870.
DOI: s10482-022-01740-w

Fawzy, A., Giel, A., Fenske, L., Bach, A., Herden, C., Engel, K., Heuser, E., Boelhauve, M., Ulrich, R., Vogel, K., Schmidt, K., Eisenberg, T.. (2022). Development and validation of a triplex real-time qPCR for sensitive detection and quantification of major rat bite fever pathogen Streptobacillus moniliformis. J Microbiol Methods. Volume 199, 106525 DOI: 10.1016/j.mimet.2022.106525

Lau Vetter, M., Huang, B., Fenske, L., Blom, J.. (2022). Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. MDPI. Volume 10(4), 724. DOI: 10.3390/microorganisms10040724

Octaviana, S., Lorenczyk Stefan, Ackert, F., Fenske, L., Wink, J.. (2022). Four new members of the family Cytophagaceae: Chryseosolibacter histidini gen. nov., sp. nov., Chryseosolibacter indicus gen. nov., sp. nov., Dawidia cretensis, gen. nov., sp. nov., and Dawidia soli, gen. nov., sp. nov. isolated from diverse habitat . Antonie van Leeuwenhoek. Volume 115(8), 1059–1072. DOI: 10.1007/s10482-022-01756-2

Kupschus J, Janssen S, Hoek A, Kuska J, Rathjens J, Sonntag C, Ickstadt K, Budzinski L, Chang H-D, Rossi A, Esser C, Hochrath K, 2022. Rapid detection and online analysis of microbial changes through flow cytometry. Cytometry Part A, DOI: 10.1002/cyto.a.24704

2021

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial genomics 7(11), DOI:10.1099/mgen.0.000685

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild A, Schwengers O, Heider D (2021) Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics, DOI:10.1093/bioinformatics/btab681

Pulami D, Schauss T, Eisenberg T, Blom J, Schwengers O, Bender JK, Wilharm G, Kämpfer P, Glaeser SP (2021) Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions. Antonie van Leeuwenhoek 114(3): 235-251, DOI:10.1007/s10482-021-01517-7

Mahmoud W, Perniss A, Poharkar K, Soultanova A, Pfeil U, Hoek A, Bhushan S, Hain T, Gärtner U, Kummer W, 2021. CXCL13 is expressed in a subpopulation of neuroendocrine cells in the murine trachea and lung Cell Tissue Res. DOI: 10.1007/s00441-021-03552-2

Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A, 2021. WASP: a versatile, web-accessible single cell RNA-Seq processing platform. BMC Genomics. DOI: 10.1186/s12864-021-07469-6

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom, DOI:10.1099/mgen.0.000685

Dieckmann, M., Beyvers, S., Nkouamedjo-Fankep, R., Hanel, P., Jelonek, L., Blom, J., Goesmann, A.. (2021). EDGAR3. 0: comparative genomics and phylogenomics on a scalable infrastructure. Oxford University Press.Volume 49(W1), W185--W192. DOI: 10.1093/nar/gkab341

Dieckmann, M., Beyvers, S., Nkouamedjo-Fankep, R., Hanel, P., Jelonek, L., Blom, J., Goesmann, A.. (2021). EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Volume 49(W1), W185-W192. DOI: 10.1093/nar/gkab341

Schwengers, O., Jelonek, L., Dieckmann, M., Beyvers, S., Blom, J., Goesmann, Alexander. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbiology Society.Volume 7(11).  DOI: 10.1099/mgen.0.000685

Brinkrolf, K., Shukla, S., Griep, S., Rupp, O., Heise, P., Goesmann, A., Heckel, D., Vogel, H., Vilcinskas, A.. (2021). Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. Springer.Volume 22(1), 323. DOI: https://doi.org/10.1186/s12864-021-07597-z

Tegtmeier, D., Hurka, S., Klüber, P., Brinkrolf, K., Heise, P., Vilcinskas, A.. (2021). Cottonseed press cake as a potential diet for industrially farmed black soldier fly larvae triggers adaptations of their bacterial and fungal gut microbiota. Frontiers Media SA.Volume 12, 634503. DOI: 10.3389/fmicb.2021.634503

Schwabe, M., Griep, S., Schmidtberg, H., Plarre, R., Goesmann, A., Vilcinskas, A., Vogel, H., Brinkrolf, K.. (2021). Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion. MDPI.Volume 12(8), 1113. DOI: 10.3390/genes12081113

Casas-Pastor, D., Müller, R., Jaenicke, S., Brinkrolf, K., Becker, A., Buttner, M., Gross, C., Mascher, T., Goesmann, A., Fritz, G.. (2021). Expansion and re-classification of the extracytoplasmic function (ECF) $\sigma$ factor family. Oxford University Press.Volume 49(2), 986--1005. DOI: 10.1093/nar/gkaa1229

Schwengers, O., Jelonek, L., Dieckmann, M., Beyvers, S., Blom, J., Goesmann, A.. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbiology Society.Volume 7(11). DOI: 10.1099/mgen.0.000685

Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A (2021) Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14. J Fungi (Basel), DOI:10.3390/jof7100832

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild AC, Schwengers O, Heider D (2021) Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics, DOI:10.1093/bioinformatics/btab681

Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol, DOI:10.1093/gbe/evab204

Schwabe M, Griep S, Schmidtberg H, Plarre R, Goesmann A, Vilcinskas A, Vogel H, Brinkrolf K (2021) Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion. Genes (Basel), DOI:10.3390/genes12081113

Kwon S, Rupp O, Brachmann A, Blum CF, Kraege A, Goesmann A, Feldbrügge M (2021) mRNA Inventory of Extracellular Vesicles from Ustilago maydis. J Fungi (Basel), DOI:10.3390/jof7070562

Schölzel C, Blesius V, Ernst G, Goesmann A, Dominik A (2021) Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PLoS One, DOI:10.1371/journal.pone.0254749

Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L (2021) Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. Int J Syst Evol Microbiol, DOI:10.1099/ijsem.0.004822

Masello JF, Barbosa A, Kato A, Mattern T, Medeiros R, Stockdale JE, Kümmel MN, Bustamante P, Belliure J, Benzal J, Colominas-Ciuró R, Menéndez-Blázquez J, Griep S, Goesmann A, Symondson WOC, Quillfeldt P (2021) How animals distribute themselves in space: energy landscapes of Antarctic avian predators. Mov Ecol, DOI:10.1186/s40462-021-00255-9

Dieckmann MA, Beyvers S, Nkouamedjo-Fankep RC, Hanel PHG, Jelonek L, Blom J, Goesmann A (2021) EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Nucleic Acids Res, DOI:10.1093/nar/gkab341

Brinkrolf K, Shukla SP, Griep S, Rupp O, Heise P, Goesmann A, Heckel DG, Vogel H, Vilcinskas A (2021) Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. BMC Genomics, DOI:10.1186/s12864-021-07597-z

Nechitaylo TY, Sandoval-Calderón M, Engl T, Wielsch N, Dunn DM, Goesmann A, Strohm E, Svatoš A, Dale C, Weiss RB, Kaltenpoth M (2021) Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. Proc Natl Acad Sci USA, DOI:10.1073/pnas.2023047118

Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A (2021) WASP: a versatile, web-accessible single cell RNA-Seq processing platform. BMC Genomics, DOI:10.1186/s12864-021-07469-6

Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L (2021) Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Int J Syst Evol Microbiol, DOI:10.1099/ijsem.0.004652

Blifernez-Klassen O, Klassen V, Wibberg D, Cebeci E, Henke C, Rückert C, Chaudhari S, Rupp O, Blom J, Winkler A, Al-Dilaimi A, Goesmann A, Sczyrba A, Kalinowski J, Bräutigam A, Kruse O (2021) Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Sci Rep, DOI:10.1038/s41598-021-81082-1

Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G (2021) Expansion and re-classification of the extracytoplasmic function (ECF) sigma factor family. Nucleic Acids Research, DOI:10.1093/nar/gkaa1229

Blifernez-Klassen, O., Klassen, V., Wibberg, D., Cebeci, E., Henke, C., Rückert, C., Chaudhari, S., Rupp, O., Blom, J., Winkler, A., others. (2021). Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Nature Publishing Group.Volume 11(1), 1--13. DOI: 10.1038/s41598-021-81082-1

Berger, C., Rückert, C., Blom, J., Rabaey, K., Kalinowski, J., Rosenbaum, M.. (2021). Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Nature Publishing Group.Volume 11(1), 1--14. DOI: 10.1038/s41598-020-80592-8

Khilyas, I., Sorokina, A., Markelova, M., Belenikin, M., Shafigullina, L., Tukhbatova, R., Shagimardanova, E., Blom, J., Sharipova, M., Cohen, M.. (2021). Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment. Springer Berlin Heidelberg.Volume 203(2), 855--860. DOI: 10.1007/s00203-020-02057-w

Glaeser, S., Rückert, C., Abdelmohsen, U., Winkler, A., Blom, J., Goesmann, A., Kalinowski, J., Hentschel, U., Busse, H., Kämpfer, P.. (2021). Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha. Microbiology Society.Volume 71(3), 004672. DOI: 10.1099/ijsem.0.004672

Naorem, R., Blom, J., Fekete, C.. (2021). Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PeerJ Inc..Volume 9, e10185. DOI: 10.7717/peerj.10185

Lick, S., Wibberg, D., Winkler, A., Blom, J., Grimmler, C., Goesmann, A., Kalinowski, J., Kröckel, L.. (2021). Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Microbiology Society.Volume 71(2), 004652. DOI: 10.1099/ijsem.0.004652

Pulami, D., Schauss, T., Eisenberg, T., Blom, J., Schwengers, O., Bender, J., Wilharm, G., Kämpfer, P., Glaeser, S.. (2021). Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions. Springer International Publishing.Volume 114(3), 235--251. DOI: 10.1007/s10482-021-01517-7

Eisenberg, T., Gronow, S., Falgenhauer, J., Imirzalioglu, C., Mühldorfer, K., Rau, J., Blom, J., Fawzy, A., Glaeser, S., Kämpfer, P.. (2021). Sneathia vaginalis sp. nov.(Fusobacteriales, Leptotrichiaceae) as a replacement of the species ‘Sneathia amnii’Harwich et al. 2012 and ‘Leptotrichia amnionii’Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001. Microbiology Society.Volume 71(3), 004663. DOI: 10.1099/ijsem.0.004663

Fernandes, C., Martins, L., Teixeira, M., Blom, J., Pothier, J., Fonseca, N., Tavares, F.. (2021). Comparative genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis strains isolated from a single walnut host tree. MDPI.Volume 9(3), 624. DOI: 10.3390/microorganisms9030624

Panthee, S., Paudel, A., Hamamoto, H., Ogasawara, A., Iwasa, T., Blom, J., Sekimizu, K.. (2021). Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Academic Press.Volume 113(3), 1534--1542. DOI: 10.1016/j.ygeno.2021.03.021

Dieckmann, M., Beyvers, S., Nkouamedjo-Fankep, R., Hanel, P., Jelonek, L., Blom, J., Goesmann, A.. (2021). EDGAR3. 0: comparative genomics and phylogenomics on a scalable infrastructure. Oxford University Press.Volume 49(W1), W185--W192. DOI:10.1093/nar/gkab341

Volokhov, D., Zagorodnyaya, T., Shen, Z., Blom, J., Furtak, V., Eisenberg, T., Fan, P., Jeong, K., Gao, Y., Zhang, S., others. (2021). Streptococcus vicugnae sp. nov., isolated from faeces of alpacas (Vicugna pacos) and cattle (Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions (Zalophus californianus). Microbiology Society.Volume 71(5), 004826. DOI: 10.1099/ijsem.0.004826

Lick, S., Wibberg, D., Winkler, A., Blom, J., Grimmler, C., Goesmann, A., Kalinowski, J., Kröckel, L.. (2021). Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. Microbiology Society.Volume 71(6), 004822. DOI: 10.1099/ijsem.0.004822

Talamantes-Becerra, B., Carling, J., Blom, J., Georges, A.. (2021). Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov. Cold Spring Harbor Laboratory. DOI: 10.1101/2021.06.18.449068

Hudec, C., Biessy, A., Novinscak, A., St-Onge, R., Lamarre, S., Blom, J., Filion, M.. (2021). Comparative genomics of potato common scab-causing Streptomyces spp. displaying varying virulence. Frontiers Media SA.Volume 12. DOI: 10.3389/fmicb.2021.716522

Stitz, M., Chaparro, C., Lu, Z., Olzog, V., Weinberg, C., Blom, J., Goesmann, A., Grunau, C., Grevelding, C.. (2021). Satellite-like W-elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni. Oxford University Press.Volume 13(10), evab204. DOI: 10.1093/gbe/evab204

Schwengers, O., Jelonek, L., Dieckmann, M., Beyvers, S., Blom, J., Goesmann, A.. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbiology Society.Volume 7(11). DOI: 10.1099/mgen.0.000685

Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., Grosch, R., Pühler, A., Schlüter, A.. (2021). Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14. MDPI.Volume 7(10), 832. DOI: 10.3390/jof7100832

Van Le, V., Ko, S., Lee, S., Jin, L., Blom, J., Ahn, C., Oh, H.. (2021). Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. Microbiology Society.Volume 71(11), 005124. DOI: 10.1099/ijsem.0.005124

Dia, N., Van Vaerenbergh, J., Van Malderghem, C., Blom, J., Smits, T., Cottyn, B., Pothier, J.. (2021). Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Microbiology Society.Volume 71(12), 005163. DOI: 10.1099/ijsem.0.005163

Dia, N., Van Vaerenbergh, J., Van Malderghem, C., Blom, J., Smits, T., Cottyn, B., Pothier, J.. (2021). Xanthomonas hydrangeae sp: nov. Microbiology Society.Volume 71(12). DOI: 10.1099/ijsem.0.005163

Shaban, M., Müller, C., {Mayr-Buro}, C., Weiser, H., {Meier-Soelch}, J., Albert, B., Weber, A., Linne, U., Hain, T., Babayev, I., Karl, N., Hofmann, N., Becker, S., Herold, S., Schmitz, M., Ziebuhr, J., Kracht, M.. (2021). Multi-Level Inhibition of Coronavirus Replication by Chemical ER Stress. Volume 12(1), 5536. DOI: s41467-021-25551-1

Gerz U., Pfister M. (2021). Deutlich kürzere Bearbeitungszeit von Videos durch ein „MotionDetection-Programm“ – Eine einfache Methode und Anwendung zur Ermittlung der Kotsäckchenanzahl bei Nistkastenaufnahmen von Kohlmeisen Parus major. Vogelwarte. Volume 59(4), 375–382. 

2020

Biedenkopf D, Will T, Knauer T, Jelonek L, Furch ACU, Busche T, Koch A (2020) Systemic spreading of exogenous applied RNA biopesticides in the crop plant Hordeum vulgare. ExRNA 2(1), DOI:10.1186/s41544-020-00052-3

Höfle L, Biedenkopf D, Werner BT, Shrestha A, Jelonek L, Koch A (2020) Study on the efficiency of dsRNAs with increasing length in RNA-based silencing of the Fusarium CYP51 genes. RNA Biology 17(4): 463-473, DOI:10.1080/15476286.2019.1700033

Sauerhering, L., Kupke, A., Meier, L., Dietzel, E., Hoppe, J., Gruber, A., Gattenloehner, S., Witte, B., Fink, L., Hofmann, N., Zimmermann, T., Goesmann, A., Nist, A., Stiewe, T., Becker, S., Herold, S., Peteranderl, C.. (2020). Cyclophilin Inhibitors Restrict Middle East Respiratory Syndrome Coronavirus Interferon-λ in Vitro and in Mice. Volume 56(5), 1901826. DOI: 10.1183/13993003.01826-2019

Bathke J, Gauernack AS, Rupp O, Weber L, Preusser C, Lechner M, Rossbach O, Goesmann A, Evguenieva-Hackenberg E, Klug G (2020) iCLIP analysis of RNA substrates of the archaeal exosome. BMC Genomics, DOI:10.1186/s12864-020-07200-x

Lick, S., Kröckel, L., Wibberg, D., Winkler, A., Blom, J., Goesmann, A., Kalinowski, J.. (2020). Pseudomonas bubulae sp. nov., isolated from beef. Microbiology Society.Volume 70(1), 292--301. DOI: 10.1099/ijsem.0.003751

Madhaiyan, M., Saravanan, V., Blom, J., Smits, T., Rezzonico, F., Kim, S., Weon, H., Kwon, S., Whitman, W., Ji, L.. (2020). Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Microbiology Society.Volume 70(2), 841--848. DOI: 10.1099/ijsem.0.003834

Kämpfer, P., Fuglsang-Damgaard, D., Overballe-Petersen, S., Hasman, H., Hammerum, A., Fuursted, K., Blom, J., Glaeser, S., Hansen, F.. (2020). Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov.. Microbiology Society.Volume 70(2), 1315--1320. DOI: 10.1099/ijsem.0.003918

Lick, S., Kröckel, L., Wibberg, D., Winkler, A., Blom, J., Bantleon, A., Goesmann, A., Kalinowski, J.. (2020). Pseudomonas carnis sp. nov., isolated from meat. Microbiology Society.Volume 70(3), 1528--1540. DOI: 10.1099/ijsem.0.003928

Wu, L., Li, X., Ma, L., Blom, J., Wu, H., Gu, Q., Borriss, R., Gao, X.. (2020). The “pseudo-pathogenic” effect of plant growth-promoting bacilli on starchy plant storage organs is due to their $\alpha$-amylase activity which is stimulating endogenous opportunistic pathogens. Springer Berlin Heidelberg.Volume 104(6), 2701--2714. DOI: 10.1007/s00253-020-10367-8

Kumru, S., Tekedar, H., Blom, J., Lawrence, M., Karsi, A.. (2020). Genomic diversity in flavobacterial pathogens of aquatic origin. Academic Press.Volume 142, 104053. DOI: 10.1016/j.micpath.2020.104053

Tekedar, H., Blom, J., Kalindamar, S., Nho, S., Karsi, A., Lawrence, M.. (2020). Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. Microbiology Society.Volume 6(2). DOI: 10.1099/mgen.0.000322

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2020). Proposal to reclassify Leptotrichia goodfellowii into a novel genus as Pseudoleptotrichia goodfellowii gen. nov., comb. nov.. Microbiology Society.Volume 70(3), 2084--2088. DOI: 10.1099/ijsem.0.004024

Maus, I., Klocke, M., Derenkó, J., Stolze, Y., Beckstette, M., Jost, C., Wibberg, D., Blom, J., Henke, C., Willenbücher, K., others. (2020). Impact of process temperature and organic loading rate on cellulolytic/hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics. BioMed Central.Volume 15(1), 1--21. DOI: 10.1186/s40793-020-00354-x

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2020). Proposal to reclassify Streptobacillus hongkongensis into a novel genus as Pseudostreptobacillus hongkongensis gen. nov., comb. nov.. Microbiology Society.Volume 70(4), 2366--2368. DOI: 10.1099/ijsem.0.004051

Eisenberg, T., Heydel, C., Prenger-Berninghoff, E., Fawzy, A., Kling, U., Akimkin, V., Semmler, T., Mühldorfer, K., Kämpfer, P., Blom, J., others. (2020). Streptobacillus canis sp. nov. isolated from a dog. Microbiology Society.Volume 70(4), 2648--2656. DOI: 10.1099/ijsem.0.004086

Liu, Y., Rao, Q., Blom, J., Lin, Q., Luo, T.. (2020). Pseudomonas piscis sp. nov., isolated from the profound head ulcers of farmed Murray cod (Maccullochella peelii peelii). Microbiology Society.Volume 70(4), 2732--2739. DOI: 10.1099/ijsem.0.004101

Liu, A., Zhang, Y., Cheng, P., Peng, Y., Blom, J., Xue, Q.. (2020). Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia. Springer International Publishing.Volume 113(7), 919--931. DOI: 10.1007/s10482-020-01405-6

Volokhov, D., Blom, J., Amselle, M., Delmonte, P., Gao, Y., Shen, Z., Zhang, S., Gulland, F., Chizhikov, V., Eisenberg, T.. (2020). Oceanivirga miroungae sp. nov., isolated from oral cavity of northern elephant seal (Mirounga angustirostris). Microbiology Society.Volume 70(5), 3037--3048. DOI: 10.1099/ijsem.0.004127

Palmer, M., Steenkamp, E., Blom, J., Hedlund, B., Venter, S.. (2020). All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Microbiology Society.Volume 70(4), 2937--2948. DOI: 10.1099/ijsem.0.004124

Huang, C., Chen, C., Liou, J., Lee, A., Blom, J., Lin, Y., Huang, L., Watanabe, K.. (2020). Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. Microbiology Society.Volume 70(6), 3755--3762. DOI: 10.1099/ijsem.0.003969

Rothen, J., Sapugahawatte, D., Li, C., Lo, N., Vogel, G., Foucault, F., Pflüger, V., Pothier, J., Blom, J., Daubenberger, C., others. (2020). A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS. Nature Publishing Group.Volume 10(1), 1--8. DOI: 10.1038/s41598-020-65707-5

Tekedar, H., Arick, M., Hsu, C., Thrash, A., Blom, J., Lawrence, M., Abdelhamed, H.. (2020). Identification of antimicrobial resistance determinants in Aeromonas veronii strain MS-17-88 recovered from channel catfish (Ictalurus punctatus). Frontiers Media SA.Volume 10, 348. DOI: 10.3389/fcimb.2020.00348

Filippidou, S., Fatton, M., Junier, T., Berge, M., Poppleton, D., Blum, T., Kaminek, M., Odriozola, A., Blom, J., Johnson, S., others. (2020). Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. Cold Spring Harbor Laboratory. DOI: 10.1111/1462-2920.16145

Franco, A., Rückert, C., Blom, J., Busche, T., Reichert, J., Schubert, P., Goesmann, A., Kalinowski, J., Wilke, T., Kämpfer, P., others. (2020). High diversity of Vibrio spp. associated with different ecological niches in a marine aquaria system and description of Vibrio aquimaris sp. nov. Urban \& Fischer.Volume 43(5), 126123. DOI: 10.1016/j.syapm.2020.126123

Eisenberg, T., Schlez, K., Fawzy, A., Völker, I., Hechinger, S., Curić, M., Schauerte, N., Geiger, C., Blom, J., Scholz, H.. (2020). Expanding the host range: infection of a reptilian host (Furcifer pardalis) by an atypical Brucella strain. Springer International Publishing.Volume 113(10), 1531--1537. DOI: 10.1007/s10482-020-01448-9

Liou, J., Huang, C., Ikeyama, N., Lee, A., Chen, I., Blom, J., Chen, C., Chen, C., Lin, Y., Hsieh, S., others. (2020). Prevotella hominis sp. nov., isolated from human faeces. Microbiology Society.Volume 70(8), 4767--4773. DOI: 10.1099/ijsem.0.004342

Gétaz, M., Blom, J., Smits, T., Pothier, J.. (2020). Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra-and interspecies variations. BioMed Central.Volume 2(1), 1--19. DOI: 10.1186/s42483-020-00061-y

Rocha, D., Azevedo, V., Brenig, B., Silva, A., Blom, J., Ramos, R., Aguiar, E., Chapartegui-González, I., Fernández-Martínez, M., Martínez-Martínez, L., others. (2020). Whole-genome sequencing reveals misidentification of a multidrug-resistant urine clinical isolate as Corynebacterium urealyticum. Elsevier.Volume 23, 16--19. DOI: 10.1016/j.jgar.2020.07.020

Fawzy, A., Rau, J., Riße, K., Schauerte, N., Geiger, C., Blom, J., Imirzalioglu, C., Falgenhauer, J., Bach, A., Herden, C., others. (2020). Streptobacillus felis, a member of the oropharynx microbiota of the Felidae, isolated from a tropical rusty-spotted cat. Springer International Publishing.Volume 113(10), 1455--1465. DOI: 10.1007/s10482-020-01454-x

Clawson, M., Schuller, G., Dickey, A., Bono, J., Murray, R., Sweeney, M., Apley, M., DeDonder, K., Capik, S., Larson, R., others. (2020). Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BioMed Central.Volume 20(1), 1--18. DOI: 10.1186/s12866-020-01932-2

Pulami, D., Schauss, T., Eisenberg, T., Wilharm, G., Blom, J., Goesmann, A., Kämpfer, P., Glaeser, S.. (2020). Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. Oxford University Press.Volume 96(10), fiaa176. DOI: 10.1093/femsec/fiaa176

Glaeser, S., Pulami, D., Blom, J., Eisenberg, T., Goesmann, A., Bender, J., Wilharm, G., Kämpfer, P.. (2020). The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992). Microbiology Society.Volume 70(9), 5165--5171. DOI: 10.1099/ijsem.0.004404

Martins, L., Fernandes, C., Blom, J., Dia, N., Pothier, J., Tavares, F.. (2020). Xanthomonas euroxanthea sp. nov., a new xanthomonad species including pathogenic and non-pathogenic strains of walnut. Microbiology Society.Volume 70(12), 6024. DOI: 10.1099/ijsem.0.004386

Mühldorfer, K., Szentiks, C., Wibbelt, G., van der Linden, M., Ewers, C., Semmler, T., Akimkin, V., Blom, J., Rau, J., Eisenberg, T.. (2020). Streptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries (Catagonus wagneri). Microbiology Society.Volume 70(11), 5734--5739. DOI: 10.1099/ijsem.0.004471

Herrera-Belaroussi, A., Normand, P., Pawlowski, K., Fernandez, M., Wibberg, D., Kalinowski, J., Brachmann, A., Berckx, F., Lee, N., Blom, J., others. (2020). Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta. Urban \& Fischer.Volume 43(6), 126134. DOI: 10.1016/j.syapm.2020.126134

Wibberg, D., Price-Carter, M., Rückert, C., Blom, J., Möbius, P.. (2020). Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. MDPI.Volume 9(1), 70. DOI: 10.3390/microorganisms9010070

Vazquez-Armendariz AI, Heiner M, El Agha E, Salwig I, Hoek A, Hessler MC, Shalashova I, Shrestha A, Carraro G, Mengel JP, Günther A, Morty RE, Vadász I, Schwemmle M, Kummer W, Hain T, Goesmann A, Bellusci S, Seeger W, Braun T, Herold S (2020) Multilineage murine stem cells generate complex organoids to model distal lung development and disease. EMBO J, DOI:10.15252/embj.2019103476

Franco A, Rückert C, Blom J, Busche T, Reichert J, Schubert P, Goesmann A, Kalinowski J, Wilke T, Kämpfer P, Glaeser SP (2020) High diversity of Vibrio spp. associated with different ecological niches in a marine aquaria system and description of Vibrio aquimaris sp. nov. Syst Appl Microbiol, DOI:10.1016/j.syapm.2020.126123

Glaeser SP, Pulami D, Blom J, Eisenberg T, Goesmann A, Bender J, Wilharm G, Kämpfer P (2020) The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992). Int J Syst Evol Microbiol, DOI:10.1099/ijsem.0.004404

Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, Kämpfer P, Glaeser SP (2020) Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol, DOI:10.1093/femsec/fiaa176

Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J (2020) Pseudomonas bubulae sp. Nov., isolated from beef. International Journal of Systematic and Evolutionary Microbiology 70(1): 292-301, DOI:10.1099/ijsem.0.003751

Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Bantleon A, Goesmann A, Kalinowski J (2020) Pseudomonas carnis sp. Nov., isolated from meat. International Journal of Systematic and Evolutionary Microbiology 70(3): 1528-1540, DOI:10.1099/ijsem.0.003928

Sauerhering L, Kupke A, Meier L, Dietzel E, Hoppe J, Gruber AD, Gattenloehner S, Witte B, Fink L, Hofmann N, Zimmermann T, Goesmann A, Nist A, Stiewe T, Becker S, Herold S, Peteranderl C (2020) Cyclophilin Inhibitors Restrict Middle East Respiratory Syndrome Coronavirus Via Interferon λ In Vitro And In Mice. European Respiratory Journal: 1901826, DOI:10.1183/13993003.01826-2019

Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial genomics, DOI:10.1099/mgen.0.000398

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS computational biology 16(3): e1007134, DOI:10.1371/journal.pcbi.1007134

Vilcinskas, A., Schwabe, M., Brinkrolf, K., Plarre, R., Wielsch, N., Vogel, H.. (2020). Larvae of the clothing moth Tineola bisselliella maintain gut bacteria that secrete enzyme cocktails to facilitate the digestion of keratin. MDPI.Volume 8(9), 1415. DOI: 10.3390/microorganisms8091415

Vazquez-Armendariz AI, Heiner M, El Agha E, Salwig I, Hoek A, Hessler MC, Shalashova I, Shrestha A, Carraro G, Mengel JP, Günther A, Morty RE, Vadász I, Schwemmle M, Kummer W, Hain T, Goesmann A, Bellusci S, Seeger W, Braun T, Herold S, 2020. Multilineage murine stem cells generate complex organoids to model distal lung development and disease. EMBO J. DOI: 10.15252/embj.2019103476

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A, 2020. ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol DOI: 10.1371/journal.pcbi.1007134

Lori, M., Piton, G., Symanczik, S., Legay, N., Brussaard, L., Jaenicke, S., Nascimento, E., Reis, F., Sousa, J.P., Mäder, P. and others, 2020. Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes. Scientific Reports, 10(1), pp.1-15.

Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L (2020) Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. The Journal of antimicrobial chemotherapy, DOI:10.1093/jac/dkaa293

Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial Genomics, DOI:10.1099/mgen.0.000398

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS computational biology 16(3): e1007134, DOI:10.1371/journal.pcbi.1007134

Schwengers O, Hain T, Chakraborty T, Goesmann A (2020) ReferenceSeeker: rapid determination of appropriate reference genomes. Journal of Open Source Software 5(46): 1994, DOI:10.21105/joss.01994

2019

Suarez C, Ratering S, Hain T, Fritzenwanker M, Goesmann A, Blom J, Chakraborty T, Bunk B, Spröer C, Overmann J, Schnell S (2019) Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. International journal of genomics: 7586430, DOI:10.1155/2019/7586430

Ludueña LM, Anzuay MS, Angelini JG, McIntosh M, Becker A, Rupp O, Goesmann A, Blom J, Fabra A, Taurian T (2019) Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics 111(4): 913-920, DOI:10.1016/j.ygeno.2018.05.021

Falgenhauer J, Imirzalioglu C, Falgenhauer L, Yao Y, Hauri AM, Erath B, Schwengers O, Goesmann A, Seifert H, Chakraborty T, Doijad S (2019) Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany. Microbiology Resource Announcements 8(29), DOI:10.1128/mra.00465-19

Farr M, Ferreira S, Al-Dilaimi A, Bögeholz S, Goesmann A, Kalinowski J, Knabbe C, Faber L, Oliveira JP, Rudolph V (2019) Fabry disease: Detection of Alu-mediated exon duplication by NGS. Molecular and Cellular Probes: 79-83, DOI:10.1016/j.mcp.2019.03.008

López JL, Lozano MJ, Lagares A, Fabre ML, Draghi WO, Del Papa MF, Pistorio M, Becker A, Wibberg D, Schlüter A, Pühler A, Blom J, Goesmann A, Lagares A (2019) Codon usage heterogeneity in the multipartite prokaryote genome: Selection-based coding bias associated with gene location, expression level, and ancestry. mBio 10(3), DOI:10.1128/mBio.00505-19

Biessy, A., Novinscak, A., Blom, J., Léger, G., Thomashow, L., Cazorla, F., Josic, D., Filion, M.. (2019). Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp.. John Wiley \& Sons, Inc. Hoboken, USA.Volume 21(1), 437--455. DOI: 10.1111/1462-2920.14476

Tekedar, H., Abdelhamed, H., Kumru, S., Blom, J., Karsi, A., Lawrence, M.. (2019). Comparative genomics of Aeromonas hydrophila secretion systems and mutational analysis of hcp1 and vgrG1 genes from T6SS. Frontiers Media SA.Volume 9, 3216. DOI: 10.3389/fmicb.2018.03216

Rupp, O., 2019. Nuclear factor of activated T-cells, NFATC1, governs FLT3ITD-driven hematopoietic stem cell transformation and a poor prognosis in AML. Journal of Hematology & Oncology, DOI:10.1186/s13045-019-0765-y.

Rupp, O., 2019. Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035. Microbiology resource announcements, DOI:10.1128/mra.00050-19.

Baal, N., Cunningham, S., Obermann, H., Thomas, J., Lippitsch, A., Dietert, K., Gruber, A., Kaufmann, A., Michel, G., Nist, A., Stiewe, T., Rupp, O., Goesmann, A., Zukunft, S., Fleming, I., Bein, G., Lohmeyer, J., Bauer, S. and Hackstein, H., 2019. ADAR1 is required for dendritic cell subset homeostasis and alveolar macrophage function. Journal of Immunology, 202(4), pp.1099-1111.

Herbert, D.B., Gross, T., Rupp, O. and Becker, A., 2019. Transcriptional changes suggest a major involvement of Gibberellins in Trifolium pratense regrowth after mowing., DOI:10.1101/775841.

Ludueña, L.M., Anzuay, M.S., Angelini, J.G., McIntosh, M., Becker, A., Rupp, O., Goesmann, A., Blom, J., Fabra, A. and Taurian, T., 2019. Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics, 111(4), pp.913-920, DOI:10.1016/j.ygeno.2018.05.021.

Jaswal, R., Pathak, A., Edwards III, B., Lewis III, R., Seaman, J.C., Stothard, P., Krivushin, K., Blom, J., Rupp, O. and Chauhan, A., 2019. Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes, 10(5), p.325, DOI:10.3390/genes10050325.

Rutz, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J., Smits, T.. (2019). High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 8(3), e01502--18. DOI: https://doi.org/10.1128/mra.01502-18

Ludueña, L., Anzuay, M., Angelini, J., McIntosh, M., Becker, A., Rupp, O., Goesmann, A., Blom, J., Fabra, A., Taurian, T.. (2019). Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Academic Press.Volume 111(4), 913--920.  DOI: 10.1016/j.ygeno.2018.05.021

Amiri Moghaddam, J., Dávila-Céspedes, A., Alanjary, M., Blom, J., König, G., Schäberle, T.. (2019). Genome analysis of the marine bacterium Labrenzia sp. strain 011, a potential protective agent of mollusks. MDPI.Volume 4(1), 33. DOI: 10.3390/data4010033

Rothen, J., Pothier, J., Foucault, F., Blom, J., Nanayakkara, D., Li, C., Ip, M., Tanner, M., Vogel, G., Pflüger, V., others. (2019). Subspecies typing of Streptococcus agalactiae based on ribosomal subunit protein mass variation by MALDI-TOF MS. Frontiers Media SA.Volume 10, 471. DOI: 10.3389/fmicb.2019.00471

Ruinelli, M., Blom, J., Smits, T., Pothier, J.. (2019). Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp. BioMed Central.Volume 20(1), 1--16. DOI: 10.1186/s12864-019-5555-y

Falgenhauer L, Schwengers O, Schmiedel J, Baars C, Lambrecht O, Heß S, Berendonk TU, Falgenhauer J, Chakraborty T, Imirzalioglu C (2019) Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters. Frontiers in microbiology: 2779, DOI:10.3389/fmicb.2019.02779

Falgenhauer J, Imirzalioglu C, Falgenhauer L, Yao Y, Hauri AM, Erath B, Schwengers O, Goesmann A, Seifert H, Chakraborty T, Doijad S (2019) Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany. Microbiology resource announcements 8(29), DOI:10.1128/MRA.00465-19

Smits, T., Duffy, B., Blom, J., Ishimaru, C., Stockwell, V.. (2019). Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species. Springer Berlin Heidelberg.Volume 201(6), 713--722. DOI: 10.1007/s00203-019-01647-7

Liou, J., Huang, C., Wang, C., Lee, A., Mori, K., Tamura, T., Watanabe, M., Blom, J., Huang, L., Watanabe, K.. (2019). Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Microbiology Society.Volume 69(5), 1484--1489. DOI: 10.1099/ijsem.0.003346

Avontuur, J., Palmer, M., Beukes, C., Chan, W., Coetzee, M., Blom, J., Stępkowski, T., Kyrpides, N., Woyke, T., Shapiro, N., others. (2019). Genome-informed Bradyrhizobium taxonomy: where to from here?. Urban \& Fischer.Volume 42(4), 427--439. DOI: 10.1016/j.syapm.2019.03.006

Guan, Y., Ngugi, D., Vinu, M., Blom, J., Alam, I., Guillot, S., Ferry, J., Stingl, U.. (2019). Comparative genomics of the genus Methanohalophilus, including a newly isolated strain from Kebrit deep in the Red Sea. Frontiers Media SA.Volume 10, 839. DOI: 10.3389/fmicb.2019.00839

Ramdhan, N., Blom, J., Sutcliffe, I., Pereira-Ribeiro, P., Santos, C., Mattos-Guaraldi, A., Burkovski, A., Sangal, V.. (2019). Genomic analysis of a novel nontoxigenic Corynebacterium diphtheriae strain isolated from a cancer patient. Elsevier.Volume 30, 100544. DOI: 10.1016/j.nmni.2019.100544

Palmer, M., Venter, S., McTaggart, A., Coetzee, M., Van Wyk, S., Avontuur, J., Beukes, C., Fourie, G., Santana, Q., Van Der Nest, M., others. (2019). The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ Inc..Volume 7, e6698. DOI: 10.7717/peerj.6698

Bouhired, S., Rupp, O., Blom, J., Schäberle, T., Schiefer, A., Kehraus, S., Pfarr, K., Goesmann, A., Hoerauf, A., König, G.. (2019). Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 8(17), e00050--19. DOI: 10.1128/MRA.00050-19

López, J., Lozano, M., Lagares Jr, A., Fabre, M., Draghi, W., Del Papa, M., Pistorio, M., Becker, A., Wibberg, D., Schlüter, A., others. (2019). Codon usage Heterogeneity in the multipartite prokaryote genome: selection-based coding bias associated with gene location, expression level, and ancestry. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 10(3), e00505--19. DOI: https://doi.org/10.1128/mbio.00505-19

Chen, S., Soehnlen, M., Blom, J., Terrapon, N., Henrissat, B., Walker, E.. (2019). Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains. Public Library of Science San Francisco, CA USA.Volume 14(10), e0222648. DOI: 10.1371/journal.pone.0222648

Wu, H., Gu, Q., Xie, Y., Lou, Z., Xue, P., Fang, L., Yu, C., Jia, D., Huang, G., Zhu, B., others. (2019). Cold-adapted Bacilli isolated from the Qinghai--Tibetan Plateau are able to promote plant growth in extreme environments. John Wiley \& Sons, Inc. Hoboken, USA.Volume 21(9), 3505--3526. DOI: 10.1111/1462-2920.14722

Panthee, S., Paudel, A., Blom, J., Hamamoto, H., Sekimizu, K.. (2019). Complete genome sequence of Weissella hellenica 0916-4-2 and its comparative genomic analysis. Frontiers Media SA.Volume 10, 1619. DOI: 10.3389/fmicb.2019.01619

Paterson, M., Ranasinghe, D., Blom, J., Dover, L., Sutcliffe, I., Lopes, B., Sangal, V.. (2019). Genomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host. Springer Berlin Heidelberg.Volume 201(9), 1317--1321. DOI: 10.1007/s00203-019-01695-z

Silva, S., Blom, J., Keller-Costa, T., Costa, R.. (2019). Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species. John Wiley \& Sons, Inc. Hoboken, USA.Volume 21(11), 4002--4019. DOI: 10.1111/1462-2920.14747

Nguyen, T., Wibberg, D., Vigil-Stenman, T., Berckx, F., Battenberg, K., Demchenko, K., Blom, J., Fernandez, M., Yamanaka, T., Berry, A., others. (2019). Frankia-enriched metagenomes from the earliest diverging symbiotic Frankia cluster: they come in teams. Oxford University Press.Volume 11(8), 2273--2291. DOI: 10.1093/gbe/evz153

Huang, C., Wang, C., Liou, J., Lee, A., Blom, J., Huang, L., Watanabe, K.. (2019). Reclassification of Micrococcus aloeverae and Micrococcus yunnanensis as later heterotypic synonyms of Micrococcus luteus. Microbiology Society.Volume 69(11), 3512--3518. DOI: 10.1099/ijsem.0.003654

Tekedar, H., Kumru, S., Blom, J., Perkins, A., Griffin, M., Abdelhamed, H., Karsi, A., Lawrence, M.. (2019). Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. Public Library of Science San Francisco, CA USA.Volume 14(8), e0221018. DOI: 10.1371/journal.pone.0221018

Suarez, C., Ratering, S., Hain, T., Fritzenwanker, M., Goesmann, A., Blom, J., Chakraborty, T., Bunk, B., Spröer, C., Overmann, J., others. (2019). Complete genome sequence of the plant growth-promoting bacterium hartmannibacter diazotrophicus strain E19T. Hindawi.Volume 2019. DOI: 10.1155/2019/7586430

Smits, T., Rezzonico, F., Frasson, D., Vesga, P., Vacheron, J., Blom, J., Pothier, J., Keel, C., Maurhofer, M., Sievers, M.. (2019). Updated genome sequence and annotation for the full genome of Pseudomonas protegens CHA0. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 8(39), e01002--19. DOI: 10.1128/mra.01002-19

Rutz, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J., Smits, T.. (2019). Comparative genomic analysis of the biotechnological potential of the novel species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T. MDPI.Volume 11(11), 204. DOI: 10.3390/d11110204

Wibberg, D., Batut, B., Belmann, P., Blom, J., Glöckner, F., Grüning, B., Hoffmann, N., Kleinbölting, N., Rahn, R., Rey, M., others. (2019). The de. NBI/ELIXIR-DE training platform-Bioinformatics training in Germany and across Europe within ELIXIR. Faculty of 1000 Ltd.Volume 8. DOI: 10.12688/f1000research.20244.2

Alexandraki, V., Kazou, M., Blom, J., Pot, B., Papadimitriou, K., Tsakalidou, E.. (2019). Comparative genomics of Streptococcus thermophilus support important traits concerning the evolution, biology and technological properties of the species. Frontiers Media SA.Volume 10, 2916. DOI: 10.3389/fmicb.2019.02916

Bouhired S, Rupp O, Blom J, Schäberle TF, Schiefer A, Kehraus S, Pfarr K, Goesmann A, Hoerauf A, König G (2019) Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035. Microbiology Resource Announcements 8(17), DOI:10.1128/mra.00050-19

Gerresheim GK, Bathke J, Michel AM, Andreev DE, Shalamova LA, Rossbach O, Hu P, Glebe D, Fricke M, Marz M, Goesmann A, Kiniry SJ, Baranov PV, Shatsky IN, Niepmann M (2019) Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling. International journal of molecular sciences 20(6), DOI:10.3390/ijms20061321

Baal N, Cunningham S, Obermann H, Thomas J, Lippitsch A, Dietert K, Gruber AD, Kaufmann A, Michel G, Nist A, Stiewe T, Rupp O, Goesmann A, Zukunft S, Fleming I, Bein G, Lohmeyer J, Bauer S, Hackstein H (2019) ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function. Journal of immunology (Baltimore, Md. : 1950) 202(4): 1099-1111, DOI:10.4049/jimmunol.1800269

Nelkner, J., Henke, C., Lin, T.W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A. and Schlüter, A., 2019. Effect of long-term farming practices on agricultural soil microbiome members represented by metagenomically assembled genomes (MAGs) and their predicted plant-beneficial genes. Genes, 10(6), p.424.

Koch, A., Höfle, L., Werner, B.T., Imani, J., Schmidt, A., Jelonek, L. and Kogel, K., 2019. SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. Molecular plant pathology, pp.1636-1644, DOI:10.1111/mpp.12866.

2018

Landwehr, W., Kämpfer, P., Glaeser, S., Rückert, C., Kalinowski, J., Blom, J., Goesmann, A., Mack, M., Schumann, P., Atasayar, E., others. (2018). Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.. Microbiology Society.Volume 68(1), 382--393. DOI: 10.1099/ijsem.0.002519

Ludueña, L., Anzuay, M., Angelini, J., McIntosh, M., Becker, A., Rupp, O., Goesmann, A., Blom, J., Fabra, A., Taurian, T.. (2018). Strain Serratia sp. S119: a potential biofertilizer for peanut and maize and a model bacterium to study phosphate solubilization mechanisms. Elsevier.Volume 126, 107--112. DOI: 10.1016/j.apsoil.2017.12.024

Kazou, M., Alexandraki, V., Blom, J., Pot, B., Tsakalidou, E., Papadimitriou, K.. (2018). Comparative genomics of Lactobacillus acidipiscis ACA-DC 1533 isolated from traditional Greek Kopanisti cheese against species within the Lactobacillus salivarius clade. Frontiers Media SA.Volume 9, 1244. DOI: 10.3389/fmicb.2018.01244

Verwaaijen, B., Wibberg, D., Nelkner, J., Gordin, M., Rupp, O., Winkler, A., Bremges, A., Blom, J., Grosch, R., Pühler, A., others. (2018). Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Elsevier.Volume 267, 12--18. DOI: 10.1016/j.jbiotec.2017.12.021

Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., Blom, J., Pühler, A., Schlüter, A., others. (2018). Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. BioMed Central.Volume 11(1), 1--13. DOI: 10.1186/s13068-018-1162-4

Gétaz, M., Baeyen, S., Blom, J., Maes, M., Cottyn, B., Pothier, J.. (2018). High-quality draft genome sequences of five Xanthomonas arboricola pv. fragariae isolates. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 6(7), e01585--17. DOI: 10.1128/genomea.01585-17

Douriet-Gámez, N., Maldonado-Mendoza, I., Ibarra-Laclette, E., Blom, J., Calderón-Vázquez, C.. (2018). Genomic analysis of Bacillus sp. strain B25, a biocontrol agent of maize pathogen Fusarium verticillioides. Springer US.Volume 75(3), 247--255. DOI: 10.1007/s00284-017-1372-1

Pillonetto, M., Arend, L., Faoro, H., D’Espindula, H., Blom, J., Smits, T., Mira, M., Rezzonico, F.. (2018). Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.. Microbiology Society.Volume 68(1), 176--184. DOI: 10.1099/ijsem.0.002477

Riesco, R., Carro, L., Román-Ponce, B., Prieto, C., Blom, J., Klenk, H., Normand, P., Trujillo, M.. (2018). Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Frontiers Media SA.Volume 9, 1360. DOI:10.3389/fmicb.2018.01360 

Palmer, M., Steenkamp, E., Coetzee, M., Avontuur, J., Chan, W., Van Zyl, E., Blom, J., Venter, S.. (2018). Mixta gen. nov., a new genus in the Erwiniaceae. Microbiology Society. DOI: 10.1099/ijsem.0.002540

Ludueña, L., Anzuay, M., Angelini, J., McIntosh, M., Becker, A., Rupp, O., Goesmann, A., Blom, J., Fabra, A. and Taurian, T., 2018. Strain Serratia sp. S119: A potential biofertilizer for peanut and maize and a model bacterium to study phosphate solubilization mechanisms. Applied Soil Ecology.

JS, C., D, W., C, R., O, R., A, S., A, W., J, K. and T, W., 2018. Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience, DOI:10.1093/gigascience/giy075.

Rupp, O., MacDonald, M.L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., Samoudi, M., Hao, H., Kingham, B., Goesmann, A., Betenbaugh, M.J., Lewis, N.E., Borth, N. and Lee, K.H., 2018. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnology and Bioengineering, DOI:10.1002/bit.26722.

Perniss A, Schmidt N, Gurtner C, Dietert K, Schwengers O, Weigel M, Hempe J, Ewers C, Pfeil U, Gärtner U, Gruber AD, Hain T, Kummer W (2018) Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice. Scientific reports 8(1): 5681, DOI:10.1038/s41598-018-23830-4

Falgenhauer L, Imirzalioglu C, Oppong K, Akenten CW, Hogan B, Krumkamp R, Poppert S, Levermann V, Schwengers O, Sarpong N, Owusu-Dabo E, May J, Eibach D (2018) Detection and Characterization of ESBL-Producing Escherichia coli From Humans and Poultry in Ghana. Frontiers in microbiology: 3358, DOI:10.3389/fmicb.2018.03358

B, V., D, W., J, N., M, G., O, R., A, W., A, B., J, B., R, G., A, P. and A, S., 2018. Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of biotechnology, DOI:10.1016/j.jbiotec.2017.12.021.

Bartz, J., Blom, J., Busse, H., Mvie, J., Hardt, M., Schubert, P., Wilke, T., Goessmann, A., Wilharm, G., Bender, J., others. (2018). Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas. Elsevier.Volume 41(2), 73--84. DOI: 10.1016/j.syapm.2017.11.004

Palmer, M., Steenkamp, E., Coetzee, M., Blom, J., Venter, S.. (2018). Genome-based characterization of biological processes that differentiate closely related bacteria. Frontiers Media SA.Volume 9, 113. DOI: 10.3389/fmicb.2018.00113

Karimi, E., Slaby, B., Soares, A., Blom, J., Hentschel, U., Costa, R.. (2018). Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges. Oxford University Press.Volume 94(6), fiy074. DOI: 10.1093/femsec/fiy074

Wei, Y., Mao, H., Xu, Y., Zou, W., Fang, J., Blom, J.. (2018). Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Microbiology Society.Volume 68(8), 2462--2467. DOI: 10.1099/ijsem.0.002785

Kämpfer, P., Rückert, C., Blom, J., Goesmann, A., Wink, J., Kalinowski, J., Glaeser, S.. (2018). Streptomyces ciscaucasicus Sveshnikova et al. 1983 is a later subjective synonym of Streptomyces canus Heinemann et al. 1953. Microbiology Society.Volume 68(1), 42--46. DOI: 10.1099/ijsem.0.002418

Åvall-Jääskeläinen, S., Taponen, S., Kant, R., Paulin, L., Blom, J., Palva, A., Koort, J.. (2018). Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes. PeerJ Inc..Volume 6, e4560. DOI: 10.7717/peerj.4560

Aliyu, H., Lebre, P., Blom, J., Cowan, D., De Maayer, P.. (2018). Corrigendum to" Phylogenomic re-assessment of the thermophilic genus Geobacillus"[Syst. Appl. Microbiol. 39 (2016) 527-533].. Volume 41(5), 529--530. DOI: 10.1016/j.syapm.2018.07.001

Sangal, V., Goodfellow, M., Blom, J., Tan, G., Klenk, H., Sutcliffe, I.. (2018). Revisiting the taxonomic status of the biomedically and industrially important genus Amycolatopsis, using a phylogenomic approach. Frontiers Media SA.Volume 9, 2281. DOI: 10.3389/fmicb.2018.02281

Shibl, A., Ngugi, D., Talarmin, A., Thompson, L., Blom, J., Stingl, U.. (2018). The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis. Oxford University Press.Volume 94(12), fiy182. DOI: 10.1093/femsec/fiy182

Fernandes, C., Blom, J., Pothier, J., Tavares, F.. (2018). High-quality draft genome sequence of Xanthomonas sp. strain CPBF 424, a Walnut-Pathogenic strain with atypical features. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 7(15), e00921--18. DOI: 10.1128/mra.00921-18

Rutz, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J., Smits, T.. (2018). High-quality draft genome sequence of Pseudomonas wadenswilerensis CCOS 864T. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 7(16), e01059--18. DOI: 10.1128/MRA.01059-18

Fernandes, C., Blom, J., Pothier, J., Tavares, F.. (2018). High-quality draft genome sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, isolated from leaves of a symptomatic walnut tree in Portugal without a past of phytosanitary treatment. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 7(16), e00887--18. DOI: 10.1128/MRA.00887-18

Amiri Moghaddam, J., Crüsemann, M., Alanjary, M., Harms, H., Dávila-Céspedes, A., Blom, J., Poehlein, A., Ziemert, N., König, G., Schäberle, T.. (2018). Analysis of the genome and metabolome of marine myxobacteria reveals high potential for biosynthesis of novel specialized metabolites. Nature Publishing Group.Volume 8(1), 1--14. DOI: 10.1038/s41598-018-34954-y

Schult F, Le TN, Albersmeier A, Rauch B, Blumenkamp P, van der Does C, Goesmann A, Kalinowski J, Albers S, Siebers B (2018) Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response. Nucleic acids research 46(14): 7179-7192, DOI:10.1093/nar/gky527

Pati NB, Doijad SP, Schultze T, Mannala GK, Yao Y, Jaiswal S, Ryan D, Suar M, Gwozdzinski K, Bunk B, Mraheil MA, Marahiel MA, Hegemann JD, Spröer C, Goesmann A, Falgenhauer L, Hain T, Imirzalioglu C, Mshana SE, Overmann J, Chakraborty T (2018) Enterobacter bugandensis: A novel enterobacterial species associated with severe clinical infection. Scientific Reports 8(1), DOI:10.1038/s41598-018-23069-z

Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, others (2018) Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. International journal of systematic and evolutionary microbiology 68(1): 382-393.

Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH (2018) A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnology and Bioengineering 115(8): 2087-2100, DOI:10.1002/bit.26722

Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A (2018) Flexible metagenome analysis using the MGX framework. Microbiome 6(1): 76, DOI:10.1186/s40168-018-0460-1

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2018) Streptomyces ciscaucasicus sveshnikova et al. 1983 is a later subjective synonym of streptomyces canus heinemann et al. 1953. International Journal of Systematic and Evolutionary Microbiology 68(1): 42-46, DOI:10.1099/ijsem.0.002418

Rupp, O., MacDonald, M.L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., Samoudi, M., Hao, H., Kingham, B., Goesmann, A., Betenbaugh, M.J., Lewis, N.E., Borth, N. and Lee, K.H., 2018. A reference genome of the Chinese hamster based on a hybrid assembly strategy., 115(8), pp.2087-2100, DOI:10.1002/bit.26722.

Lori, M., Symanczik, S., Maeder, P., Efosa, N., Jaenicke, S., Buegger, F., Tresch, S., Goesmann, A. and Gattinger, A., 2018. Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime. Frontiers in Environmental Science, p.40.

Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., Blom, J., Pühler, A., Schlüter, A., Sczyrba, A. and Klocke, M., 2018. Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels, 11(1), p.167, DOI:10.1186/s13068-018-1162-4.

Jaenicke, S., Albaum, S.P., Blumenkamp, P., Linke, B., Stoye, J. and Goesmann, A., 2018. Flexible metagenome analysis using the MGX framework. Microbiome, 6(1), p.76, DOI:10.1186/s40168-018-0460-1.

Zanini, S., Šečić, E., Jelonek, L. and Kogel, K., 2018. A bioinformatics pipeline for the analysis and target prediction of RNA effectors in bidirectional communication during plant-microbe interactions. Frontiers in Plant Science, p.1212.

2017

Mannala GK, Izar B, Rupp O, Schultze T, Goesmann A, Chakraborty T, Hain T (2017) Listeria monocytogenes induces a virulence-dependent microRNA signature that regulates the immune response in Galleria mellonella. Frontiers in Microbiology 8(DEC), DOI:10.3389/fmicb.2017.02463

Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, Lacono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN (2017) Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. Scientific Reports 7(1), DOI:10.1038/s41598-017-03904-5

Brinkrolf, K., Heise, P., Griep, S.. (2017). Genome Analyses of Insect-associated Microbes. Volume 72(9-10), E3--E3.

Wippermann, A., Rupp, O., Brinkrolf, K., Hoffrogge, R., Noll, T.. (2017). Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells. Elsevier.Volume 257, 150--161. DOI: 10.1016/j.jbiotec.2016.11.020

Beukes, C., Palmer, M., Manyaka, P., Chan, W., Avontuur, J., van Zyl, E., Huntemann, M., Clum, A., Pillay, M., Palaniappan, K., others. (2018). Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato (vol 8, 1154, 2017). FRONTIERS MEDIA SA PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE~….Volume 9. DOI: 10.3389/fmicb.2017.01154

Ngugi, D., Miyake, S., Cahill, M., Vinu, M., Hackmann, T., Blom, J., Tietbohl, M., Berumen, M., Stingl, U.. (2017). Genomic diversification of giant enteric symbionts reflects host dietary lifestyles. National Academy of Sciences.Volume 114(36), E7592--E7601. DOI: 10.1073/pnas.1703070114

Palmer, M., Steenkamp, E., Coetzee, M., Chan, W., Van Zyl, E., De Maayer, P., Coutinho, T., Blom, J., Smits, T., Duffy, B., others. (2017). Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Springer International Publishing.Volume 110(10), 1287--1309. DOI: 10.1007/s10482-017-0852-4

Duar, R., Frese, S., Lin, X., Fernando, S., Burkey, T., Tasseva, G., Peterson, D., Blom, J., Wenzel, C., Szymanski, C., others. (2017). Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 83(12), e00132--17. DOI: 10.1128/AEM.00132-17

Petkauskaite, R., Blom, J., Goesmann, A., Kuisiene, N.. (2017). Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594. Sociedade Brasileira de Microbiologia.Volume 48, 7--8. DOI: 10.1016/j.bjm.2016.06.013

Lopes, R., Cerdeira, L., Tavares, G., Ruiz, J., Blom, J., Horácio, E., Mantovani, H., Queiroz, M.. (2017). Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens. Springer Netherlands.Volume 33(10), 1--15. DOI: 10.1007/s11274-017-2347-x

Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A (2017) A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Journal of biotechnology: 2-9, DOI:10.1016/j.jbiotec.2017.07.010

Pappesch R, Warnke P, Mikkat S, Normann J, Wisniewska-Kucper A, Huschka F, Wittmann M, Khani A, Schwengers O, Oehmcke-Hecht S, Hain T, Kreikemeyer B, Patenge N (2017) The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes. Scientific reports 7(1): 12241, DOI:10.1038/s41598-017-12507-z

Celis, J., Edgell, D., Stelbrink, B., Wibberg, D., Hauffe, T., Blom, J., Kalinowski, J., Wilke, T.. (2017). Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Public Library of Science San Francisco, CA USA.Volume 12(3), e0173734. DOI: 10.1371/journal.pone.0173734

Tomazetto, G., Hahnke, S., Langer, T., Wibberg, D., Blom, J., Maus, I., Pühler, A., Klocke, M., Schlüter, A.. (2017). The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor. Elsevier.Volume 257, 178--186. DOI: 10.1016/j.jbiotec.2017.05.027

Klughammer, J., Dittrich, M., Blom, J., Mitesser, V., Vogel, U., Frosch, M., Goesmann, A., Müller, T., Schoen, C.. (2017). Comparative genome sequencing reveals within-host genetic changes in Neisseria meningitidis during invasive disease. Public Library of Science San Francisco, CA USA.Volume 12(1), e0169892. DOI: 10.1371/journal.pone.0169892

Eisenberg, T., Riße, K., Schauerte, N., Geiger, C., Blom, J., Scholz, H.. (2017). Isolation of a novel ‘atypical’Brucella strain from a bluespotted ribbontail ray (Taeniura lymma). Springer International Publishing.Volume 110(2), 221--234. DOI: 10.1007/s10482-016-0792-4

Wöchtl, B., Gunzer, F., Gerner, W., Gasse, H., Koch, M., Bagó, Z., Ganter, M., Weissenböck, H., Dinhopl, N., Coldewey, S., others. (2017). Comparison of clinical and immunological findings in gnotobiotic piglets infected with Escherichia coli O104: H4 outbreak strain and EHEC O157: H7. BioMed Central.Volume 9(1), 1--18. DOI: 10.1186/s13099-017-0179-8

Kämpfer, P., Rückert, C., Blom, J., Goesmann, A., Wink, J., Kalinowski, J., Glaeser, S.. (2017). Streptomyces phaeopurpureus Shinobu 1957 (Approved Lists 1980) and Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980) are heterotypic subjective synonyms. Microbiology Society.Volume 67(8), 3111--3116. DOI: 10.1099/ijsem.0.002110

Chen, S., Blom, J., Walker, E.. (2017). Genomic, physiologic, and symbiotic characterization of Serratia marcescens strains isolated from the mosquito Anopheles stephensi. Frontiers Media SA.Volume 8, 1483. DOI: 10.3389/fmicb.2017.01483

Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., Grosch, R., Pühler, A., Schlüter, A.. (2017). Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Springer Berlin Heidelberg.Volume 199(7), 1065--1068. DOI: 10.1007/s00203-017-1394-x

Makarewicz, O., Lucas, M., Brandt, C., Herrmann, L., Albersmeier, A., Rückert, C., Blom, J., Goesmann, A., van der Linden, M., Kalinowski, J., others. (2017). Whole genome sequencing of 39 invasive Streptococcus pneumoniae sequence type 199 isolates revealed switches from serotype 19A to 15B. Public Library of Science.Volume 12(1), e0169370. DOI: 10.1371/journal.pone.0169370

De Maayer, P., Aliyu, H., Vikram, S., Blom, J., Duffy, B., Cowan, D., Smits, T., Venter, S., Coutinho, T.. (2017). Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers. DOI: 10.3389/fmicb.2017.01755

Gétaz, M., van der Wolf, J., Blom, J., Pothier, J.. (2017). Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 5(32), e00642--17. DOI: 10.1128/genomeA.00642-17

Glaeser, S., Alabid, I., Guo, H., Kumar, N., Imani, J., Kämpfer, P., Hardt, M., Busche, T., Kalinowski, J., Blom, J., others. (2017). Detection and characterization of endobacteria in the fungal endophyte Piriformospora indica. Springer, Cham.

Stadermann, K., Blom, J., Borgmeier, C., Sciberras, N., Herbold, S., Kipker, M., Meurer, G., Molck, S., Petri, D., Pelzer, S., others. (2017). First complete genome sequence of Bacillus glycinifermentans B-27. Elsevier.Volume 257, 187--191. DOI: 10.1016/j.jbiotec.2017.04.021

Alexandraki, V., Kazou, M., Blom, J., Pot, B., Tsakalidou, E., Papadimitriou, K.. (2017). The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. BioMed Central.Volume 12(1), 1-DOI: 10.1186/s40793-017-0227-5-10. 

Chen, S., Blom, J., Loch, T., Faisal, M., Walker, E.. (2017). The emerging fish pathogen Flavobacterium spartansii isolated from chinook salmon: comparative genome analysis and molecular manipulation. Frontiers Media SA.Volume 8, 2339. DOI: 10.3389/fmicb.2017.02339

Fan, B., Blom, J., Klenk, H., Borriss, R.. (2017). Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis form an “operational group B. amyloliquefaciens” within the B. subtilis species complex. Frontiers Media SA.Volume 8, 22. DOI: 10.3389/fmicb.2017.00022

Schatschneider, S., Schneider, J., Blom, J., Létisse, F., Niehaus, K., Goesmann, A., Vorhölter, F.. (2017). Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology Society.Volume 163(8), 1117--1144. DOI: 10.1099/mic.0.000473

Hersemann, L., Wibberg, D., Blom, J., Goesmann, A., Widmer, F., Vorhölter, F., Kölliker, R.. (2017). Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BioMed Central.Volume 18(1), 1--18. DOI: 10.1186/s12864-016-3422-7

Jeong, D., Heo, S., Ryu, S., Blom, J., Lee, J.. (2017). Genomic insights into the virulence and salt tolerance of Staphylococcus equorum. Nature Publishing Group.Volume 7(1), 1--11. DOI: 10.1038/s41598-017-05918-5

Yu, J., Blom, J., Sczyrba, A., Goesmann, A.. (2017). Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Elsevier.Volume 257, 58--60. DOI: https://doi.org/10.1016/j.jbiotec.2017.02.020

Langlois, P., Snelling, J., Hamilton, J., Bragard, C., Koebnik, R., Verdier, V., Triplett, L., Blom, J., Tisserat, N., Leach, J.. (2017). Characterization of the Xanthomonas translucens complex using draft genomes, comparative genomics, phylogenetic analysis, and diagnostic LAMP assays. Volume 107(5), 519--527. DOI: 10.1094/PHYTO-08-16-0286-R

Yu, J., Blom, J., Glaeser, S., Jaenicke, S., Juhre, T., Rupp, O., Schwengers, O., Spänig, S., Goesmann, A.. (2017). A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Elsevier.Volume 261, 2--9. DOI: 10.1016/j.jbiotec.2017.07.010

Grosse-Kock, S., Kolodkina, V., Schwalbe, E., Blom, J., Burkovski, A., Hoskisson, P., Brisse, S., Smith, D., Sutcliffe, I., Titov, L., others. (2017). Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s. BioMed Central.Volume 18(1), 1--10. DOI: 10.1186/s12864-017-4276-3

Jimenez-Infante, F., Ngugi, D., Vinu, M., Blom, J., Alam, I., Bajic, V., Stingl, U.. (2017). Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade. Oxford University Press.Volume 93(7). DOI: 10.1093/femsec/fix083

Beukes, C., Palmer, M., Manyaka, P., Chan, W., Avontuur, J., van Zyl, E., Huntemann, M., Clum, A., Pillay, M., Palaniappan, K., others. (2017). Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers Media SA.Volume 8, 1154. DOI: 10.3389/fmicb.2017.01154

Ampattu, B., Hagmann, L., Liang, C., Dittrich, M., Schlüter, A., Blom, J., Krol, E., Goesmann, A., Becker, A., Dandekar, T., others. (2017). Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BioMed Central.Volume 18(1), 1--36. DOI: 10.1186/s12864-017-3616-7

Entfellner, E., Frei, M., Christiansen, G., Deng, L., Blom, J., Kurmayer, R.. (2017). Evolution of anabaenopeptin peptide structural variability in the cyanobacterium Planktothrix. Frontiers Media SA.Volume 8, 219. DOI: 10.3389/fmicb.2017.00219

Ruinelli, M., Blom, J., Pothier, J.. (2017). Complete genome sequence of Pseudomonas viridiflava CFBP 1590, isolated from diseased cherry in France. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 5(30), e00662--17. DOI: 10.1128/genomeA.00662-17

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2017) Streptomyces phaeopurpureus shinobu 1957 (Approved lists 1980) and streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (approved lists 1980) are heterotypic subjective synonyms. International Journal of Systematic and Evolutionary Microbiology 67(8): 3111-3116, DOI:10.1099/ijsem.0.002110

Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A (2017) A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.: 2-9, DOI:10.1016/j.jbiotec.2017.07.010

Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J (2017) Bioinformatics for NGS-based metagenomics and the application to biogas research.: 10-23, DOI:10.1016/j.jbiotec.2017.08.012

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L (2017) Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713. Genome announcements, DOI:10.1128/genomea.01262-17

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L (2017) Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing. Genome announcements 5(40), DOI:10.1128/genomeA.01127-17

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L (2017) Draft genome sequence of the fruiting myxobacterium Nannocystis exedens DSM 71. Genome Announcements 5(43), DOI:10.1128/genomeA.01227-17

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L (2017) Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655. Genome announcements 5(43), DOI:10.1128/genomeA.01196-17

Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A (2017) Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of microbiology 199(7): 1065-1068, DOI:10.1007/s00203-017-1394-x

Serranía J, Johner T, Rupp O, Goesmann A, Becker A (2017) Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library. Journal of Biotechnology: 9-12, DOI:10.1016/j.jbiotec.2017.02.019

Yu J, Blom J, Sczyrba A, Goesmann A (2017) Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology: 58-60, DOI:10.1016/j.jbiotec.2017.02.020

Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ (2017) Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium xanthomonas campestris. 163(8): 1117-1144, DOI:10.1099/mic.0.000473

Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O (2017) Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for biofuels 10(1): 197, DOI:10.1186/s13068-017-0882-1

Schmautz Z, Graber A, Jaenicke S, Goesmann A, Junge R, Smits TH (2017) Microbial diversity in different compartments of an aquaponics system. Archives of Microbiology 199(4): 613-620, DOI:10.1007/s00203-016-1334-1

Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, Müller T, Schoen C (2017) Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC Genomics 18(1), DOI:10.1186/s12864-017-3616-7

Cardoso SD, Gonçalves D, Goesmann A, Canário AV, Oliveira RF (2017) Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish. Molecular Ecology 27(3): 789-803, DOI:10.1111/mec.14408

Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C (2017) Comparative genome sequencing reveals within-host genetic changes in neisseria meningitidis during invasive disease. PLoS ONE 12(1), DOI:10.1371/journal.pone.0169892

Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R (2017) Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC Genomics 18(1), DOI:10.1186/s12864-016-3422-7

Petkauskaite R, Blom J, Goesmann A, Kuisiene N (2017) Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594. Brazilian Journal of Microbiology 48(1): 7-8, DOI:10.1016/j.bjm.2016.06.013

Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, Van Der Linden M, Kalinowski J, Pletz MW (2017) Whole genome sequencing of 39 invasive Streptococcus pneumoniae sequence type 199 isolates revealed switches from serotype 19A to 15B. PLoS ONE 12(1), DOI:10.1371/journal.pone.0169370

Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S.P., Schlüter, A., Goesmann, A., SWczyrba, A. and Stoye, J., 2017. Bioinformatics for NGS-based Metagenomics and the Application to Biogas Research. Journal of Biotechnology.

Yu, J., Blom, J., Glaeser, S., Jaenicke, S., Juhre, T., Rupp, O., Schwengers, O., Spänig, S. and Goesmann, A., 2017. A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Journal of Biotechnology.

Schmautz, Z., Graber, A., Jaenicke, S., Goesmann, A., Junge, R. and Smits, T.H.M., 2017. Microbial diversity in different compartments of an aquaponics system. Archives of Microbiology, pp.1-8, DOI:10.1007/s00203-016-1334-1.

GK, M., B, I., O, R., T, S., A, G., T, C. and T, H., 2017. Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella. Frontiers in microbiology, DOI:10.3389/fmicb.2017.02463.

J, Y., J, B., SP, G., S, J., T, J., O, R., O, S., S, S. and A, G., 2017. A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Journal of biotechnology, DOI:10.1016/j.jbiotec.2017.07.010.

A, T., M, B., O, R., A, G. and L, S., 2017. Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713. Genome announcements, DOI:10.1128/genomea.01262-17.

A, T., M, B., O, R., A, G. and L, S., 2017. Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing. Genome announcements, DOI:10.1128/genomea.01127-17.

A, T., M, B., O, R., A, G. and L, S., 2017. Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71. Genome announcements, DOI:10.1128/genomea.01227-17.

A, T., M, B., O, R., A, G. and L, S., 2017. Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655. Genome announcements, DOI:10.1128/genomea.01196-17.

D, W., F, G., B, V., J, B., O, R., A, G., R, Z., R, G., A, P. and A, S., 2017. Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of microbiology, DOI:10.1007/s00203-017-1394-x.

A, W., O, R., K, B., R, H. and T, N., 2017. Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells. Journal of biotechnology, DOI:10.1016/j.jbiotec.2016.11.020.

J, S., T, J., O, R., A, G. and A, B., 2017. Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library. Journal of biotechnology, DOI:10.1016/j.jbiotec.2017.02.019.

F, R., O, R. and J, F., 2017. Pathogen recognition in compatible plant-microbe interactions. Scientific reports, DOI:10.1038/s41598-017-04792-5.

RS, A., C, R., O, R., B, P., G, H., D, W., K, N., A, P. and FJ, V., 2017. Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. Journal of biotechnology, DOI:10.1016/j.jbiotec.2017.05.009.

KC, P., M, L., O, R. and A, B., 2017. Seed Plant-Specific Gene Lineages Involved in Carpel Development. Molecular biology and evolution, DOI:10.1093/molbev/msw297.

2016

Jimenez-Infante, F., Ngugi, D., Vinu, M., Alam, I., Kamau, A., Blom, J., Bajic, V., Stingl, U.. (2016). Comprehensive genomic analyses of the OM43 clade, including a novel species from the Red Sea, indicate ecotype differentiation among marine methylotrophs. American Society for Microbiology.Volume 82(4), 1215--1226. DOI: https://doi.org/10.1128/AEM.02852-15

Aliyu, H., Lebre, P., Blom, J., Cowan, D., De Maayer, P.. (2016). Phylogenomic re-assessment of the thermophilic genus Geobacillus. Elsevier.Volume 39(8), 527--533. DOI: 10.1016/j.syapm.2016.09.004

Anton, B., Harhay, G., Smith, T., Blom, J., Roberts, R.. (2016). Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi. Public Library of Science San Francisco, CA USA.Volume 11(8), e0161499. DOI: 10.1371/journal.pone.0161499

Pathak, A., Chauhan, A., Blom, J., Indest, K., Jung, C., Stothard, P., Bera, G., Green, S., Ogram, A.. (2016). Comparative genomics and metabolic analysis reveals peculiar characteristics of Rhodococcus opacus strain M213 particularly for naphthalene degradation. Public Library of Science San Francisco, CA USA.Volume 11(8), e0161032. DOI: 10.1371/journal.pone.0161032

Nguyen, T., Wibberg, D., Battenberg, K., Blom, J., Vanden Heuvel, B., Berry, A., Kalinowski, J., Pawlowski, K.. (2016). An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH. BioMed Central.Volume 17(1), 1--17. DOI: 10.1186/s12864-016-3140-1

Dickey, A., Loy, J., Bono, J., Smith, T., Apley, M., Lubbers, B., DeDonder, K., Capik, S., Larson, R., White, B., others. (2016). Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. BioMed Central.Volume 47(1), 1--11. DOI: 10.1186/s13567-016-0316-2

Ngugi, D., Blom, J., Stepanauskas, R., Stingl, U.. (2016). Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. Nature Publishing Group.Volume 10(6), 1383--1399. DOI: 10.1038/ismej.2015.214

Scholz, H., Revilla-Fernández, S., Al Dahouk, S., Hammerl, J., Zygmunt, M., Cloeckaert, A., Koylass, M., Whatmore, A., Blom, J., Vergnaud, G., others. (2016). Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes (Vulpes vulpes). Microbiology Society.Volume 66(5), 2090--2098. DOI: 10.1099/ijsem.0.000998

Sun, Y., Wang, Z., Zhang, S., Li, X., Gao, H., Zhang, C., Abdel-Shafy, H., Mansour, M., Kuppusamy, S., Thavamani, P., others. (2016). Purification and properties of NADH-ferredoxinNAP reductase, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816.. orgz.Volume 16(4-6), 107--123. DOI: 10.1128/jb.172.1.457-464.1990

Scholz, H., Mühldorfer, K., Shilton, C., Benedict, S., Whatmore, A., Blom, J., Eisenberg, T.. (2016). The change of a medically important genus: worldwide occurrence of genetically diverse novel Brucella species in exotic frogs. Public Library of Science San Francisco, CA USA.Volume 11(12), e0168872. DOI: 10.1371/journal.pone.0168872

Ghatak, S., Blom, J., Das, S., Sanjukta, R., Puro, K., Mawlong, M., Shakuntala, I., Sen, A., Goesmann, A., Kumar, A., others. (2016). Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila. Springer International Publishing.Volume 109(7), 945--956. DOI: 10.1007/s10482-016-0693-6

Jaenicke, S., Bunk, B., Wibberg, D., Spröer, C., Hersemann, L., Blom, J., Winkler, A., Schatschneider, S., Albaum, S.P., Kölliker, R. and others, 2016. Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome Announcements, 4(6), pp.e01334-16.

Hilker, R., Bernd Stadermann, K., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T. and Goesmann, A., 2016. ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics, p.btw541, DOI:10.1093/bioinformatics/btw541.

Maus, I., Koeck, D.E., Cibis, K.G., Hahnke, S., Kim, Y.S., Langer, T., Kreubel, J., Erhard, M., Bremges, A., Off, S., Stolze, Y., Jaenicke, S., Goesmann, A., Sczyrba, A., Scherer, P., König, H., Schwarz, W.H., Zverlov, V.V., Liebl, W., Pühler, A., Schlüter, A. and Klocke, M., 2016. Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnology for Biofuels, 9(1), pp.1-28, DOI:10.1186/s13068-016-0581-3.

Martini, M.C., Wibberg, D., Lozano, M., Tejerizo, G.T., Albicoro, F.J., Jaenicke, S., Van Elsas, J.D., Petroni, A., Garcillán-Barcia, M.P., De La Cruz, F. and others, 2016. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports, DOI:10.1038/srep28284.

Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S.P., Jaenicke, S., Fracowiak, J., Pühler, A. and Schlüter, A., 2016. An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology, pp.268-279, DOI:10.1016/j.jbiotec.2016.06.014.

Gómez-Consarnau, L., González, J.M., Riedel, T., Jaenicke, S., Wagner-Döbler, I., Sañudo-Wilhelmy, S.A. and Fuhrman, J.A., 2016. Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. The ISME Journal, 10(5), pp.1102-1112, DOI:10.1038/ismej.2015.196.

Gonzalez-Perez, M., Murcia, M., Parra-Lopez, C., Blom, J., Tauch, A.. (2016). Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense. Elsevier.Volume 14, 98--105. DOI: 10.1016/j.nmni.2016.09.007

Papadimitriou, K., Baharidis, P., Georgoulis, A., Engel, M., Louka, M., Karamolegkou, G., Tsoka, A., Blom, J., Pot, B., Malecki, P., others. (2016). Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus). Springer Japan.Volume 20(3), 351--361. DOI: 10.1007/s00792-016-0826-x

Maus, I., Cibis, K., Bremges, A., Stolze, Y., Wibberg, D., Tomazetto, G., Blom, J., Sczyrba, A., König, H., Pühler, A., others. (2016). Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. Elsevier.Volume 232, 50--60. DOI: 10.1016/j.jbiotec.2016.05.001

Hofer, E., Hammerl, J., Zygmunt, M., Cloeckaert, A., Koylass, M., Whatmore, A., Blom, J., Revilla-Fernández, S., Witte, A., Scholz, H., others. (2016). Brucella vulpis sp. nov., a novel Brucella species isolated from mandibular lymph nodes of red foxes (Vulpes vulpes) in Austria. Volume 66(5), 2090--2098. DOI: 10.1099/ijsem.0.000998

Blom, J., Kreis, J., Spänig, S., Juhre, T., Bertelli, C., Ernst, C., Goesmann, A.. (2016). EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Oxford University Press.Volume 44(W1), W22--W28. DOI: 10.1093/nar/gkw255

Azarbaijani, R., Yeganeh, L., Blom, J., Younesi, H., Fazeli, S., Tabatabaei, M., Salekdeh, G.. (2016). Comparative genome analysis of Oceanimonas sp. GK1, a halotolerant bacterium with considerable xenobiotics degradation potentials. BioMed Central.Volume 66(2), 703--716. DOI: 10.1007/s13213-015-1156-4

Fernández-Natal, I., Saez-Nieto, J., Rodríguez-Lázaro, D., Valdezate-Ramos, S., Parras-Padilla, T., Medina, M., Rodríguez-Pollán, R., Blom, J., Tauch, A., Soriano, F.. (2016). Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples. Elsevier.Volume 10, 116--121. DOI: 10.1016/j.nmni.2016.01.007

Hersemann, L., Wibberg, D., Blom, J., Widmer, F., Kölliker, R.. (2016). Draft genome sequence of the Xanthomonas bromi type strain LMG 947. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 4(5), e00961--16. DOI: 10.1128/genomeA.00961-16

Kupferschmied, P., Chai, T., Flury, P., Blom, J., Smits, T., Maurhofer, M., Keel, C.. (2016). Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties. Wiley Online Library.Volume 18(11), 4265--4281. DOI: 10.1111/1462-2920.13571

Glaeser, S., Imani, J., Alabid, I., Guo, H., Kumar, N., Kämpfer, P., Hardt, M., Blom, J., Goesmann, A., Rothballer, M., others. (2016). Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. Nature Publishing Group.Volume 10(4), 871--884. DOI: 10.1038/ismej.2015.163 

Wibberg, D., Andersson, L., Tzelepis, G., Rupp, O., Blom, J., Jelonek, L., Pühler, A., Fogelqvist, J., Varrelmann, M., Schlüter, A., others. (2016). Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BioMed Central.Volume 17(1), 1--12. DOI: 10.1186/s12864-016-2561-1

Sangal, V., Goodfellow, M., Jones, A., Schwalbe, E., Blom, J., Hoskisson, P., Sutcliffe, I.. (2016). Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Nature Publishing Group.Volume 6(1), 1--12. DOI: 10.1038/srep38392

Blifernez-Klassen, O., Wibberg, D., Winkler, A., Blom, J., Goesmann, A., Kalinowski, J., Kruse, O.. (2016). Complete chloroplast and mitochondrial genome sequences of the hydrocarbon oil-producing green microalga Botryococcus braunii Race B (Showa). American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 4(3), e00524--16. DOI: 10.1128/genomeA.00524-16

Rezzonico, F., Smits, T., Born, Y., Blom, J., Frey, J., Goesmann, A., Cleenwerck, I., De Vos, P., Bonaterra, A., Duffy, B., others. (2016). Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. Microbiology Society.Volume 66(3), 1583--1592. DOI: 10.1099/ijsem.0.000920

Flury, P., Aellen, N., Ruffner, B., Péchy-Tarr, M., Fataar, S., Metla, Z., Dominguez-Ferreras, A., Bloemberg, G., Frey, J., Goesmann, A., others. (2016). Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. Nature Publishing Group.Volume 10(10), 2527--2542. DOI: 10.1038/ismej.2016.5

Jaenicke, S., Bunk, B., Wibberg, D., Spröer, C., Hersemann, L., Blom, J., Winkler, A., Schatschneider, S., Albaum, S., Kölliker, R., others. (2016). Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 4(6), e01334--16. DOI: 10.1128/genomeA.01334-16

Wegmann U, Goesmann A, Carding SR (2016) Complete Genome Sequence of Bacteroides ovatus V975. Genome Announcements 4(6), DOI:10.1128/genomea.01335-16

Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW (2016) Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in genetics 7(FEB): 5, DOI:10.3389/fgene.2016.00005

Blifernez-Klassen O, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J, Kruse O (2016) Complete chloroplast and mitochondrial genome sequences of the hydrocarbon oil-producing green microalga Botryococcus braunii race B (Showa). Genome Announcements 4(3), DOI:10.1128/genomeA.00524-16

Jaenicke S, Bunk B, Wibberg D, Spröer C, Hersemann L, Blom J, Winkler A, Schatschneider S, Albaum SP, Kölliker R, Goesmann A, Pühler A, Overmann J, Vorhölter FJ (2016) Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome Announcements 4(6), DOI:10.1128/genomeA.01334-16

Bertelli C, Cissé OH, Rusconi B, Kebbi-Beghdadi C, Croxatto A, Goesmann A, Collyn F, Greub G (2016) CRISPR system acquisition and evolution of an obligate intracellular chlamydia-related bacterium. Genome Biology and Evolution 8(8): 2376-2386, DOI:10.1093/gbe/evw138

Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Oliver Glöckner F, Czjzek M, Amann R, Michel G (2016) Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT. Environmental Microbiology 18(12): 4610-4627, DOI:10.1111/1462-2920.13584

Franta Z, Vogel H, Lehmann R, Rupp O, Goesmann A, Vilcinskas A (2016) Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. BioMed research international: 8285428, DOI:10.1155/2016/8285428

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A (2016) ReadXplorer 2-detailed read mapping analysis and visualization from one single source. Bioinformatics 32(24): 3702-3708, DOI:10.1093/bioinformatics/btw541

Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M (2016) Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnology for Biofuels 9(1), DOI:10.1186/s13068-016-0581-3

Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkovc-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Buendia GR, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Jeddou FB, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, Van Der Meer JR (2016) The genome of the toluene-degrading Pseudomonas veronii strain 1YdBTEX2 and its differential gene expression in contaminated sand. PLoS ONE 11(11), DOI:10.1371/journal.pone.0165850

Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A, Cardoza V, McMillan J, Mentzel T, Kogel KH (2016) An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery. PLoS Pathogens 12(10), DOI:10.1371/journal.ppat.1005901

Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits THM, Keel C, Maurhofer M (2016) Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. The ISME journal 10(10): 2527-42, DOI:10.1038/ismej.2016.5

Falgenhauer L, Waezsada SE, Gwozdzinski K, Ghosh H, Doijad S, Bunk B, Spröer C, Imirzalioglu C, Seifert H, Irrgang A, Fischer J, Guerra B, Käsbohrer A, Overmann J, Goesmann A, Chakraborty T (2016) Chromosomal locations of mcr-1 and blaCTX-M-15 in fluoroquinolone-resistant Escherichia coli ST410. 22(9): 1689-1691, DOI:10.3201/eid2209.160692

Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A (2016) EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic acids research 44(W1): W22-W28, DOI:10.1093/nar/gkw255

Sobetzko, P., Jelonek, L., Strickert, M., Han, W., Goesmann, A. and Waldminghaus, T., 2016. DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes. Frontiers in microbiology, p.283, DOI:10.3389/fmicb.2016.00283.

Langenkämper, D., Jakobi, T., Feld, D., Jelonek, L., Goesmann, A. and Nattkemper, T.W., 2016. Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in genetics, p.5, DOI:10.3389/fgene.2016.00005.

Koch, A., Biedenkopf, D., Furch, A., Weber, L., Rossbach, O., Abdellatef, E., Linicus, L., Johannsmeier, J., Jelonek, L., Goesmann, A., Cardoza, V., McMillan, J., Mentzel, T. and Kogel, K., 2016. An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery. PLoS pathogens, p.e1005901, DOI:10.1371/journal.ppat.1005901.

Wibberg, D., Andersson, L., Tzelepis, G., Rupp, O., Blom, J., Jelonek, L., Pühler, A., Fogelqvist, J., Varrelmann, M., Schlüter, A. and Dixelius, C., 2016. Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC genomics, p.245, DOI:10.1186/s12864-016-2561-1.

Ghatak S, Blom J, Das S, Sanjukta R, Puro K, Mawlong M, Shakuntala I, Sen A, Goesmann A, Kumar A, Ngachan SV (2016) Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila. Antonie van Leeuwenhoek 109(7): 945-56, DOI:10.1007/s10482-016-0693-6

Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T (2016) Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. International Journal of Antimicrobial Agents 47(6): 457-465, DOI:10.1016/j.ijantimicag.2016.03.019

Barbuddhe SB, Doijad SP, Goesmann A, Hilker R, Poharkar KV, Rawool DB, Kurkure NV, Kalorey DR, Malik SS, Shakuntala I, Chaudhari S, Waskar V, D'Costa D, Kolhe R, Arora R, Roy A, Raorane A, Kale S, Pathak A, Negi M, Kaur S, Waghmare R, Warke S, Shoukat S, Harish B, Poojary A, Madhavaprasad C, Nagappa K, Das S, Zende R, Garg S, Bhosle S, Radriguez S, Paturkar A, Fritzenwanker M, Ghosh H, Hain T, Chakraborty T (2016) Presence of a widely disseminated Listeria monocytogenes serotype 4b clone in India. 5(6), DOI:10.1038/emi.2016.55

Fischer S, Klockgether J, Morán Losada P, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Dorda M, Goesmann A, Hilker R, Mielke S, Schönfelder T, Suerbaum S, Türk O, Woltemate S, Wiehlmann L, Tümmler B (2016) Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14. Environmental microbiology reports 8(2): 227-34, DOI:10.1111/1758-2229.12372

Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M, Hartmann A, Kogel KH (2016) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME Journal 10(4): 871-884, DOI:10.1038/ismej.2015.163

Falgenhauer L, Waezsada S, Yao Y, Imirzalioglu C, Käsbohrer A, Roesler U, Michael GB, Schwarz S, Werner G, Kreienbrock L, Chakraborty T, consortium R (2016) Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. The Lancet. Infectious diseases 16(3): 282-3, DOI:10.1016/S1473-3099(16)00009-8

Sobetzko P, Jelonek L, Strickert M, Han W, Goesmann A, Waldminghaus T (2016) DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes. Frontiers in microbiology 7(MAR): 283, DOI:10.3389/fmicb.2016.00283

Wibberg D, Andersson L, Rupp O, Goesmann A, Pühler A, Varrelmann M, Dixelius C, Schlüter A (2016) Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670. Journal of biotechnology: 11-2, DOI:10.1016/j.jbiotec.2016.02.001

Rezzonico F, Smits THM, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E (2016) Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. International journal of systematic and evolutionary microbiology 66(3): 1583-1592, DOI:10.1099/ijsem.0.000920

Z, F., H, V., R, L., O, R., A, G. and A, V., 2016. Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. BioMed research international, DOI:10.1155/2016/8285428.

D, W., L, A., O, R., A, G., A, P., M, V., C, D. and A, S., 2016. Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670. Journal of biotechnology, DOI:10.1016/j.jbiotec.2016.02.001.

D, W., L, A., G, T., O, R., J, B., L, J., A, P., J, F., M, V., A, S. and C, D., 2016. Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC genomics, DOI:10.1186/s12864-016-2561-1.

2015

M, P., N, C., O, R., J, K., A, G., MD, S., O, K. and JI, H., 2015. De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC genomics, DOI:10.1186/s12864-015-2254-1.

D, W., O, R., J, B., L, J., M, K., B, V., A, G., S, A., R, G., A, P. and A, S., 2015. Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates. PloS one, DOI:10.1371/journal.pone.0144769.

O, R., K, B., C, B., M, K., J, S., S, J., A, G., A, P., KE, J. and JF, E., 2015. The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Journal of biotechnology, DOI:10.1016/j.jbiotec.2015.06.423.

D, W., O, R., L, J., M, K., B, V., J, B., A, W., A, G., R, G., A, P. and A, S., 2015. Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system. Journal of biotechnology, DOI:10.1016/j.jbiotec.2015.03.005.

A, W., O, R., K, B., R, H. and T, N., 2015. The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells. Journal of biotechnology, DOI:10.1016/j.jbiotec.2015.02.014.

Schultze T, Hilker R, Mannala GK, Gentil K, Weigel M, Farmani N, Windhorst AC, Goesmann A, Chakraborty T, Hain T (2015) A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq. Frontiers in Microbiology 6(OCT), DOI:10.3389/fmicb.2015.01199

Zschüttig A, Auerbach C, Meltke S, Eichhorn C, Brandt M, Blom J, Goesmann A, Jarek M, Scharfe M, Zimmermann K, Wassenaar TM, Gunzer F (2015) Complete sequence of probiotic Symbioflor 2 Escherichia coli strain G3/10 and draft sequences of Symbioflor 2 E. coli strains G1/2, G4/9, G5, G6/7 and G8. Genome Announcements 3(2), DOI:10.1128/genomeA.01330-14

Pauli M, Chakarov N, Rupp O, Kalinowski J, Goesmann A, Sorenson MD, Krüger O, Hoffman JI (2015) De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC Genomics 16(1), DOI:10.1186/s12864-015-2254-1

Zischka, M., Künne, C., Blom, J., Wobser, D., Sakınç, T., Schmidt-Hohagen, K., Dabrowski, P., Nitsche, A., Hübner, J., Hain, T., others. (2015). Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BioMed Central.Volume 16(1), 1--20. DOI: 10.1186/s12864-015-1367-x

Doijad, S., Weigel, M., Barbuddhe, S., Blom, J., Goesmann, A., Hain, T., Chakraborty, T.. (2015). Phylogenomic grouping of Listeria monocytogenes. NRC Research Press.Volume 61(9), 637--646. DOI: 10.1139/cjm-2015-0281

Kamanda Ngugi, D., Blom, J., Alam, I., Rashid, M., Ba-Alawi, W., Zhang, G., Hikmawan, T., Guan, Y., Antunes, A., Siam, R., others. (2015). Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. Nature Publishing Group.Volume 9(2), 396--411. DOI: 10.1038/ismej.2014.137

De Maayer, P., Chan, W., Martin, D., Blom, J., Venter, S., Duffy, B., Cowan, D., Smits, T., Coutinho, T.. (2015). Integrative conjugative elements of the ICE Pan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Frontiers Media SA.Volume 6, 576. DOI: 10.3389/fmicb.2015.00576

Rückert, C., Kriete, M., Jaenicke, S., Winkler, A. and Tauch, A., 2015. Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise. Genome Announcements, 3(4), DOI:10.1128/genomeA.00784-15.

Rückert, C., Kriete, M., Jaenicke, S., Winkler, A. and Tauch, A., 2015. Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare. Genome Announcements, 3(4), DOI:10.1128/genomeA.00783-15.

Rupp, O., Brinkrolf, K., Buerth, C., Kunigo, M., Schneider, J., Jaenicke, S., Goesmann, A., Pühler, A., Jaeger, K. and Ernst, J.F., 2015. The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Journal of Biotechnology, DOI:10.1016/j.jbiotec.2015.06.423.

Stolze, Y., Zakrzewski, M., Maus, I., Eikmeyer, F.G., Jaenicke, S., Rottmann, N., Siebner, C., Pühler, A. and Schlüter, A., 2015. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for Biofuels, 8(1), DOI:10.1186/s13068-014-0193-8.

Rückert, C., Albersmeier, A., Busche, T., Jaenicke, S., Winkler, A., Friðjónsson, Ó.H., Hreggviðsson, G.Ó., Lambert, C., Badcock, D., Bernaerts, K., Anne, J., Economou, A. and Kalinowski, J., 2015. Complete genome sequence of Streptomyces lividans TK24. Journal of Biotechnology, pp.21-22, DOI:10.1016/j.jbiotec.2015.02.004.

Vinardell, J., Acosta-Jurado, S., Göttfert, M., Zehner, S., Becker, A., Baena-Ropero, I., Blom, J., Crespo-Rivas, J., Goesmann, A., Jaenicke, S., Krol, E., McIntosh, M., Margaret, I., Pérez-Montaño, F., Schneiker-Bekel, S., Serrania, J., Szczepanowski, R., Buendia-Claveria, A., Lloret, J., Bonilla, I., Pühler, A., Ruiz-Sainz, J. and Weidner, S., 2015. The Sinorhizobium fredii HH103 genome: a comparative analysis with S. fredii strains differing in their symbiotic behaviour with soybean. Molecular Plant-Microbe Interactions, DOI:10.1094/mpmi-12-14-0397-fi.

Maus, I., Wibberg, D., Stantscheff, R., Stolze, Y., Blom, J., Eikmeyer, F., Fracowiak, J., König, H., Pühler, A., Schlüter, A.. (2015). Insights into the annotated genome sequence of Methanoculleus bourgensis MS2T, related to dominant methanogens in biogas-producing plants. Elsevier.Volume 201, 43--53. DOI: 10.1016/j.jbiotec.2014.11.020

Smits, T., Pothier, J., Ruinelli, M., Blom, J., Frasson, D., Koechli, C., Fabbri, C., Brandl, H., Duffy, B., Sievers, M.. (2015). Complete genome sequence of the cyanogenic phosphate-solubilizing Pseudomonas sp. strain CCOS 191, a close relative of Pseudomonas mosselii. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(3), e00616--15. DOI: 10.1128/genomeA.00616-15

Heggelund, L., Gaustad, P., Håvelsrud, O., Blom, J., Borgen, L., Sundset, A., Sørum, H., Frøland, S.. (2015). Corynebacterium pseudotuberculosis pneumonia in a veterinary student infected during laboratory work. Volume 2(2), ofv053. DOI: 10.1093/ofid/ofv053

Wibberg, D., Rupp, O., Jelonek, L., Kröber, M., Verwaaijen, B., Blom, J., Winkler, A., Goesmann, A., Grosch, R., Pühler, A., others. (2015). Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system. Elsevier.Volume 203, 19--21. DOI: 10.1016/j.jbiotec.2015.03.005

Wibberg, D., Rupp, O., Blom, J., Jelonek, L., Kröber, M., Verwaaijen, B., Goesmann, A., Albaum, S., Grosch, R., Pühler, A., others. (2015). Development of a Rhizoctonia solani AG1-IB specific gene model enables comparative genome analyses between phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 isolates. Public Library of Science San Francisco, CA USA.Volume 10(12), e0144769. DOI: 10.1371/journal.pone.0144769

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Leptotrichiaceae. John Wiley \& Sons, Ltd. DOI: 10.1002/9781118960608.gbm00774.pub2

Li, X., Blom, J., Zeng, Y.. (2015). Whole genome sequences of a free-living Pseudomonas sp. strain ML96 isolated from a freshwater Maar Lake. Elsevier.Volume 24, 219--221. DOI: 10.1016/j.margen.2015.05.016

Arnold, M., Wibberg, D., Blom, J., Schatschneider, S., Winkler, A., Kutter, Y., Rückert, C., Albersmeier, A., Albaum, S., Goesmann, A., others. (2015). Draft genome sequence of Pseudomonas aeruginosa strain WS136, a highly cytotoxic ExoS-positive wound isolate recovered from pyoderma gangrenosum. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(4), e00680--15. DOI: 10.1128/genomeA.00680-15

Burgsdorf, I., Slaby, B., Handley, K., Haber, M., Blom, J., Marshall, C., Gilbert, J., Hentschel, U., Steindler, L.. (2015). Lifestyle evolution in cyanobacterial symbionts of sponges. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 6(3), e00391--15. DOI: https://doi.org/10.1128/mbio.00391-15

Guimarães, L., Soares, S., Trost, E., Blom, J., Ramos, R., Silva, A., Barh, D., Azevedo, V.. (2015). Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology. BioMed Central.Volume 16(5), 1--9. DOI: 10.1186/1471-2164-16-S5-S7

Kweon, O., Kim, S., Blom, J., Kim, S., Kim, B., Baek, D., Park, S., Sutherland, J., Cerniglia, C.. (2015). Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium. BioMed Central.Volume 15(1), 1--23. DOI: 10.1186/s12862-015-0302-8

Morley, L., McNally, A., Paszkiewicz, K., Corander, J., Méric, G., Sheppard, S., Blom, J., Manning, G.. (2015). Gene loss and lineage-specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni sequence type 403 clonal complex. American Society for Microbiology.Volume 81(11), 3641--3647. DOI: 10.1128/AEM.00546-15

Vorhölter, F., Tielen, P., Wibberg, D., Narten, M., Schobert, M., Tüpker, R., Blom, J., Schatschneider, S., Winkler, A., Albersmeier, A., others. (2015). Genome sequence of the urethral catheter isolate Pseudomonas aeruginosa MH19. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(2), e00115--15. DOI: 10.1128/genomeA.00115-15

Sangal, V., Blom, J., Sutcliffe, I., von Hunolstein, C., Burkovski, A., Hoskisson, P.. (2015). Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome. BioMed Central.Volume 16(1), 1--15. DOI: 10.1186/s12864-015-1980-8

Huja, S., Oren, Y., Trost, E., Brzuszkiewicz, E., Biran, D., Blom, J., Goesmann, A., Gottschalk, G., Hacker, J., Ron, E., others. (2015). Genomic avenue to avian colisepticemia. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 6(1), e01681--14. DOI: 10.1128/mBio.01681-14

Zschüttig, A., Auerbach, C., Meltke, S., Eichhorn, C., Brandt, M., Blom, J., Goesmann, A., Jarek, M., Scharfe, M., Zimmermann, K., others. (2015). Complete sequence of probiotic symbioflor 2 Escherichia coli strain G3/10 and draft sequences of symbioflor 2 E. coli strains G1/2, G4/9, G5, G6/7, and G8. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(2), e01330--14. DOI: 10.1128/genomeA.01330-14

Wibberg, D., Tielen, P., Narten, M., Schobert, M., Blom, J., Schatschneider, S., Meyer, A., Neubauer, R., Albersmeier, A., Albaum, S., others. (2015). Genome sequence of the urethral isolate Pseudomonas aeruginosa RN21. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(4), e00788--15. DOI: 10.1128/genomeA.00788-15

Humphreys, C., McLean, S., Schatschneider, S., Millat, T., Henstra, A., Annan, F., Breitkopf, R., Pander, B., Piatek, P., Rowe, P., others. (2015). Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BioMed Central.Volume 16(1), 1--10. DOI: 10.1186/s12864-015-2287-5

Smits, T., Rezzonico, F., Blom, J., Goesmann, A., Abelli, A., Kron Morelli, R., Vanneste, J., Duffy, B.. (2015). Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 3(6), e01448--15. DOI: 10.1128/genomea.01448-15

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Sebaldella. John Wiley \& Sons, Ltd.

Eisenberg, T., Glaeser, S., Blom, J., Rau, J., Kämpfer, P.. (2015). Streptobacillus. John Wiley \& Sons, Ltd Chichester, UK.

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Leptotrichia. John Wiley \& Sons, Ltd Chichester, UK.

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Caviibacter. John Wiley \& Sons, Ltd Chichester, UK.

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Oceanivirga. John Wiley \& Sons, Ltd Chichester, UK.

Blom, J., Glaeser, S., Juhre, T., Kreis, J., Hanel, P., Schrader, J., Kämpfer, P., Goesmann, A.. (2015). EDGAR: a versatile tool for phylogenomics. John Wiley \& Sons, Ltd Chichester, UK. DOI: 10.1002/9781118960608.bm00038

Eisenberg, T., Glaeser, S., Blom, J., Kämpfer, P.. (2015). Sneathia. John Wiley \& Sons, Ltd Chichester, UK

Wibberg D, Rupp O, Blom J, Jelonek L, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, Schlüter A (2015) Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates. PLoS ONE 10(12), DOI:10.1371/journal.pone.0144769

Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M, Vorhölter FJ (2015) Draft genome sequence of Pseudomonas aeruginosa strain WS136, a highly cytotoxic ExoS-positive wound isolate recovered from pyoderma gangrenosum. Genome Announcements 3(4), DOI:10.1128/genomeA.00680-15

Smits TH, Rezzonico F, Blom J, Goesmann A, Abelli A, Morelli RK, Vanneste JL, Duffy B (2015) Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c. Genome Announcements 3(6), DOI:10.1128/genomeA.01448-15

Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer AK, Neubauer R, Albersmeier A, Albaum S, Jahn M, Goesmann A, Vorhölter FJ, Pühler A, Jahn D (2015) Genome sequence of the urethral isolate Pseudomonas aeruginosa RN21. Genome Announcements 3(4), DOI:10.1128/genomeA.00788-15

Kessler N, Bonte A, Albaum SP, Mäder P, Messmer M, Goesmann A, Niehaus K, Langenkämper G, Nattkemper TW (2015) Learning to classify organic and conventional wheat - A machine learning driven approach using the MeltDB 2.0 metabolomics analysis platform. Frontiers in Bioengineering and Biotechnology 3(MAR), DOI:10.3389/fbioe.2015.00035

Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G (2015) Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: Training students and biological insights. Frontiers in Microbiology 6(FEB), DOI:10.3389/fmicb.2015.00101

Wegmann U, MacKenzie DA, Zheng J, Goesmann A, Roos S, Swarbreck D, Walter J, Crossman LC, Juge N (2015) The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics 16(1), DOI:10.1186/s12864-015-2216-7

Rupp O, Brinkrolf K, Buerth C, Kunigo M, Schneider J, Jaenicke S, Goesmann A, Pühler A, Jaeger KE, Ernst JF (2015) The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Journal of Biotechnology: 20-30, DOI:10.1016/j.jbiotec.2015.06.423

Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S (2015) The Sinorhizobium fredii HH103 genome: A comparative analysis with S. fredii strains differing in their symbiotic behavior with soybean. Molecular Plant-Microbe Interactions 28(7): 811-824, DOI:10.1094/MPMI-12-14-0397-FI

Wibberg D, Rupp O, Jelonek L, Kröber M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Pühler A, Schlüter A (2015) Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system. Journal of Biotechnology: 19-21, DOI:10.1016/j.jbiotec.2015.03.005

Chakarov N, Linke B, Boerner M, Goesmann A, Krüger O, Hoffman JI (2015) Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite. Molecular Ecology 24(6): 1355-1363, DOI:10.1111/mec.13115

Zischka M, Künne CT, Blom J, Wobser D, Sakinç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, Chakraborty T, Linke B, Goesmann A, Voget S, Daniel R, Schomburg D, Hauck R, Hafez HM, Tielen P, Jahn D, Solheim M, Sadowy E, Larsen J, Jensen LB, Ruiz-Garbajosa P, Quiñones Pérez D, Mikalsen T, Bender J, Steglich M, Nübel U, Witte W, Werner G (2015) Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC Genomics 16(1), DOI:10.1186/s12864-015-1367-x

Vorhölter F, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, Goesmann A, Pühler A, Jahn D (2015) Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19. Genome announcements 3(2), DOI:10.1128/genomeA.00115-15

Doijad S, Weigel M, Barbuddhe S, Blom J, Goesmann A, Hain T, Chakraborty T (2015) Phylogenomic grouping of listeria monocytogenes. Canadian Journal of Microbiology 61(9): 637-646, DOI:10.1139/cjm-2015-0281

Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Siebenthal AV, Falquet L, van der Meer JR (2015) Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology 17(1): 91-104, DOI:10.1111/1462-2920.12498

Huja S, Oren Y, Trost E, Brzuszkiewicz E, Biran D, Blom J, Goesmann A, Gottschalk G, Hacker J, Ron EZ, Dobrindt U (2015) Genomic avenue to avian colisepticemia. mBio 6(1), DOI:10.1128/mBio.01681-14

Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B (2015) Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment. Environmental Microbiology 17(1): 29-46, DOI:10.1111/1462-2920.12606

Rupp, O., Brinkrolf, K., Buerth, C., Kunigo, M., Schneider, J., Jaenicke, S., Goesmann, A., Pühler, A., Jaeger, K., Ernst, J.. (2015). The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Elsevier.Volume 211, 20--30. DOI: 10.1016/j.jbiotec.2015.06.423

Wippermann, A., Rupp, O., Brinkrolf, K., Hoffrogge, R., Noll, T.. (2015). The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells. Elsevier.Volume 199, 38--46. DOI: 10.1016/j.jbiotec.2015.02.014

Merten, M., Brinkrolf, K., Albersmeier, A., Kutter, Y., Rückert, C., Tauch, A.. (2015). Complete genome sequence and annotation of Corynebacterium singulare DSM 44357, isolated from a human semen specimen. Am Soc Microbiol.Volume 3(2), e00183--15. DOI: 10.1128/genomeA.00183-15

2014

Langenkämper D, Goesmann A, Nattkemper TW (2014) AKE - the Accelerated -mer Exploration web-tool for rapid taxonomic classification and visualization. BMC Bioinformatics 15(1), DOI:10.1186/s12859-014-0384-0

Brinkrolf, K., Hoffrogge, R., Hackl, M., Tauch, A., Baumann, M., Noll, T., Goesmann, A., Pühler, A., Borth, N.. (2014). Animal Cell Biotechnology In Biologics P - Functional-Omics for Cell Lines and Processes: The-Omics Technologies on the Example of CHO Cells.

Glaub, A., Bomholt, C., Gravermann, K., Brinkrolf, K., Albersmeier, A., Rückert, C., Tauch, A.. (2014). Complete genome sequence of Corynebacterium falsenii DSM 44353 to study the evolution of Corynebacterium cluster 3 species. Am Soc Microbiol.Volume 2(2), e00158--14. DOI: 10.1128/genomeA.00158-14

Rupp, O., Becker, J., Brinkrolf, K., Timmermann, C., Borth, N., Pühler, A., Noll, T., Goesmann, A.. (2014). Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. Public Library of Science San Francisco, USA.Volume 9(1), e85568. DOI: 10.1371/journal.pone.0085568

Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A., Goesmann, A.. (2014). Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Elsevier.Volume 190, 64--75. DOI: 10.1016/j.jbiotec.2014.07.437

Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., Abe, F., Takahashi, K., Kaiser, O., Goesmann, A., Jaenicke, S., Grote, R., Horikoshi, K. and Antranikian, G., 2014. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), pp.853-863, DOI:10.1007/s00792-014-0676-3.

Tippelt, A., Möllmann, S., Albersmeier, A., Jaenicke, S., Rückert, C. and Tauch, A., 2014. Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849. Genome Announcements, 2(4), DOI:10.1128/genomeA.00845-14.

Becker, J., Timmermann, C., Rupp, O., Albaum, S., Brinkrolf, K., Goesmann, A., Pühler, A., Tauch, A., Noll, T.. (2014). Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR3. Elsevier.Volume 178, 23--31. DOI: 10.1016/j.jbiotec.2014.02.021

Tippelt, A., Albersmeier, A., Brinkrolf, K., Rückert, C., Fernández-Natal, I., Soriano, F., Tauch, A.. (2014). Complete genome sequence of Corynebacterium ureicelerivorans DSM 45051, a lipophilic and urea-splitting isolate from the blood culture of a septicemia patient. Am Soc Microbiol.Volume 2(6), e01211--14. DOI: 10.1128/genomeA.01211-14

Bertelli C, Goesmann A, Greub G (2014) Criblamydia sequanensis harbors a megaplasmid encoding arsenite resistance. Genome Announcements 2(5), DOI:10.1128/genomeA.00949-14

O, R., J, B., K, B., C, T., N, B., A, P., T, N. and A, G., 2014. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PloS one, DOI:10.1371/journal.pone.0085568.

D, W., L, J., O, R., M, K., A, G., R, G., A, P. and A, S., 2014. Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal biology, DOI:10.1016/j.funbio.2014.06.007.

J, B., C, T., O, R., SP, A., K, B., A, G., A, P., A, T. and T, N., 2014. Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology, DOI:10.1016/j.jbiotec.2014.02.021.

A, W., S, K., O, R., SP, A., H, B., T, N. and R, H., 2014. Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells. Applied microbiology and biotechnology, DOI:10.1007/s00253-013-5282-2.

JC, D., AE, M., D, H., S, C., F, Z., H, T., O, R., TR, S., R, S., R, R., A, G., T, K. and H, H., 2014. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature, DOI:10.1038/nature12817.

BA, C., ET, K., R, H., M, K., O, R., K, R. and S, S., 2014. The more the better - polyandry and genetic similarity are positively linked to reproductive success in a natural population of terrestrial salamanders (Salamandra salamandra). Molecular ecology, DOI:10.1111/mec.12577.

Vorhölter FJ, Arnold M, Wibberg D, Blom J, Winkler A, Viehoever P, Albersmeier A, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M (2014) Draft genome sequence of Pseudomonas aeruginosa strain WS394, a multidrug-resistant and highly cytotoxic wound isolate from chronic ulcus cruris. Genome Announcements 2(6), DOI:10.1128/genomeA.01325-14

Christiansen G, Goesmann A, Kurmayer R (2014) Elucidation of insertion elements carried on plasmids and in vitro construction of shuttle vectors from the toxic cyanobacterium Planktothrix. Applied and Environmental Microbiology 80(16): 4887-4897, DOI:10.1128/AEM.01188-14

Wibberg D, Tielen P, Blom J, Rosin N, Schobert M, Tüpker R, Schatschneider S, Spilker D, Albersmeier A, Goesmann A, Vorhölter FJ, Pühler A, Jahn D (2014) Genome sequence of the acute urethral catheter isolate Pseudomonas aeruginosa MH38. Genome Announcements 2(2), DOI:10.1128/genomeA.00161-14

Ismail, E., Blom, J., Bultreys, A., Ivanović, M., Obradović, A., van Doorn, J., Bergsma-Vlami, M., Maes, M., Willems, A., Duffy, B., others. (2014). A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids. Springer Berlin Heidelberg.Volume 196(12), 891--899. DOI: 10.1007/s00203-014-1028-5

Sangal, V., Burkovski, A., Hunt, A., Edwards, B., Blom, J., Hoskisson, P.. (2014). A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. Elsevier.Volume 21, 54--57. DOI: 10.1016/j.meegid.2013.10.019

Smits, T., Guerrero-Prieto, V., Hernández-Escarcega, G., Blom, J., Goesmann, A., Rezzonico, F., Duffy, B., Stockwell, V.. (2014). Whole-genome sequencing of Erwinia amylovora strains from Mexico detects SNPs in rpsL conferring streptomycin resistance and in the avrRpt2 effector altering host interactions. American Society for Microbiology.Volume 2(1). DOI: 10.1128/genomeA.01229-13

Anastasiou, R., Mavrogonatou, E., Blom, J., Papandreou, N., Hamodrakas, S., Ferreira, S., Renault, P., Supply, P., Pot, B., Tsakalidou, E.. (2014). Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. DOI: 10.1186/1471-2164-15-272

Tielen, P., Wibberg, D., Blom, J., Rosin, N., Meyer, A., Bunk, B., Schobert, M., Tüpker, R., Schatschneider, S., Rückert, C., others. (2014). Genome sequence of the small-colony variant Pseudomonas aeruginosa MH27, isolated from a chronic urethral catheter infection. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 2(1), e01174--13. DOI: 10.1128/genomeA.01174-13

Vorhölter, F., Arnold, M., Wibberg, D., Blom, J., Winkler, A., Viehoever, P., Albersmeier, A., Goesmann, A., Zange, S., Heesemann, J., others. (2014). Draft genome sequence of Pseudomonas aeruginosa strain WS394, a multidrug-resistant and highly cytotoxic wound isolate from chronic ulcus cruris. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 2(6), e01325--14. DOI: 10.1128/genomeA.01325-14

Papadimitriou, K., Anastasiou, R., Mavrogonatou, E., Blom, J., Papandreou, N., Hamodrakas, S., Ferreira, S., Renault, P., Supply, P., Pot, B., others. (2014). Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BioMed Central.Volume 15(1), 1--21. DOI: 10.1186/1471-2164-15-272

Guan, Y., Ngugi, D., Blom, J., Ali, S., Ferry, J., Stingl, U.. (2014). Draft genome sequence of an obligately methylotrophic methanogen, Methanococcoides methylutens, isolated from marine sediment. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 2(6), e01184--14. DOI: 10.1128/genomeA.01184-14

Wibberg, D., Tielen, P., Blom, J., Rosin, N., Schobert, M., Tüpker, R., Schatschneider, S., Spilker, D., Albersmeier, A., Goesmann, A., others. (2014). Genome sequence of the acute urethral catheter isolate Pseudomonas aeruginosa MH38. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 2(2), e00161-DOI: https://doi.org/10.1128/genomea.00161-14. 

Liu, Y., Chen, X., Blom, J., Yi, Z., Wen, J., Zeng, R.. (2014). Draft genome of formaldehyde-degrading strain, Pseudomonas monteilii IOFA19. Elsevier.Volume 15, 1--2. DOI: 10.1016/j.margen.2014.04.005

Bonte A, Neuweger H, Goesmann A, Thonar C, Mäder P, Langenkämper G, Niehaus K (2014) Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems. Journal of the Science of Food and Agriculture 94(13): 2605-2612, DOI:10.1002/jsfa.6566

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484): 546-549, DOI:10.1038/nature12817

Wibberg D, Jelonek L, Rupp O, Kröber M, Goesmann A, Grosch R, Pühler A, Schlüter A (2014) Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal Biology 118(9): 800-813, DOI:10.1016/j.funbio.2014.06.007

Kessler N, Walter F, Persicke M, Albaum SP, Kalinowski J, Goesmann A, Niehaus K, Nattkemper TW (2014) Allocator: An interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis. PLoS ONE 9(11), DOI:10.1371/journal.pone.0113909

Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014) Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology: 64-75, DOI:10.1016/j.jbiotec.2014.07.437

Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G (2014) Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 18(5): 853-863, DOI:10.1007/s00792-014-0676-3

Wegmann U, Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ (2014) Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans. Environmental microbiology 16(9): 2879-90, DOI:10.1111/1462-2920.12217

Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D (2014) GABenchToB: A genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS ONE 9(9), DOI:10.1371/journal.pone.0107014

Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Fischer N, Steinkämper A, Pühler A, Biener R, Schwartz D, Kalinowski J (2014) Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin. Journal of Biotechnology 178(1): 41-42, DOI:10.1016/j.jbiotec.2014.03.011

Becker J, Timmermann C, Rupp O, Albaum SP, Brinkrolf K, Goesmann A, Pühler A, Tauch A, Noll T (2014) Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR3. Journal of Biotechnology 178(1): 23-31, DOI:10.1016/j.jbiotec.2014.02.021

Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A (2014) Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS ONE 9(1), DOI:10.1371/journal.pone.0085568

Tielen P, Wibberg D, Blom J, Rosin N, Meyer A, Bunk B, Schobert M, Tupker R, Schatschneider S, Ruckert C, Albersmeier A, Goesmann A, Vorholter F, Jahn D, Puhler A (2014) Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection. Genome Announcements 2(1), DOI:10.1128/genomea.01174-13

Smits THM, Guerrero-Prieto VM, Hernandez-Escarcega G, Blom J, Goesmann A, Rezzonico F, Duffy B, Stockwell VO (2014) Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in rpsL Conferring Streptomycin Resistance and in the avrRpt2 Effector Altering Host Interactions. Genome Announcements 2(1), DOI:10.1128/genomea.01229-13

2013

Bolzan de Campos S, Youn J, Farina R, Jaenicke S, Jünemann S, Szczepanowski R, Beneduzi A, Vargas LK, Wendisch VF, Passaglia L (2013) Changes in Root Bacterial Communities associated to two different development stages of Canola (Brassica napus L. var oleifera) evaluated through Next-Generation Sequencing. Microbial Ecology 65(3): 593-601, DOI:10.1007/s00248-012-0132-9

Köhler KAK, Rückert C, Schatschneider S, Vorhölter F, Szczepanowski R, Blank LM, Niehaus K, Goesmann A, Pühler A, Kalinowski J, Schmid A (2013) Complete genome sequence of Pseudomonas sp. strain VLB120 a solvent tolerant, styrene degrading bacterium, isolated from forest soil. Journal of biotechnology 168(4): 729-30, DOI:10.1016/j.jbiotec.2013.10.016

Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Iftime D, Musiol EM, Blin K, Wohlleben W, Pühler A, Kalinowski J, Weber T (2013) Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids. Journal of biotechnology 168(4): 739-40, DOI:10.1016/j.jbiotec.2013.10.004

Bogen C, Al-Dilaimi A, Albersmeier A, Wichmann J, Grundmann M, Rupp O, Lauersen KJ, Blifernez-Klassen O, Kalinowski J, Goesmann A, Mussgnug JH, Kruse O (2013) Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. BMC Genomics 14(1), DOI:10.1186/1471-2164-14-926

Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, Von Haeseler A, Stoye J, Harmsen D (2013) Updating benchtop sequencing performance comparison. 31(4): 294-296, DOI:10.1038/nbt.2522

Kessler N, Neuweger H, Bonte A, Langenkämper G, Niehaus K, Nattkemper TW, Goesmann A (2013) MeltDB 2.0-advances of the metabolomics software system. Bioinformatics (Oxford, England) 29(19): 2452-9, DOI:10.1093/bioinformatics/btt414

Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B (2013) Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Systematic and Applied Microbiology 36(7): 449-456, DOI:10.1016/j.syapm.2013.04.003

Bolzan de Campos, S., Youn, J., Farina, R., Jaenicke, S., Jünemann, S., Szczepanowski, R., Beneduzi, A., Vargas, L.K., Wendisch, V.F. and Passaglia, L., 2013. Changes in Root Bacterial Communities associated to two different development stages of Canola (Brassica napus L. var oleifera) evaluated through Next-Generation Sequencing. Microbial Ecology, 65(3), pp.593-601, DOI:10.1007/s00248-012-0132-9.

Roetzer, A., Diel, R., Kohl, T.A., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch-Gerdes, S., Supply, P., Kalinowski, J. and Niemann, S., 2013. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS Medicine, 10(2), DOI:10.1371/journal.pmed.1001387.

Koeck, D.E., Wibberg, D., Koellmeier, T., Blom, J., Jaenicke, S., Winkler, A., Albersmeier, A., Zverlov, V.V., Pühler, A., Schwarz, W.H. and Schlüter, A., 2013. Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. Journal of Biotechnology, 168(1), pp.62-63, DOI:10.1016/j.jbiotec.2013.08.011.

Toepel, J., Illmer-Kephalides, M., Jaenicke, S., Straube, J., May, P., Goesmann, A. and Kruse, O., 2013. New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant Biotechnology Journal, 11(6), pp.717-733, DOI:10.1111/pbi.12062.

Luque-Almagro, V.M., Acera, F., Igeño, M.I., Wibberg, D., Roldán, M.D., Sáez, L.P., Hennig, M., Quesada, A., Huertas, M.J., Blom, J., Merchán, F., Escribano, M.P., Jaenicke, S., Estepa, J., Guijo, M.I., Mart\ńez-Luque, M., Mac\'ś, D., Szczepanowski, R., Becerra, G., Ramirez, S., Carmona, M.I., Gutiérrez, O., Manso, I., Pühler, A., Castillo, F., Moreno-Vivián, C., Schlüter, A. and Blasco, R., 2013. Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Environmental Microbiology, 15(1), pp.253-270, DOI:10.1111/j.1462-2920.2012.02875.x.

Weidner, S., Baumgarth, B., Göttfert, M., Jaenicke, S., Pühler, A., Schneiker-Bekel, S., Serrania, J., Szczepanowski, R. and Becker, A., 2013. Genome Sequence of Sinorhizobium meliloti Rm41. Genome Announcements, 1(1), DOI:10.1128/genomeA.00013-12.

Eikmeyer, F.G., Rademacher, A., Hanreich, A., Hennig, M., Jaenicke, S., Maus, I., Wibberg, D., Zakrzewski, M., Pühler, A., Klocke, M. and Schlüter, A., 2013. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnology for Biofuels, 6(1), DOI:10.1186/1754-6834-6-49.

Guimarães, L.C., Soares, S.C., Albersmeier, A., Blom, J., Jaenicke, S., Azevedo, V., Soriano, F., Tauch, A. and Trost, E., 2013. Complete Genome Sequence of Corynebacterium urealyticum Strain DSM 7111, Isolated from a 9-Year-Old Patient with Alkaline-Encrusted Cystitis. Genome Announcements, 1(3), DOI:10.1128/genomeA.00264-13.

Vences M, Susanne Hauswaldt J, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA (2013) Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Molecular Phylogenetics and Evolution 68(3): 657-670, DOI:10.1016/j.ympev.2013.04.014

Brinkrolf K, Rupp O, Laux H, Kollin F, Ernst W, Linke B, Kofler R, Romand S, Hesse F, Budach WE, Galosy S, Müller D, Noll T, Wienberg J, Jostock T, Leonard M, Grillari J, Tauch A, Goesmann A, Helk B, Mott JE, Pühler A, Borth N (2013) Chinese hamster genome sequenced from sorted chromosomes. 31(8): 694-695, DOI:10.1038/nbt.2645

Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A (2013) Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of biotechnology 167(2): 142-55, DOI:10.1016/j.jbiotec.2012.12.010

Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüterd A, Goesmann A (2013) MetaSAMS-A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology 167(2): 156-165, DOI:10.1016/j.jbiotec.2012.09.013

Toepel J, Illmer-Kephalides M, Jaenicke S, Straube J, May P, Goesmann A, Kruse O (2013) New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant biotechnology journal 11(6): 717-33, DOI:10.1111/pbi.12062

Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I (2013) Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PloS one 8(3): e57487, DOI:10.1371/journal.pone.0057487

Mann RA, Smits TH, Bühlmann A, Blom J, Goesmann A, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B (2013) Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core. PLoS ONE 8(2), DOI:10.1371/journal.pone.0055644

Fritzenwanker M, Kuenne C, Billion A, Hain T, Zimmermann K, Goesmann A, Chakraborty T, Domann E (2013) Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431. Genome announcements 1(1), DOI:10.1128/genomeA.00165-12

Smits, T., Rezzonico, F., López, M., Blom, J., Goesmann, A., Frey, J., Duffy, B.. (2013). Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Elsevier.Volume 36(7), 449--456. DOI: 10.1016/j.syapm.2013.04.003

Ruijter, J., Pfaffl, M., Zhao, S., Spiess, A., Boggy, G., Blom, J., Rutledge, R., Sisti, D., Lievens, A., De Preter, K., others. (2013). Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications. Elsevier.Volume 59(1), 32--46. DOI: 10.1016/j.ymeth.2012.08.011

Wichmann, F., Vorhölter, F., Hersemann, L., Widmer, F., Blom, J., Niehaus, K., Reinhard, S., Conradin, C., Kölliker, R.. (2013). The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Wiley Online Library.Volume 14(6), 576--588. DOI: 10.1111/mpp.12030

Soares, S., Silva, A., Trost, E., Blom, J., Ramos, R., Carneiro, A., Ali, A., Santos, A., Pinto, A., Diniz, C., others. (2013). The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. Public Library of Science.Volume 8(1), e53818. DOI: 10.1371/journal.pone.0053818

Brinkrolf, K., Rupp, O., Laux, H., Kollin, F., Ernst, W., Linke, B., Kofler, R., Romand, S., Hesse, F., Budach, W., others. (2013). Chinese hamster genome sequenced from sorted chromosomes. Nature Publishing Group US New York.Volume 31(8), 694--695. DOI: 10.1038/nbt.2645

Bomholt, C., Glaub, A., Gravermann, K., Albersmeier, A., Brinkrolf, K., Rückert, C., Tauch, A.. (2013). Whole-genome sequence of the clinical strain Corynebacterium argentoratense DSM 44202, isolated from a human throat specimen. Am Soc Microbiol.Volume 1(5), e00793--13. DOI: 10.1128/genomeA.00793-13

Barbé, S., Llop, P., Blom, J., Cabrefiga, J., Goesmann, A., Duffy, B., Montesinos, E., Smits, T., López, M.. (2013). Complete sequence of Erwinia piriflorinigrans plasmids p EPIR 37 and p EPIR 5 and role of p EPIR 37 in pathogen virulence. Volume 62(4), 786--798. : DOI: 10.1111/ppa.12002

Pereira, U., Soares, S., Blom, J., Leal, C., Ramos, R., Guimaraes, L., Oliveira, L., Almeida, S., Hassan, S., Santos, A., others. (2013). In silico prediction of conserved vaccine targets in Streptococcus agalactiae strains isolated from fish, cattle, and human samples. Volume 12(3), 2902--2912. DOI: 10.4238/2013.August.12.6

Dam, B., Dam, S., Blom, J., Liesack, W.. (2013). Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. Public Library of Science.Volume 8(10), e74767. DOI: 10.1371/journal.pone.0074767

Mann, R., Smits, T., Bühlmann, A., Blom, J., Goesmann, A., Frey, J., Plummer, K., Beer, S., Luck, J., Duffy, B., others. (2013). Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. Public Library of Science.Volume 8(2), e55644. DOI: 10.1371/journal.pone.0055644

Wu, H., Qiao, J., Blom, J., Rueckert, C., Reva, O., Gao, X., Borriss, R.. (2013). The rhizobacterium Bacillus amyloliquefaciens subsp. plantarum NAU-B3 contains a large inversion within the central portion of the genome. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 1(6), e00941--13. DOI: 10.1128/genomeA.00941-13

Vassen, V., Eichhorn, C., Goesmann, A., Blom, J., Strauch, E., Gunzer, F.. (2013). Characterization and curing of plasmid pVN0028 from the Vibrio parahaemolyticus patient isolate VN-0028. Volume 303, 110--110.

Guimarães, L., Soares, S., Albersmeier, A., Blom, J., Jaenicke, S., Azevedo, V., Soriano, F., Tauch, A., Trost, E.. (2013). Complete genome sequence of Corynebacterium urealyticum strain DSM 7111, isolated from a 9-year-old patient with alkaline-encrusted cystitis. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 1(3), e00264--13. DOI: 10.1128/genomeA.00264-13

Koeck, D., Wibberg, D., Koellmeier, T., Blom, J., Jaenicke, S., Winkler, A., Albersmeier, A., Zverlov, V., Pühler, A., Schwarz, W., others. (2013). Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. Elsevier.Volume 168(1), 62--63. DOI: 10.1016/j.jbiotec.2013.08.011

Eichhorn, C., Claudia, Z., Auerbach, C., Goesmann, A., Blom, J., Alter, T., Huehn, S., Strauch, E., Gunzer, F.. (2013). Genome sequencing, annotation and gap closure of four V. parahaemolyticus strains isolated in Germany. Volume 303, 112--112.

He, P., Hao, K., Blom, J., Rückert, C., Vater, J., Mao, Z., Wu, Y., Hou, M., He, P., He, Y., others. (2013). Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. Elsevier.Volume 164(2), 281--291. DOI: 10.1016/j.jbiotec.2012.12.014

Niu, B., Vater, J., Rueckert, C., Blom, J., Lehmann, M., Ru, J., Chen, X., Wang, Q., Borriss, R.. (2013). Polymyxin P is the active principle in suppressing phytopathogenic Erwinia spp. by the biocontrol rhizobacterium Paenibacillus polymyxa M-1. BioMed Central.Volume 13(1), 1--13. DOI: 10.1186/1471-2180-13-137

Roetzer, A., Diel, R., Kohl, T., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch-Gerdes, S., others. (2013). Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. Public Library of Science San Francisco, USA.Volume 10(2), e1001387. DOI: 10.1371/journal.pmed.1001387

Wibberg, D., Blom, J., Rückert, C., Winkler, A., Albersmeier, A., Pühler, A., Schlüter, A., Scharf, B.. (2013). Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis. Elsevier.Volume 168(4), 731--733. DOI: 10.1016/j.jbiotec.2013.10.015

Luque-Almagro, V., Acera, F., Igeño, M., Wibberg, D., Roldán, M., Sáez, L., Hennig, M., Quesada, A., Huertas, M., Blom, J., others. (2013). Draft whole genome sequence of the cyanide-degrading bacterium P seudomonas pseudoalcaligenes CECT 5344. Wiley Online Library.Volume 15(1), 253--270. DOI: 10.1111/j.1462-2920.2012.02875.x

Kuenne C, Billion A, Mraheil MA, Strittmatter A, Daniel R, Goesmann A, Barbuddhe S, Hain T, Chakraborty T (2013) Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC genomics 14(1): 47, DOI:10.1186/1471-2164-14-47

A, W., S, K., O, R., T, N. and R, H., 2013. First CpG island microarray for genome-wide analyses of DNA methylation in Chinese hamster ovary cells: new insights into the epigenetic answer to butyrate treatment. BMC proceedings, DOI:10.1186/1753-6561-7-s6-o5.

J, G., C, T., J, B., T, T., O, R., H, B., A, L., A, G. and T, N., 2013. Multidimension cultivation analysis by standard and omics methods for optimization of therapeutics production. BMC proceedings, DOI:10.1186/1753-6561-7-s6-p5.

C, B., A, A., A, A., J, W., M, G., O, R., KJ, L., O, B., J, K., A, G., JH, M. and O, K., 2013. Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. BMC genomics, DOI:10.1186/1471-2164-14-926.

A, D., D, G., K, F., DS, S., S, K., O, R., A, L., M, D., E, V. and S, S., 2013. What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina-based approaches. Ecology and evolution, DOI:10.1002/ece3.764.

M, V., JS, H., S, S., O, R., A, G., S, K., P, O., DR, V., S, N., S, H., C, L., M, G. and NA, S., 2013. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Molecular phylogenetics and evolution, DOI:10.1016/j.ympev.2013.04.014.

K, B., O, R., H, L., F, K., W, E., B, L., R, K., S, R., F, H., WE, B., S, G., D, M., T, N., J, W., T, J. and N, B., 2013. Chinese hamster genome sequenced from sorted chromosomes. Nature biotechnology, DOI:10.1038/nbt.2645.

D, W., L, J., O, R., M, H., F, E., A, G., A, H., R, B., R, G., A, P. and A, S., 2013. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of biotechnology, DOI:10.1016/j.jbiotec.2012.12.010.

M, Z., T, B., C, A., A, P., O, R., J, S., A, S. and A, G., 2013. MetaSAMS-a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of biotechnology, DOI:10.1016/j.jbiotec.2012.09.013.

2012

P, M., R, H., M, H., O, R., JH, B., C, C., K, B., S, K., B, M., P, D., M, H., TF, B., T, N., J, G. and N, B., 2012. Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics. Biotechnology and bioengineering, DOI:10.1002/bit.24476.

J, S., O, R., E, T., S, J., V, P., A, G., A, T. and K, B., 2012. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS yeast research, DOI:10.1111/j.1567-1364.2012.00791.x.

M, H., V, J., T, J., O, R., K, B., A, G., A, P., T, N., N, B. and J, G., 2012. Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of biotechnology, DOI:10.1016/j.jbiotec.2012.01.019.

Brinkrolf, K., Schneider, J., Knecht, M., Rückert, C., Tauch, A.. (2012). Draft genome sequence of Turicella otitidis ATCC 51513, isolated from middle ear fluid from a child with otitis media. Am Soc Microbiol. DOI: https://doi.org/10.1128/jb.01412-12

Meleady, P., Hoffrogge, R., Henry, M., Rupp, O., Bort, J., Clarke, C., Brinkrolf, K., Kelly, S., Müller, B., Doolan, P., others. (2012). Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics. Wiley Online Library.Volume 109(6), 1386--1394. DOI: 10.1002/bit.24476

Schneider, J., Andrea, H., Blom, J., Jaenicke, S., Rückert, C., Schorsch, C., Szczepanowski, R., Farwick, M., Goesmann, A., Pühler, A., others. (2012). Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Am Soc Microbiol. DOI: 10.1128/EC.00258-12

Schneider, J., Rupp, O., Trost, E., Jaenicke, S., Passoth, V., Goesmann, A., Tauch, A., Brinkrolf, K.. (2012). Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. Blackwell Publishing Ltd Oxford, UK.Volume 12(3), 382--386. DOI: 10.1111/j.1567-1364.2012.00791.x

Hackl, M., Jadhav, V., Jakobi, T., Rupp, O., Brinkrolf, K., Goesmann, A., Pühler, A., Noll, T., Borth, N., Grillari, J.. (2012). Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Elsevier.Volume 158(3), 151--155. DOI: 10.1016/j.jbiotec.2012.01.019

Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, Schaffer S, Tauch A, Köhler T, Brinkrolf K (2012) Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryotic Cell 11(12): 1582-1583, DOI:10.1128/EC.00258-12

Rose MT, Rose TJ, Pariasca-Tanaka J, Yoshihashi T, Neuweger H, Goesmann A, Frei M, Wissuwa M (2012) Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess. Planta 236(4): 959-973, DOI:10.1007/s00425-012-1648-4

Zischka M, Kuenne C, Blom J, Dabrowski PW, Linke B, Hain T, Nitsche A, Goesmann A, Larsen J, Jensen LB, Witte W, Werner G (2012) Complete genome sequence of the porcine isolate Enterococcus faecalis D32. 194(19): 5490-5491, DOI:10.1128/JB.01298-12

Heinl S, Wibberg D, Eikmeyer F, Szczepanowski R, Blom J, Linke B, Goesmann A, Grabherr R, Schwab H, Pühler A, Schlüter A (2012) Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. Journal of Biotechnology 161(2): 153-166, DOI:10.1016/j.jbiotec.2012.03.007

Rezzonico F, Braun-Kiewnick A, Mann RA, Rodoni B, Goesmann A, Duffy B, Smits TH (2012) Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora. Molecular Plant Pathology 13(8): 975-984, DOI:10.1111/j.1364-3703.2012.00807.x

Schork S, Schlüter A, Blom J, Schneiker-Bekel S, Pühler A, Goesmann A, Frosch M, Schoen C (2012) Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198. 194(18): 5144-5145, DOI:10.1128/JB.01099-12

Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D (2012) Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PloS one 7(8): e41606, DOI:10.1371/journal.pone.0041606

Mann RA, Blom J, Bühlmann A, Plummer KM, Beer SV, Luck JE, Goesmann A, Frey JE, Rodoni BC, Duffy B, Smits THM (2012) Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. Gene 504(1): 6-12, DOI:10.1016/j.gene.2012.05.002

Filippini M, Qi W, Jaenicke S, Goesmann A, Smits TH, Bagheri HC (2012) Genome sequence of the Filamentous bacterium Fibrisoma limi BUZ 3T. 194(16): 4445-4445, DOI:10.1128/JB.00869-12

Trötschel C, Albaum SP, Wolff D, Schrod S, Goesmanns A, Nattkemper TW, Poetsch A (2012) Protein turnover quantification in a multilabeling approach: From data calculation to evaluation. Molecular and Cellular Proteomics 11(8): 512-526, DOI:10.1074/mcp.M111.014134

Filippini M, Qi W, Blom J, Goesmann A, Smits TH, Bagheri HC (2012) Genome sequence of Fibrella aestuarina BUZ 2T, a filamentous marine bacterium. 194(13): 3555, DOI:10.1128/JB.00550-12

Schneider J, Rupp O, Trost E, Jaenicke S, Passoth V, Goesmann A, Tauch A, Brinkrolf K (2012) Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Research 12(3): 382-386, DOI:10.1111/j.1567-1364.2012.00791.x

Kahlke T, Goesmann A, Hjerde E, Willassen NP, Haugen P (2012) Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation. BMC Genomics 13(1), DOI:10.1186/1471-2164-13-179

Brankatschk K, Blom J, Goesmann A, Smits TH, Duffy B (2012) Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. International Journal of Food Microbiology 155(3): 247-256, DOI:10.1016/j.ijfoodmicro.2012.01.024

Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, Izar B, Mohamed W, Mraheil MA, Domann E, Schaffrath S, Kärst U, Goesmann A, Oehm S, Pühler A, Merkl R, Vorwerk S, Glaser P, Garrido P, Rusniok C, Buchrieser C, Goebel W, Chakraborty T (2012) Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics 13(1), DOI:10.1186/1471-2164-13-144

Hackl M, Jadhav V, Jakobi T, Rupp O, Brinkrolf K, Goesmann A, Pühler A, Noll T, Borth N, Grillari J (2012) Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of Biotechnology 158(3): 151-155, DOI:10.1016/j.jbiotec.2012.01.019

Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology 158(4): 248-258, DOI:10.1016/j.jbiotec.2012.01.020

Blom, J., Rueckert, C., Niu, B., Wang, Q., Borriss, R.. (2012). The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of iturin A. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.06762-11

Jankowitsch, F., Schwarz, J., Rückert, C., Gust, B., Szczepanowski, R., Blom, J., Pelzer, S., Kalinowski, J., Mack, M.. (2012). Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 194(24), 6818--6827. DOI: 10.1128/JB.01592-12

Strobel, T., Al-Dilaimi, A., Blom, J., Gessner, A., Kalinowski, J., Luzhetska, M., Pühler, A., Szczepanowski, R., Bechthold, A., Rückert, C.. (2012). Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae. BioMed Central.Volume 13(1), 1--13. DOI: 10.1186/1471-2164-13-465

Hao, K., He, P., Blom, J., Rueckert, C., Mao, Z., Wu, Y., He, Y., Borriss, R.. (2012). The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.00545-12

Zischka, M., Kuenne, C., Blom, J., Dabrowski, P., Linke, B., Hain, T., Nitsche, A., Goesmann, A., Larsen, J., Jensen, L., others. (2012). Complete genome sequence of the porcine isolate Enterococcus faecalis D32. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.01298-12

Schneider, J., Andrea, H., Blom, J., Jaenicke, S., Rückert, C., Schorsch, C., Szczepanowski, R., Farwick, M., Goesmann, A., Pühler, A., others. (2012). Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/EC.00258-12

Maus, I., Wibberg, D., Stantscheff, R., Eikmeyer, F., Seffner, A., Boelter, J., Szczepanowski, R., Blom, J., Jaenicke, S., König, H., others. (2012). Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2T, isolated from a sewage sludge digester. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: https://doi.org/10.1128/jb.01292-12

Trost, E., Blom, J., de Castro Soares, S., Huang, I., Al-Dilaimi, A., Schröder, J., Jaenicke, S., Dorella, F., Rocha, F., Miyoshi, A., others. (2012). Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 194(12), 3199--3215. DOI: 10.1128/JB.00183-12

Brankatschk, K., Blom, J., Goesmann, A., Smits, T., Duffy, B.. (2012). Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. Elsevier.Volume 155(3), 247--256. DOI: 10.1016/j.ijfoodmicro.2012.01.024

Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., Trost, E., Tauch, A.. (2012). Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BioMed Central.Volume 13(1), 1--19. DOI: 10.1186/1471-2164-13-141

Mann, R., Blom, J., Bühlmann, A., Plummer, K., Beer, S., Luck, J., Goesmann, A., Frey, J., Rodoni, B., Duffy, B., others. (2012). Comparative analysis of the Hrp pathogenicity island of Rubus-and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. Elsevier.Volume 504(1), 6--12. DOI: 10.1016/j.gene.2012.05.002

Schork, S., Schlüter, A., Blom, J., Schneiker-Bekel, S., Pühler, A., Goesmann, A., Frosch, M., Schoen, C.. (2012). Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.01099-12

Filippini, M., Qi, W., Blom, J., Goesmann, A., Smits, T., Bagheri, H.. (2012). Genome sequence of Fibrella aestuarina BUZ 2T, a filamentous marine bacterium. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.00550-12

Zschüttig, A., Zimmermann, K., Blom, J., Goesmann, A., Pöhlmann, C., Gunzer, F.. (2012). Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. Public Library of Science.Volume 7(3), e33351. DOI: 10.1371/journal.pone.0033351

Heinl, S., Wibberg, D., Eikmeyer, F., Szczepanowski, R., Blom, J., Linke, B., Goesmann, A., Grabherr, R., Schwab, H., Pühler, A., others. (2012). Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. Elsevier.Volume 161(2), 153--166. DOI: 10.1016/j.jbiotec.2012.03.007

De Maayer, P., Chan, W., Rezzonico, F., Bühlmann, A., Venter, S., Blom, J., Goesmann, A., Frey, J., Smits, T., Duffy, B., others. (2012). Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.06715-11

Parreira, V., Costa, M., Eikmeyer, F., Blom, J., Prescott, J.. (2012). Sequence of two plasmids from Clostridium perfringens chicken necrotic enteritis isolates and comparison with C. perfringens conjugative plasmids. Public Library of Science.Volume 7(11), e49753. DOI: 10.1371/journal.pone.0049753

De Maayer, P., Chan, W., Blom, J., Venter, S., Duffy, B., Smits, T., Coutinho, T.. (2012). The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. BioMed Central.Volume 13(1), 1--12. DOI: 10.1186/1471-2164-13-625

Rademacher A, Zakrzewski M, Schlüter A, Schönberg M, Szczepanowski R, Goesmann A, Pühler A, Klocke M (2012) Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiology Ecology 79(3): 785-799, DOI:10.1111/j.1574-6941.2011.01265.x

De Maayer P, Chan WY, Rezzonico F, Bühlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits TH, Duffy B, Coutinho TA (2012) Complete genome sequence of clinical isolate pantoea ananatis LMG 5342. 194(6): 1615-1616, DOI:10.1128/JB.06715-11

Zschüttig A, Zimmermann K, Blom J, Goesmann A, Pöhlmann C, Gunzer F (2012) Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. PLoS ONE 7(3), DOI:10.1371/journal.pone.0033351

Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F.G., Szczepanowski, R., Al-Soud, W.A., Sørensen, S., Pühler, A. and Schlüter, A., 2012. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology, 158(4), pp.248-258, DOI:10.1016/j.jbiotec.2012.01.020.

Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., Trost, E. and Tauch, A., 2012. Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC Genomics, 13(1), DOI:10.1186/1471-2164-13-141.

Dohrmann, A.B., Küting, M., Jünemann, S., Jaenicke, S., Schlüter, A. and Tebbe, C.C., 2012. Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. The ISME Journal, 7(1), pp.37-49, DOI:10.1038/ismej.2012.77.

Trost, E., Blom, J., de Castro Soares, S., Huang, I., Al-Dilaimi, A., Schröder, J., Jaenicke, S., Dorella, F.A., Rocha, F.S., Miyoshi, A., Azevedo, V., Schneider, M.P., Silva, A., Camello, T.C., Sabbadini, P.S., Santos, C.S., Santos, L.S., Hirata, R.J., Mattos-Guaraldi, A.L., Efstratiou, A., Schmitt, M.P., Ton-That, H. and Tauch, A., 2012. Pangenomic Study of Corynebacterium diphtheriae that provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia. Journal of Bacteriology, 194(12), pp.3199-3215, DOI:10.1128/JB.00183-12.

Schneider, J., Andrea, H., Blom, J., Jaenicke, S., Rückert, C., Schorsch, C., Szczepanowski, R., Farwick, M., Goesmann, A., Pühler, A., Schaffer, S., Tauch, A., Köhler, T. and Brinkrolf, K., 2012. Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryotic Cell, 11(12), pp.1582-1583, DOI:10.1128/EC.00258-12.

Maus, I., Wibberg, D., Stantscheff, R., Eikmeyer, F.G., Seffner, A., Boelter, J., Szczepanowski, R., Blom, J., Jaenicke, S., Konig, H., Pühler, A. and Schlüter, A., 2012. Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. Journal of Bacteriology, 194(19), pp.5487-5488, DOI:10.1128/JB.01292-12.

Weidner, S., Becker, A., Bonilla, I., Jaenicke, S., Lloret, J., Margaret, I., Pühler, A., Ruiz-Sainz, J.E., Schneiker-Bekel, S., Szczepanowski, R., Vinardell, J.M., Zehner, S. and Göttfert, M., 2012. Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103. Journal of Bacteriology, 194(6), pp.1617-1618, DOI:10.1128/JB.06729-11.

Schneider, J., Rupp, O., Trost, E., Jaenicke, S., Passoth, V., Goesmann, A., Tauch, A. and Brinkrolf, K., 2012. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Research, 12(3), pp.382-386, DOI:10.1111/j.1567-1364.2012.00791.x.

Filippini, M., Qi, W., Jaenicke, S., Goesmann, A., Smits, T.H.M. and Bagheri, H.C., 2012. Genome Sequence of the filamentous Bacterium Fibrisoma limi BUZ 3(T). Journal of Bacteriology, 194(16), DOI:10.1128/JB.00869-12.

2011

Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann K, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Pühler A, Schlüter A, Goesmann A (2011) Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE 6(1), DOI:10.1371/journal.pone.0014519

González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C (2011) Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Applied and Environmental Microbiology 77(24): 8676-8686, DOI:10.1128/AEM.06152-11

Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, FreyJü JE, Stockwell VO, Duffy B (2011) Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist pantoea vagans C9-1. PLoS ONE 6(7), DOI:10.1371/journal.pone.0022247

Becker J, Timmermann C, Jakobi T, Rupp O, Szczepanowski R, Hackl M, Goesmann A, Tauch A, Borth N, Grillari J, Pühler A, Noll T, Brinkrolf K (2011) Next-generation sequencing of the CHO cell transcriptome. BMC Proceedings 5(S8), DOI:10.1186/1753-6561-5-s8-p6

Becker J, Hackl M, Rupp O, Jakobi T, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Pühler A, Tauch A, Brinkrolf K (2011) Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology 156(3): 227-235, DOI:10.1016/j.jbiotec.2011.09.014

Joseph B, Schwarz RF, Linke B, Blom J, Becker A, Claus H, Goesmann A, Frosch M, Müller T, Vogel U, Schoen C (2011) Virulence evolution of the human pathogen neisseria meningitidis by recombination in the core and accessory genome. PLoS ONE 6(4), DOI:10.1371/journal.pone.0018441

Toepel J, Albaum SP, Arvidsson S, Goesmann A, la Russa M, Rogge K, Kruse O (2011) Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics, DOI:10.1186/1471-2164-12-579

Ausec L, Zakrzewski M, Goesmann A, Schlüter A, Mandic-Mulec I (2011) Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. PLoS ONE 6(10), DOI:10.1371/journal.pone.0025724

Pothier JF, Vorhölter FJ, Blom J, Goesmann A, Pühler A, Smits TH, Duffy B (2011) The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: Complete sequence and comparative genomic analysis. FEMS Microbiology Letters 323(1): 52-60, DOI:10.1111/j.1574-6968.2011.02352.x

Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Pühler A, Schlüter A (2011) Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology 155(1): 50-62, DOI:10.1016/j.jbiotec.2011.01.010

Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A (2011) RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology 155(1): 118-126, DOI:10.1016/j.jbiotec.2010.10.076

Krol E, Blom J, Winnebald J, Berhörster A, Barnett MJ, Goesmann A, Baumbach J, Becker A (2011) RhizoRegNet-a database of rhizobial transcription factors and regulatory networks. Journal of biotechnology 155(1): 127-34, DOI:10.1016/j.jbiotec.2010.11.004

Margaret I, Becker A, Blom J, Bonilla I, Goesmann A, Göttfert M, Lloret J, Mittard-Runte V, Rückert C, Ruiz-Sainz JE, Vinardell JM, Weidner S (2011) Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. Journal of Biotechnology 155(1): 11-19, DOI:10.1016/j.jbiotec.2011.03.016

Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorhölter FJ, Weidner S, Goesmann A, Pühler A, Schlüter A (2011) The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Journal of Biotechnology 155(1): 20-33, DOI:10.1016/j.jbiotec.2010.12.018

Küberl A, Schneider J, Thallinger GG, Anderl I, Wibberg D, Hajek T, Jaenicke S, Brinkrolf K, Goesmann A, Szczepanowski R, Pühler A, Schwab H, Glieder A, Pichler H (2011) High-quality genome sequence of Pichia pastoris CBS7435. Journal of Biotechnology 154(4): 312-320, DOI:10.1016/j.jbiotec.2011.04.014

Albaum SP, Hahne H, Otto A, Haußmann U, Becher D, Poetsch A, Goesmann A, Nattkemper TW (2011) A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: An application study. Proteome Science, DOI:10.1186/1477-5956-9-30

Thomas V, Bertelli C, Collyn F, Casson N, Telenti A, Goesmann A, Croxatto A, Greub G (2011) Lausannevirus, a giant amoebal virus encoding histone doublets. Environmental Microbiology 13(6): 1454-1466, DOI:10.1111/j.1462-2920.2011.02446.x

Linke B, Giegerich R, Goesmann A (2011) Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics (Oxford, England) 27(7): 903-11, DOI:10.1093/bioinformatics/btr040

de Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS (2011) Deep sequencing of naupliar-, cyprid- and adult-specific normalised expressed sequence tag (EST) libraries of the acorn barnacle Balanus amphitrite. Biofouling 27(4): 367-374, DOI:10.1080/08927014.2011.577211

Brankatschk K, Blom J, Goesmann A, Smits TH, Duffy B (2011) Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica Serovar Weltevreden. Journal of Bacteriology 193(8): 2066, DOI:10.1128/JB.00123-11

Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner Zu Siederdissen C, Bort JAH, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J (2011) Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of biotechnology 153(1-2): 62-75, DOI:10.1016/j.jbiotec.2011.02.011

Schoen C, Weber-Lehmann J, Blom J, Joseph B, Goesmann A, Strittmatter A, Frosch M (2011) Whole-genome sequence of the transformable Neisseria meningitidis Serogroup a strain WUE2594. 193(8): 2064-2065, DOI:10.1128/JB.00084-11

Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011) Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27(10): 1351-1358, DOI:10.1093/bioinformatics/btr151

Zschuettig, A., Eichhorn, C., Meltke, S., Zimmermann, K., Wassenaar, T., Blom, J., Goesmann, A., Jarek, M., Scharfe, M., Gunzer, F.. (2011). Genome analysis of probiotic Symbioflor 2 Escherichia coli DSM17252. Volume 301, 103--103. DOI: 10.1128/genomeA.01330-14

Brankatschk, K., Blom, J., Goesmann, A., Smits, T., Duffy, B.. (2011). Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar Weltevreden. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.00123-11

J, B., M, H., O, R., T, J., J, S., R, S., T, B., N, B., A, G., J, G., C, K., T, N., A, P., A, T. and K, B., 2011. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of biotechnology, DOI:10.1016/j.jbiotec.2011.09.014.

J, B., C, T., T, J., O, R., R, S., M, H., A, G., A, T., N, B., J, G., A, P., T, N. and K, B., 2011. Next-generation sequencing of the CHO cell transcriptome. BMC proceedings, DOI:10.1186/1753-6561-5-s8-p6.

D, W., J, B., S, J., F, K., O, R., B, S., S, S., R, S., A, G., JC, S., R, S., A, P. and A, S., 2011. Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of biotechnology, DOI:10.1016/j.jbiotec.2011.01.010.

TB, D.G., O, R., S, K., F, K., T, B., M, K., JG, B., MI, A., A, G., R, R. and AS, C., 2011. Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite. Biofouling, DOI:10.1080/08927014.2011.577211.

Smits, T., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Ishimaru, C., Frey, J., Stockwell, V., Duffy, B.. (2011). Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1. Public Library of Science.Volume 6(7), e22247. DOI: 10.1371/journal.pone.0022247

Schoen, C., Weber-Lehmann, J., Blom, J., Joseph, B., Goesmann, A., Strittmatter, A., Frosch, M.. (2011). Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.00084-11

Borriss, R., Chen, X., Rueckert, C., Blom, J., Becker, A., Baumgarth, B., Fan, B., Pukall, R., Schumann, P., Spröer, C., others. (2011). Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Microbiology Society.Volume 61(8), 1786--1801. DOI: 10.1099/ijs.0.023267-0

Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S., Zu Siederdissen, C., Bort, J., Wieser, M., others. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Elsevier.Volume 153(1-2), 62--75. DOI: 10.1016/j.jbiotec.2011.02.011

Borriss, R., Rueckert, C., Blom, J., Bezuidt, O., Reva, O., Klenk, H.. (2011). Whole genome sequence comparisons in taxonomy. Academic Press.Volume 38, 409--436. DOI: 10.1016/B978-0-12-387730-7.00018-8

Pothier, J., Vorhölter, F., Blom, J., Goesmann, A., Pühler, A., Smits, T., Duffy, B.. (2011). The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. Blackwell Publishing Ltd Oxford, UK.Volume 323(1), 52--60. DOI: 10.1111/j.1574-6968.2011.02352.x

Llop, P., Cabrefiga, J., Smits, T., Dreo, T., Barbe, S., Pulawska, J., Bultreys, A., Blom, J., Duffy, B., Montesinos, E., others. (2011). Erwinia amylovora novel plasmid pEI70: complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen. Public Library of Science.Volume 6(12), e28651. DOI: 10.1371/journal.pone.0028651

Szczepanowski, R., Eikmeyer, F., Harfmann, J., Blom, J., Rogers, L., Top, E., Schlüter, A.. (2011). Sequencing and comparative analysis of IncP-1$\alpha$ antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Elsevier.Volume 155(1), 95--103. DOI: 10.1016/j.jbiotec.2010.11.018

Imperi, F., Antunes, L., Blom, J., Villa, L., Iacono, M., Visca, P., Carattoli, A.. (2011). The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. Wiley Subscription Services, Inc., a Wiley company New York.Volume 63(12), 1068--1074. DOI: 10.1002/iub.531

Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., Goesmann, A.. (2011). RAPYD—rapid annotation platform for yeast data. Elsevier.Volume 155(1), 118--126. DOI: 10.1016/j.jbiotec.2010.10.076

Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Sczcepanowski, R., Goesmann, A., Setubal, J., others. (2011). Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Elsevier.Volume 155(1), 50--62. DOI: 10.1016/j.jbiotec.2011.01.010

Pothier, J., Smits, T., Blom, J., Vorhoelter, F., Goesmann, A., Pühler, A., Duffy, B.. (2011). Complete genome sequence of the stone fruit pathogen Xanthomonas arboricola pv. pruni. Volume 101(6), S144--S145. DOI: 10.1128/mra.00209-22

Joseph, B., Schwarz, R., Linke, B., Blom, J., Becker, A., Claus, H., Goesmann, A., Frosch, M., Müller, T., Vogel, U., others. (2011). Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. Public Library of Science.Volume 6(4), e18441. DOI: 10.1371/journal.pone.0018441

Kant, R., Blom, J., Palva, A., Siezen, R., de Vos, W.. (2011). Comparative genomics of Lactobacillus. Blackwell Publishing Ltd Oxford, UK.Volume 4(3), 323--332. DOI: 10.1111/j.1751-7915.2010.00215.x

Luetticken, R., Bruellhoff, K., van der Linden, M., Peltroche-Llacsahunga, H., Blom, J., Weber-Lehmann, J., Ferretti, J., McShan, W.. (2011). Complete genome sequence of a streptococcus dysgalactiae subsp. equisimilis possessing Lancefield's Group A antigen and its comparative genomics. Volume 301, 67--67. DOI: 10.1093/gbe/evt117

Niu, B., Rueckert, C., Blom, J., Wang, Q., Borriss, R.. (2011). The genome of the plant growth-promoting rhizobacterium Paenibacillus polymyxa M-1 contains nine sites dedicated to nonribosomal synthesis of lipopeptides and polyketides. American Society for Microbiology 1752 N St., NW, Washington, DC. DOI: 10.1128/JB.05806-11

Krol, E., Blom, J., Winnebald, J., Berhörster, A., Barnett, M., Goesmann, A., Baumbach, J., Becker, A.. (2011). RhizoRegNet—a database of rhizobial transcription factors and regulatory networks. Elsevier.Volume 155(1), 127--134. DOI: 10.1016/j.jbiotec.2010.11.004

Powney, R., Smits, T., Sawbridge, T., Frey, B., Blom, J., Frey, J., Plummer, K., Beer, S., Luck, J., Duffy, B., others. (2011). Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 193(3), 785--786. DOI: 10.1128/JB.01352-10

Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J., Goesmann, A.. (2011). Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Oxford University Press.Volume 27(10), 1351--1358. DOI: 10.1093/bioinformatics/btr151

Hinse, D., Vollmer, T., Rückert, C., Blom, J., Kalinowski, J., Knabbe, C., Dreier, J.. (2011). Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis. BioMed Central.Volume 12(1), 1--13. DOI: 10.1186/1471-2164-12-400

Borriss, R., Chen, X., Rueckert, C., Blom, J., Becker, A., Baumgarth, B., Fan, B., Pukall, R., Schumann, P., Sproer, C., others. (2011). New taxa-firmicutes and related organisms. Volume 61, 000--000.

Schneiker-Bekel, S., Wibberg, D., Bekel, T., Blom, J., Linke, B., Neuweger, H., Stiens, M., Vorhölter, F., Weidner, S., Goesmann, A., others. (2011). The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Elsevier.Volume 155(1), 20--33. DOI: 10.1016/j.jbiotec.2010.12.018

Margaret, I., Becker, A., Blom, J., Bonilla, I., Goesmann, A., Göttfert, M., Lloret, J., Mittard-Runte, V., Rückert, C., Ruiz-Sainz, J., others. (2011). Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. Elsevier.Volume 155(1), 11--19. DOI: 10.1016/j.jbiotec.2011.03.016

Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S., Zu Siederdissen, C., Bort, J., Wieser, M., others. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Elsevier.Volume 153(1-2), 62--75. DOI: 10.1016/j.jbiotec.2011.02.011

Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., Goesmann, A.. (2011). RAPYD—rapid annotation platform for yeast data. Elsevier.Volume 155(1), 118--126. DOI: 10.1016/j.jbiotec.2010.10.076

Becker, J., Hackl, M., Rupp, O., Jakobi, T., Schneider, J., Szczepanowski, R., Bekel, T., Borth, N., Goesmann, A., Grillari, J., others. (2011). Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Elsevier.Volume 156(3), 227--235. DOI: 10.1016/j.jbiotec.2011.09.014

Küberl, A., Schneider, J., Thallinger, G., Anderl, I., Wibberg, D., Hajek, T., Jaenicke, S., Brinkrolf, K., Goesmann, A., Szczepanowski, R., others. (2011). High-quality genome sequence of Pichia pastoris CBS7435. Elsevier.Volume 154(4), 312--320. DOI: 10.1016/j.jbiotec.2011.04.014

Becker, J., Timmermann, C., Jakobi, T., Rupp, O., Szczepanowski, R., Hackl, M., Goesmann, A., Tauch, A., Borth, N., Grillari, J., others. (2011). Next-generation sequencing of the CHO cell transcriptome. Volume 5, 1--2. DOI: 10.1186/1753-6561-5-S8-P6

Rückert, C., Blom, J., Chen, X., Reva, O., Borriss, R.. (2011). Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. Elsevier.Volume 155(1), 78--85. DOI: 10.1016/j.jbiotec.2011.01.006

Jaenicke, S., Zakrzewski, M., Jünemann, S., Pühler, A., Goesmann, A. and Schlüter, A., 2011. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods., pp.403-414, DOI:10.1002/9781118010549.

Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Szczepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Pühler, A. and Schlüter, A., 2011. Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology, 155(1), pp.50-62, DOI:10.1016/j.jbiotec.2011.01.010.

Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A. and Goesmann, A., 2011. RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology, 155(1), pp.118-126, DOI:10.1016/j.jbiotec.2010.10.076.

Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J. and Goesmann, A., 2011. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics, 27(10), pp.1351-1358, DOI:10.1093/bioinformatics/btr151.

Kueberl, A., Schneider, J., Thallinger, G.G., Anderl, I., Wibberg, D., Hajek, T., Jaenicke, S., Brinkrolf, K., Goesmann, A., Szczepanowski, R., Pühler, A., Schwab, H., Glieder, A. and Pichler, H., 2011. High-quality genome sequence of Pichia pastoris CBS7435. Journal of Biotechnology, 154(4), pp.312-320, DOI:10.1016/j.jbiotec.2011.04.014.

Gonzalez, J.M., Pinhassi, J., Fernández-Gómez, B., Coll-Llado, M., Gonzalez-Velazquez, M., Puigbo, P., Jaenicke, S., Gomez-Consarnau, L., Fernandez-Guerra, A., Goesmann, A. and Pedros-Alio, C., 2011. Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology, 77(24), pp.8676-8686, DOI:10.1128/aem.06152-11.

Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K., Jünemann, S., Kaiser, O., Krause, L., Tille, F., Zakrzewski, M., Pühler, A., Schlüter, A. and Goesmann, A., 2011. Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE, 6(1), DOI:10.1371/journal.pone.0014519.

2010

Mittard-Runte, V., Bekel, T., Blom, J., Dondrup, M., Henckel, K., Jaenicke, S., Krause, L., Linke, B., Neuweger, H., Schneiker-Bekel, S. and Goesmann, A., 2010. Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions., pp.315-396, DOI:10.1007/978-90-481-8639-6.

Trost, E., Ott, L., Schneider, J., Schröder, J., Jaenicke, S., Goesmann, A., Husemann, P., Stoye, J., Alves Dorella, F., Souza Rocha, F., de Castro Soares, S., D'Afonseca, V., Miyoshi, A., Ruiz, J., Silva, A., Azevedo, V., Burkovski, A., Guiso, N., Join-Lambert, O.F., Kayal, S. and Tauch, A., 2010. The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-728.

Smits, T.H.M., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J.E. and Duffy, B., 2010. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-2.

Schlüter, J., Reinkensmeier, J., Daschkey, S., Evguenieva-Hackenberg, E., Janssen, S., Jaenicke, S., Becker, J.D., Giegerich, R. and Becker, A., 2010. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-245.

Smits THM, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B (2010) Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics 11(1), DOI:10.1186/1471-2164-11-2

Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B (2010) Genome sequence of the biocontrol agent Pantoea vagans strain C9-1. Journal of Bacteriology 192(24): 6486-6487, DOI:10.1128/JB.01122-10

Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Dorella FA, Rocha FS, de Castro Soares S, D'Afonseca V, Miyoshi A, Ruiz J, Silva A, Azevedo V, Burkovski A, Guiso N, Join-Lambert OF, Kayal S, Tauch A (2010) The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics 11(1), DOI:10.1186/1471-2164-11-728

Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G (2010) The waddlia genome: A window into chlamydial biology. PLoS ONE 5(5), DOI:10.1371/journal.pone.0010890

Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC (2010) Visualization of omics data for systems biology. 7(3): S56-S68, DOI:10.1038/nmeth.1436

Joseph B, Schneiker-Bekel S, Schramm-Glück A, Blom J, Claus H, Linke B, Schwarz RF, Becker A, Goesmann A, Frosch M, Schoen C (2010) Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. Journal of Bacteriology 192(20): 5363-5377, DOI:10.1128/JB.00883-10

Henckel K, Küster H, Stutz LJ, Goesmann A (2010) MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. BMC research notes: 262, DOI:10.1186/1756-0500-3-262

Kuenne C, Voget S, Pischimarov J, Oehm S, Goesmann A, Daniel R, Hain T, Chakraborty T (2010) Comparative analysis of plasmids in the genus Listeria. PloS one 5(9): 1-7, DOI:10.1371/journal.pone.0012511

Schneider J, Vorhölter F, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A (2010) CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. Genetics and molecular research : GMR 9(3): 1660-72, DOI:10.4238/vol9-3gmr901

Smits TH, Rezzonico F, Pelludat C, Goesmann A, Frey JE, Duffy B (2010) Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3. FEMS Microbiology Letters 308(1): 48-54, DOI:10.1111/j.1574-6968.2010.01994.x

Farnbacher M, Jahns T, Willrodt D, Daniel R, Haas R, Goesmann A, Kurtz S, Rieder G (2010) Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics 11(1), DOI:10.1186/1471-2164-11-335

Yang I, John U, Beszteri S, Glöckner G, Krock B, Goesmann A, Cembella AD (2010) Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. BMC Genomics 11(1), DOI:10.1186/1471-2164-11-248

Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B (2010) Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Molecular plant-microbe interactions : MPMI 23(4): 384-93, DOI:10.1094/MPMI-23-4-0384

Steinweg C, Kuenne CT, Billion A, Mraheil MA, Domann E, Ghai R, Barbuddhe SB, Kärst U, Goesmann A, Pühler A, Weisshaar B, Wehland J, Lampidis R, Kreft J, Goebel W, Chakraborty T, Hain T (2010) Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria. Journal of bacteriology 192(5): 1473-4, DOI:10.1128/JB.01415-09

Schneider, J., Vorhölter, F., Trost, E., Blom, J., Musa, Y., Neuweger, H., Niehaus, K., Schatschneider, S., Tauch, A., Goesmann, A., others. (2010). CARMEN-Comparative analysis and in silico reconstruction of organism-specific metabolic networks. Volume 9(3), 1660--1672. DOI: 10.4238/vol9-3gmr901

Mittard-Runte, V., Bekel, T., Blom, J., Dondrup, M., Henckel, K., Jaenicke, S., Krause, L., Linke, B., Neuweger, H., Schneiker-Bekel, S., others. (2010). Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions. Springer. DOI: 10.1007/978-90-481-8639-6_9

Trost, E., Götker, S., Schneider, J., Schneiker-Bekel, S., Szczepanowski, R., Tilker, A., Viehoever, P., Arnold, W., Bekel, T., Blom, J., others. (2010). Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BioMed Central.Volume 11(1), 1--16. DOI: 10.1186/1471-2164-11-91

Smits, T., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Frey, J., Duffy, B.. (2010). Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp.. The American Phytopathological Society.Volume 23(4), 384--393. DOI: 10.1094/MPMI-23-4-0384

Joseph, B., Schneiker-Bekel, S., Schramm-Glück, A., Blom, J., Claus, H., Linke, B., Schwarz, R., Becker, A., Goesmann, A., Frosch, M., others. (2010). Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. American Society for Microbiology.Volume 192(20), 5363--5377. DOI: 10.1128/JB.00883-10

Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, Gartemann KH, Linke B, Goesmann A, Pühler A, Shukla SK, Tauch A (2010) Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics 11(1), DOI:10.1186/1471-2164-11-91

Brinkrolf, K., Schröder, J., Pühler, A., Tauch, A.. (2010). The transcriptional regulatory repertoire of Corynebacterium glutamicum: reconstruction of the network controlling pathways involved in lysine and glutamate production. Elsevier.Volume 149(3), 173--182. DOI: 10.1016/j.jbiotec.2009.12.004

Griep, S. and Hobohm, U., 2010. PDBselect 1992–2009 and PDBfilter-select., pp.D318-D319, DOI:10.1093/nar/gkp786.

2009

Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A (2009) Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics (Oxford, England) 25(23): 3128-34, DOI:10.1093/bioinformatics/btp568

Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A (2009) Truncatulix - A data warehouse for the legume community. BMC Plant Biology, DOI:10.1186/1471-2229-9-19

Jochmann, N., Kurze, A., Czaja, L., Brinkrolf, K., Brune, I., Huser, A., Hansmeier, N., Puhler, A., Borovok, I., Tauch, A.. (2009). Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. Microbiology Society.Volume 155(5), 1459--1477. DOI: 10.1099/mic.0.025841-0

Nentwich, S., Brinkrolf, K., Gaigalat, L., Huser, A., Rey, D., Mohrbach, T., Marin, K., Puhler, A., Tauch, A., Kalinowski, J.. (2009). Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032. Microbiology Society.Volume 155(1), 150--164. DOI: 10.1099/mic.0.020388-0

Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009) WebCARMA: A web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, DOI:10.1186/1471-2105-10-430

Wegmann U, Overweg K, Horn N, Goesmann A, Narbad A, Gasson MJ, Shearman C (2009) Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry. Journal of Bacteriology 191(22): 7142-7143, DOI:10.1128/JB.01182-09

Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009) Visualizing post genomics data-sets on customized pathway maps by ProMeTra - Aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology: 82, DOI:10.1186/1752-0509-3-82

Krawczyk J, Goesmann A, Nolte R, Werber M, Weisshaar B (2009) Trace2PS and FSA2PS: Two software toolkits for converting trace and fsa files to PostScript format., DOI:10.1186/1751-0473-4-4

Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology 142(1): 38-49, DOI:10.1016/j.jbiotec.2009.02.010

Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A (2009) EDGAR: A software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, DOI:10.1186/1471-2105-10-154

Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R (2009) Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environmental Microbiology 11(5): 1038-1055, DOI:10.1111/j.1462-2920.2008.01825.x

Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A (2009) A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data. Journal of Biotechnology 140(1-2): 45-50, DOI:10.1016/j.jbiotec.2008.11.006

Dondrup M, Hüser AT, Mertens D, Goesmann A (2009) An evaluation framework for statistical tests on microarray data. Journal of Biotechnology 140(1-2): 18-26, DOI:10.1016/j.jbiotec.2009.01.009

Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A (2009) The Sequence Analysis and Management System - SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of biotechnology 140(1-2): 3-12, DOI:10.1016/j.jbiotec.2009.01.006

Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A (2009) EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics, DOI:10.1186/1471-2105-10-50

Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW (2009) TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, DOI:10.1186/1471-2105-10-56

Kröber, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K.J., Viehöver, P., Pühler, A. and others, 2009. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology, 142(1), pp.38-49, DOI:10.1016/j.jbiotec.2009.02.010.

2008

Schoen, C., Blom, J., Claus, H., Schramm-Glück, A., Brandt, P., Müller, T., Goesmann, A., Joseph, B., Konietzny, S., Kurzai, O., others. (2008). Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. National Acad Sciences.Volume 105(9), 3473--3478. DOI: 10.1073/pnas.0800151105

Brinkrolf, K., Plöger, S., Solle, S., Brune, I., Nentwich, S., Hüser, A., Kalinowski, J., Pühler, A., Tauch, A.. (2008). The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences. Microbiology Society.Volume 154(4), 1068--1081. DOI: 10.1099/mic.0.2007/014001-0

Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehoever, P., Gartemann, K., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., others. (2008). Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Elsevier.Volume 136(1-2), 22--30. DOI: 10.1016/j.jbiotec.2008.03.004

Brinkrolf, K.. (2008). Das transkriptionelle Regulationsnetzwerk von Corynebacterium glutamicum unter Einbeziehung des LacI/GaIR-Regulators UriR.

Tauch, A., Trost, E., Tilker, A., Ludewig, U., Schneiker, S., Goesmann, A., Arnold, W., Bekel, T., Brinkrolf, K., Brune, I., others. (2008). The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. Elsevier.Volume 136(1-2), 11--21. DOI: 10.1016/j.jbiotec.2008.02.009

Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehoever, P., Gartemann, K., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., others. (2008). Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Elsevier.Volume 136(1-2), 22--30. DOI: 10.1016/j.jbiotec.2008.03.004

Schoen, C., Blom, J., Schramm-Glueck, A., Linke, B., Schneiker-Bekel, S., Joseph, B., Goesmann, A., Schwarz, R., Claus, H., Vogel, U., others. (2008). In search for the genetic basis of virulence in Neisseria meningitidis. Volume 298. DOI: 10.1371/journal.pone.0018441

Strauch E, Hammerl JA, Konietzny A, Schneiker-Bekel S, Arnold W, Goesmann A, Pühler A, Beutin L (2008) Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. Infection and Immunity 76(12): 5466-5477, DOI:10.1128/IAI.00875-08

Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A (2008) Comparative Pathway Analyzer-a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic acids research 36(Web Server issue), DOI:10.1093/nar/gkn284

Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008) MeltDB: A software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 24(23): 2726-2732, DOI:10.1093/bioinformatics/btn452

Gross R, Guzman CA, Sebaihia M, Martins dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R (2008) The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics, DOI:10.1186/1471-2164-9-449

Stiens M, Becker A, Bekel T, Gödde V, Goesmann A, Niehaus K, Schneiker-Bekel S, Selbitschka W, Weidner S, Schlüter A, Pühler A (2008) Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11. Journal of Biotechnology 136(1-2): 31-37, DOI:10.1016/j.jbiotec.2008.04.014

Schlüter A, Krause L, Szczepanowski R, Goesmann A, Pühler A (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. Journal of biotechnology 136(1-2): 65-76, DOI:10.1016/j.jbiotec.2008.03.017

Szczepanowski R, Bekel T, Goesmann A, Krause L, Krömeke H, Kaiser O, Eichler W, Pühler A, Schlüter A (2008) Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. Journal of Biotechnology 136(1-2): 54-64, DOI:10.1016/j.jbiotec.2008.03.020

Krause L, Diaz NN, Edwards RA, Gartemann KH, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A (2008) Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. Journal of Biotechnology 136(1-2): 91-101, DOI:10.1016/j.jbiotec.2008.06.003

Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Götker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Dröge M, Pühler A (2008) The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. Journal of Biotechnology 136(1-2): 11-21, DOI:10.1016/j.jbiotec.2008.02.009

Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann K, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. Journal of biotechnology 136(1-2): 77-90, DOI:10.1016/j.jbiotec.2008.05.008

Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Götker S, Weisshaar B, Goesmann A, Dröge M, Pühler A (2008) Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology 136(1-2): 22-30, DOI:10.1016/j.jbiotec.2008.03.004

Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research 36(7): 2230-2239, DOI:10.1093/nar/gkn038

Vorhölter F, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A (2008) The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. Journal of biotechnology 134(1-2): 33-45, DOI:10.1016/j.jbiotec.2007.12.013

Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, Kaup O, Kirchner O, Krause L, Linke B, McHardy A, Meyer F, Pohle S, Rückert C, Sehneiker S, Zeilermann EM, Pühler A, Eichenlaub R, Kaiser O, Bartels D (2008) The genome sequence of the tomato-pathogenic actinomycete Chvibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. Journal of Bacteriology 190(6): 2138-2149, DOI:10.1128/JB.01595-07

Schoen C, Blom J, Claus H, Schramm-Glück A, Brandt P, Müller T, Goesmann A, Joseph B, Konietzny S, Kurzai O, Schmitt C, Friedrich T, Linke B, Vogel U, Frosch M (2008) Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proceedings of the National Academy of Sciences of the United States of America 105(9): 3473-3478, DOI:10.1073/pnas.0800151105

2007

Meisinger-Henschel C, Schmidt M, Lukassen S, Linke B, Krause L, Konietzny S, Goesmann A, Howley P, Chaplin P, Suter M, Hausmann J (2007) Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara. The Journal of general virology 88(Pt 12): 3249-59, DOI:10.1099/vir.0.83156-0

Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Mũoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotechnology 25(11): 1281-1289, DOI:10.1038/nbt1354

Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A (2007) CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology, DOI:10.1186/1752-0509-1-55

Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A (2007) Ecological genomics of marine roseobacters. Applied and Environmental Microbiology 73(14): 4559-4569, DOI:10.1128/AEM.02580-06

Bahl MI, Hansen LH, Goesmann A, Sørensen SJ (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups. Plasmid 58(1): 31-43, DOI:10.1016/j.plasmid.2006.11.007

Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, Van Sinderen D, Kok J (2007) Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology 189(8): 3256-3270, DOI:10.1128/JB.01768-06

Küster H, Becker A, Firnhaber C, Hohnjec N, Manthey K, Perlick AM, Bekel T, Dondrup M, Henckel K, Goesmann A, Meyer F, Wipf D, Requena N, Hildebrandt U, Hampp R, Nehls U, Krajinski F, Franken P, Pühler A (2007) Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry 68(1): 19-32, DOI:10.1016/j.phytochem.2006.09.026

Baumbach, J., Wittkop, T., Rademacher, K., Rahmann, S., Brinkrolf, K., Tauch, A.. (2007). CoryneRegNet 3.0—an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. Elsevier.Volume 129(2), 279--289. DOI: 10.1016/j.jbiotec.2006.12.012

Brinkrolf, K., Brune, I., Tauch, A.. (2007). The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. Elsevier.Volume 129(2), 191--211. DOI: 10.1016/j.jbiotec.2006.12.013

Brune, I., Jochmann, N., Brinkrolf, K., Hüser, A., Gerstmeir, R., Eikmanns, B., Kalinowski, J., Pühler, A., Tauch, A.. (2007). The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum. Am Soc Microbiol.Volume 189(7), 2720--2733. DOI: 10.1128/JB.01876-06

2006

Baumbach, J., Brinkrolf, K., Czaja, L., Rahmann, S., Tauch, A.. (2006). CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Springer.Volume 7(1), 1--12. DOI: 10.1186/1471-2164-7-24

Baumbach, J., Brinkrolf, K., Wittkop, T., Tauch, A., Rahmann, S.. (2006). CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes. De Gruyter.Volume 3(2), 1--13. DOI: 10.1515/jib-2006-24

Brinkrolf, K., Brune, I., Tauch, A.. (2006). Transcriptional regulation of catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Volume 5(4), 773--789. PMID: 17183485

Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter F, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A (2006) Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nature biotechnology 24(11): 1385-91, DOI:10.1038/nbt1243

Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Karst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Pühler A, Weisshaar B, Wehland J, Liang C, Dandekar T, Lampidis R, Kreft J, Goebel W, Chakraborty T (2006) Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to listeria monocytogenes. Journal of Bacteriology 188(21): 7405-7415, DOI:10.1128/JB.00758-06

Schneiker S, Dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nature Biotechnology 24(8): 997-1004, DOI:10.1038/nbt1232

2005

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rül;ckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 33(17): 5691-5702, DOI:10.1093/nar/gki866

Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O (2005) Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. Journal of Bacteriology 187(21): 7254-7266, DOI:10.1128/JB.187.21.7254-7266.2005

Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F (2005) BRIGEP - The BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research 33(SUPPL. 2), DOI:10.1093/nar/gki400

Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A (2005) Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. Journal of Bacteriology 187(13): 4671-4682, DOI:10.1128/JB.187.13.4671-4682.2005

Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC (2005) BACCardl - A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21(7): 853-859, DOI:10.1093/bioinformatics/bti091

Brune, I., Brinkrolf, K., Kalinowski, J., Pühler, A., Tauch, A.. (2005). The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. Springer.Volume 6, 1--10. DOI: 10.1186/1471-2164-6-86

2004

Szczepanowski R, Krahn I, Linke B, Goesmann A, Pühler A, Schlüter A (2004) Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system. Microbiology 150(11): 3613-3630, DOI:10.1099/mic.0.27317-0

McHardy AC, Goesmann A, Pühler A, Meyer F (2004) Development of joint application strategies for two microbial gene finders. Bioinformatics (Oxford, England) 20(10): 1622-31, DOI:10.1093/bioinformatics/bth137

Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson KE, Pettersson B, Uhlén M (2004) The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Research 14(2): 221-227, DOI:10.1101/gr.1673304

Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC (2004) A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science (New York, N.Y.) 303(5658): 689-92, DOI:10.1126/science.1093027

2003

Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F (2003) Bioinformatics support for high-throughput proteomics. Journal of biotechnology 106(2-3): 147-56, DOI:10.1016/j.jbiotec.2003.08.009

Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F (2003) Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. Journal of Biotechnology 106(2-3): 157-167, DOI:10.1016/j.jbiotec.2003.08.007

Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F (2003) EMMA: a platform for consistent storage and efficient analysis of microarray data. Journal of biotechnology 106(2-3): 135-46, DOI:10.1016/j.jbiotec.2003.08.010

Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (2003) Whole genome shotgun sequencing guided by bioinformatics pipelines-an optimized approach for an established technique. Journal of biotechnology 106(2-3): 121-33, DOI:10.1016/j.jbiotec.2003.08.008

Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Krämer R, Linke B, McHardy AC, Meyer F, Möckel B, Pfefferle W, Pühler A, Rey DA, Rückert C, Rupp O, Sahm H, Wendisch VF, Wiegräbe I, Tauch A (2003) The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. Journal of Biotechnology 104(1-3): 5-25, DOI:10.1016/S0168-1656(03)00154-8

Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A (2003) GenDB - An open source genome annotation system for prokaryote genomes. Nucleic Acids Research 31(8): 2187-2195, DOI:10.1093/nar/gkg312

Tauch A, Schlüter A, Bischoff N, Goesmann A, Meyer F, Pühler A (2003) The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resi. Molecular genetics and genomics : MGG 268(5): 570-84, DOI:10.1007/s00438-002-0785-z

2002

Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R (2002) PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (Oxford, England) 18(1): 124-9, DOI:10.1093/bioinformatics/18.1.124