Personal Homepage of Prof. Dr. Alexander Goesmann
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Contact
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Ludwigsplatz 13-15 Raum: 105 Tel.: +49 (0)641 99 35-800 |
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CV
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2021 - present |
Vice President for Academic Infrastructure |
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2013 - present |
Professor of Bioinformatics and Systems Biology, Gießen University, Germany, with a focus on Genomics, Proteomics and Transcriptomics |
| 2010 - 2013 | Member of the CeBiTec board of directors, CeBiTec, Bielefeld University, Germany |
| 2009 - 2013 | Vice speaker of the Institute for Bioinformatics, CeBiTec, Bielefeld University, Germany |
| 2007 - 2013 | Leader of the Junior Research Group “Computational Genomics”, Institute for Bioinformatics, CeBiTec, Bielefeld University, Germany |
| 2006 - 2013 | Head of the Bioinformatics Resource Facility (BRF), CeBiTec, Bielefeld University, Germany |
| 2004 - 2006 | PostDoc at Bielefeld University, Germany |
| 2004 | PhD - Faculty of Technology, Bielefeld University, Bielefeld, Germany |
| 2001 - 2006 | Employment within the BMBF competence network for “Genome Research on Bacteria relevant for Agriculture, Environment and Biotechnology” (GenoMik) at Bielefeld University, Germany |
| 2000 - 2001 | PhD grant “Graduiertenkolleg Bioinformatik”, Bielefeld University, Germany |
| 2000 | Diploma - Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University, Bielefeld, Germany |
| 1993 | School leaving examination (Abitur), Gymnasium Warstein |
| 1974 | Born in Warstein, Germany |
Publications
2024
Meier, D., Rauch, C., Wagner, M., Klemm, P., Blumenkamp, P., Müller, R., Ellenberger, E., Karia, K., Vecchione, S., Serrania, J., Goesmann, A., others. (2024). A MoClo-compatible toolbox of ECF sigma factor-based regulatory switches for proteobacterial chassis. BioDesign Research. Volume 6, 0025. DOI: 10.34133/bdr.0025
Höhn, D., Masello, J., Kümmel, M., Griep, S., Goesmann, A., Quillfeldt, P.. (2024). Nestling diet of two sympatric insectivorous passerines in different habitats—a metabarcoding study. Birds. Volume 5(1), 67-89. DOI: 10.3390/birds5010005
Jünemann, S., Prior, K., Albersmeier, A., Albaum, S., Kalinowski, J., Goesmann, A., Stoye, J., Harmsen, D.. (2024). Correction: GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. Plos one. Volume 19(2), e0299269. DOI: 10.1371/journal.pone.0299269
Zumkeller, C., Bletz, M., Rakotoarison, A., Sabino-Pinto, J., Reiter, S., Spohn, M., Schwengers, O., Goesmann, A., Vences, M., Mihajlovic, S., others. (2024). Draft genome sequences of 21 Pedobacter strains isolated from amphibian specimens. Microbiology Resource Announcements. Volume 13(4), e01185-23. DOI: 10.1128/mra.01185-23
Blumenkamp, P., Pfister, M., Diedrich, S., Brinkrolf, K., Jaenicke, S., Goesmann, A. (2024). Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data. BMC bioinformatics. Volume 25(1), 138. DOI: 10.1186/s12859-024-05761-2
Lick, S., Wibberg, D., Busche, T., Blom, J., Grimmler, C., Goesmann, A., Kalinowski, J. (2024). Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. International Journal of Systematic and Evolutionary Microbiology. Volume 74(4), 006293. DOI: 10.1099/ijsem.0.006293
Juenemann, S., Prior, K., Albersmeier, A., Albaum, S., Kalinowski, J., Goesmann, A., Stoye, J., Harmsen, D. (2024). GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. PLOS ONE. Volume 19(2), e0229269. DOI: 10.1371/journal.pone.0107014
Fenske, L., Jelonek, L., Goesmann, A., Schwengers, O.. (2024). BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata. Microbial Genomics.Volume 10(10). , DOI: 10.1099/mgen.0.001305
Hahnfeld, J., Schwengers, O., Jelonek, L., Diedrich, S., Cemic, F., Goesmann, A. (2024). sORFdb-A database for sORFs, small proteins, and small protein families in bacteria. bioRxiv. DOI: 10.1101/2024.06.19.599710
Ruf, A., Thieron, H., Nasfi, S., Lederer, B., Fricke, S., Adeshara, T., Postma, J., Blumenkamp, P., Kwon, S., Brinkrolf, K., Goesmann, A., others. (2024). Broad-scale phenotyping in Arabidopsis reveals varied involvement of RNA interference across diverse plant-microbe interactions. bioRxiv. DOI: 10.1101/2024.06.25.600702
Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Riviani, R., Meinita, M., Hastuti, D., Prihatiningsih, I., Dewi, R., others. (2024). Draft genome sequence of Galbibacter sp. PAP. 153, isolated from a marine sponge in Papua, Indonesia. Microbiology Resource Announcements. Volume 13(6). DOI: 10.1128/mra.01297-23
Shalamova, L., Barth, P., Pickin, M., Kouti, K., Ott, B., Humpert, K., Janssen, S., Lorenzo, G., Brun, A., Goesmann, A., others. (2024). Nucleocapsids of the Rift Valley fever virus ambisense S segment contain an exposed RNA element in the center that overlaps with the intergenic region. Nature Communications. Volume 15(1), 7602. DOI: 10.1038/s41467-024-52058-2
Hofmann, N., Bartkuhn, M., Becker, S., Biedenkopf, N., Böttcher-Friebertshäuser, E., Brinkrolf, K., Dietzel, E., Fehling, S., Goesmann, A., Heindl, M., others. (2024). Distinct negative-sense RNA viruses induce a common set of transcripts encoding proteins forming an extensive network. Journal of Virology. DOI: 10.1128/jvi.00935-24
2023
Riyanti, Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Choironi, N., Schäberle, T., Harwoko, H. (2023). Draft Genome Sequences of Algoriphagus sp. Strain PAP. 12 and Roseivirga sp. Strain PAP. 19, Isolated from Marine Samples from Papua, Indonesia. Microbiology Resource Announcements.Volume 12(4), e01264-22. DOI: 10.1128/mra.01264-22
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. Microbiology Resource Announcements. 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 in Plant Science. 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. Applied and Environmental Microbiology.Volume 89(7), e00238-23. DOI: 10.1128/aem.00238-23
Förstner, K., Becker, A., Blom, J., Bork, P., Clavel, T., Dieckmann, M., Goesmann, A., Götz, B., Gübitz, T., Hufsky, F., others. (2023). NFDI4Microbiota-national research data infrastructure for microbiota research. Research Ideas and Outcomes. Volume 9, e110501. DOI: 10.3897/rio.9.e110501
Diepenbroek, M., Kostadinov, I., Seeger, B., Glöckner, F., Dieckmann, M., Goesmann, A., Ebert, B., Schimmler, S., Sure-Vetter, Y. (2023). Towards a research data commons in the german national research data infrastructure NFDI: vision, governance, architecture. Proceedings of the Conference on Research Data Infrastructure. Volume 1. DOI: 10.52825/cordi.v1i.355
Dieckmann, M., Beyvers, S., Hochmuth, J., Rehm, A., Förster, F., Goesmann, A. (2023). The Aruna Object Storage: A Distributed Multi Cloud Object Storage System for Scientific Data Management. Proceedings of the Conference on Research Data Infrastructure. Volume 1. DOI: 10.52825/cordi.v1i.404
Hoffmann, N., Maus, I., Beier, S., Belmann, P., Krüger, J., Tauch, A., Goesmann, A., Eils, R., Bork, P., Kohlbacher, O., others. (2023). Embedding the de. NBI Cloud in the National Research Data Infrastructure Activities. Proceedings of the Conference on Research Data Infrastructure. Volume 1. DOI: 10.52825/cordi.v1i.387
Jaenicke, S., Diedrich, S., Goesmann, A.. (2023). MGX 2.0: Shotgun-and assembly-based metagenome and metatranscriptome analysis from a single source. bioRxiv. 2023-09. DOI: 10.1101/2023.09.21.558800
2022
Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., others. (2022). Characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting. Oxford University Press US.Volume 74(6), 1039-1046 DOI: 10.1093/cid/ciab588.
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 DOI: 10.1093/bioinformatics/btab681.
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. American Society for Microbiology 1752 N St., NW, Washington, DC.Volume 13(1), e00044-22 DOI: 10.1128/mbio.00044-22.
Djahanschiri, B., Di Venanzio, G., Distel, J., Breisch, J., Dieckmann, M., Goesmann, A., Averhoff, B., Göttig, S., Wilharm, G., Feldman, M., others. (2022). Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. Public Library of Science San Francisco, CA USA.Volume 18(6), e1010020 DOI: 10.1371/journal.pgen.1010020 .
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 DOI: 10.1039/d1qo01652k.
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. Elsevier.Volume 20, 1264-1270. DOI: 10.1016/j.csbj.2022.03.007
(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
2021
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
2020
(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
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
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
2018
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
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
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
2016
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
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
2015
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
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
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
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
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
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
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
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
2012
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
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
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
2010
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
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
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
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
2008
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
2006
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
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