References
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.
L Shalamova, P Barth, MJ Pickin, K Kouti, B Ott, K Humpert, S Janssen, G Lorenzo, A Brun, A Goesmann, T Hain, RK Hartmann, O Rossbach and F Weber
Nature Communications, 2024
Robustness of cancer microbiome signals over a broad range of methodological variation.
GD Sepich-Poore, D McDonald, E Kopylova, C Guccione, Q Zhu, G Austin, C Carpenter, S Fraraccio, S Wandro, T Kosciolek, S Janssen, J Metcalf, SJ Song, J Kanbar, S Miller-Montgomery, R Heaton, R Mckay, SP Patel, AD Swafford, T Korem, R Knight
Oncogene, 2024
The host genotype actively shapes its microbiome across generations.
L Benga, A Rehm, C Gougoula, P Westhoff, T Wachtmeister, WPM Benten, E Engelhardt, APM Weber, K Koehrer, M Sager, S Janssen
Microbiome, 2024 (accepted)
2023
Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis.
K Siems, K Runzheimer, K Rebrošova, L Etzbach, A Auerhammer, A Rehm, O Schwengers, M Šiler, O Samek, F Růžička and R Moeller
Frontiers in Microbiology, 2023
Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies.
P Shi, C Martino, R Han, S Janssen, G Buck, M Serrano, K Owzar, R Knight, L Shenhav, AR Zhang
bioRxiv
Exploring the frequency and distribution of ecological non-monotonicity in associations among ecosystem constituents.
M Hanusch, X He, S Janssen, J Selke, W Trutschnig, R Junker
Ecosystems, 2023
Proglacial slopes are protected against erosion by trait diverse and dense plant communities associated with specific microbial communities.
LM Ohler, S Haselberger, S Janssen, JC Otto, S Kraushaar, RR Junker
Basic and Applied Ecology, 2023 (71), 57-71
Sequence-structure-function relationships in the microbial protein universe.
J Koehler Leman, P Szczerbiak, PD Renfrew, V Gligorijevic, D Berenberg, T Vatanen, BC Taylor, C Chandler, S Janssen, N Carriero, A Pataki, N Carriero, I Fisk, RJ Xavier, R Knight, R Bonneau, T Kosciolek
Nature communications, 2023
2022
Cytokine hyperresponsiveness in Children with ETV6::RUNX1-positive Acute Lymphoblastic Leukemia (ALL) after Challenge with Common Pathogens.
N Rüchel N, M Oldenburg, S Janssen, A Pandyra, W Liu, E Vasileiou, D Hein, VH Jepsen, U Fischer, D Picard, G Kögler, J Hauer, F Auer, A Beer, O Adams, C MacKenzie, M Jaeger, MG Netea, A Borkhardt, KL Gössling
HemaSphere 2023, 7(2)
Rapid detection and online analysis of microbial changes through flow cytometry.
J Kupschus, S Janssen, A Hoek, J Kuska, J Rathjens, C Sonntag, K Ickstadt, L Budzinski, HD Chang, A Rossi, C Esser, K Hochrath
Cytometry Part A, 2022
Phenotypic and genomic assessment of the potential threat of human spaceflight-relevant Staphylococcus capitis isolates under stress conditions.
K Siems, K Runzheimer, A Rehm, O Schwengers, D Heidler Von Heilborn, L Kaser, F Arndt, C Neidhöfer, JP Mengel, M Parcina, A Lipski, T Hain, R Moeller
Frontiers in Microbiology, section Extreme Microbiology, accepted
2021
The microbiome in childhood acute lymphoblastic leukemia.
M Oldenburg, N Rüchel, S Janssen, A Borkhardt, KL Gössling
Cancers (Basel) 2021, 13(19), 4947
Results from a pilot study on the Oral Microbiome in Children and Adolescents with Chronic non-Bacterial Osteomyelitis.
M Zeus, S Janssen, HJ Laws, U Fischer, A Borkhardt, PT Oommen
Zeitschrift für Rheumatologie, 2021
Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing.
N Apostolopoulos, SP Glaeser, R Bagwe, S Janssen, U Mayer, C Ewers, P Kämpfer, R Neiger, N Thom
PLoSONE, 2021
Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources.
SC Brandt, H Brognaro, A Ali, B Ellinger, K Maibach, M Rühl, C Wrenger, H Schlüter, W Schäfer, C Betzel, S Janssen and M Gand
Biotechnology for Biofuels, 2021
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.
K Cantrell, MW Fedarko, G Rahman, D McDonald, Y Yang, T Zaw, A Gonzalez, S Janssen, M Estaki, N Haiminen, KL Beck, Q Zhu, E Sayyari, JT Morton, A Tripathi, JM Gauglitz, C Marotz, NL Matteson, C Martino, JG Sanders, AP Carrieri, SJ Song, AD Swafford, P Dorrestein, KG Andersen, L Parida, HC Kim, Y Vázquez-Baeza, R Knight
mSystems, 2021
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
A Hoek, K Maibach, E Özmen, AI Vazquez-Armendariz, JP Mengel, T Hain, S Herold, A Goesmann
BMC Genomics, 2021
2020
Vitamin D metabolites and the gut microbiome in older men.
RL Thomas, L Jiang, JS Adams, ZZ Xu, J Shen, S Janssen, G Ackermann, D Vanderschueren, S Pauwels, R Knight, ES Orwoll, DM Kado
Nature Communications 5997, 2020
An intact gut microbiome protects genetically predisposed mice against leukemia.
C Vicente Dueñas, S Janssen, M Oldenburg, F Auer, I González Herrero, A Casado-García, M Isidro-Hernández, J Raboso-Gallego, P Westhoff, A Pandyra, D Hein, K Gössling, D Alonso-López, J De Las Rivas, S Bhatia, F Garcia-Criado, M Begoña García Cenador, A Weber, K Köhrer, J Hauer, U Fischer, I Sanchez-Garcia, A Borkhardt
Blood 136:18, 2020
The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months.
MI Ordiz, S Janssen, G Humphrey, G Ackermann, K Stephenson, S Agapova, O Divala, Y Kaimila, K Maleta, C Zhong, R Knight, I Trehan, PI Tarr, B Rusconi, MJ Manary
The American Journal of Clinical Nutrition, 2020
A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice.
TR Sampson, C Challis, N Jain, A Moiseyenko, MS Ladinsky, GG Shastri, T Thron, BD Needham, I Horvath, JW Debelius, S Janssen, ...
eLife, 9:e53111, Feb 2020
2019
Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID.
G Rodríguez-Hernández, FV Opitz, P Delgado, C Walter, ÁF Álvarez-Prado, I González-Herrero, F Auer, U Fischer, S Janssen, ...
Nature Communications 5563, 2019
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
Q Zhu, U Mai, W Pfeiffer, S Janssen, F Asnicar, JG Sanders, P Belda-Ferre, GA Al-Ghalith, E Kopylova, ...
Nature Communications 5477 (10) 2019
The impact of skin care products on skin chemistry and microbiome dynamics.
A Bouslimani, R da Silva, T Kosciolek, S Janssen, C Callewaert, A Amir, ...
BMC biology 17 (1), 47 2019
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.
N Iszatt, S Janssen, V Lenters, C Dahl, H Stigum, R Knight, S Mandal, ...
Microbiome 7 (1), 34 2019
Assessing taxonomic metagenome profilers with OPAL.
F Meyer, A Bremges, P Belmann, S Janssen, AC McHardy, D Koslicki
Genome biology 20 (1), 51 2019
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, CC Abnet, GA Al-Ghalith, ...
Nature biotechnology 37 (8), 852-857 2019
2018
Qiita: rapid, web-enabled microbiome meta-analysis.
A Gonzalez, JA Navas-Molina, T Kosciolek, D McDonald, Y Vázquez-Baeza, G Ackermann, J DeReus, S Janssen...
Nature methods 15 (10), 796 2018
American gut: an open platform for citizen science microbiome research.
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ...
mSystems 3 (3), e00031-18 2018
Phylogenetic placement of exact amplicon sequences improves associations with clinical information.
S Janssen, D McDonald, A Gonzalez, JA Navas-Molina, L Jiang, ZZ Xu, ...
Msystems 3 (3), e00021-18 2018
KatharoSeq enables high-throughput microbiome analysis from low-biomass samples.
JJ Minich, Q Zhu, S Janssen, R Hendrickson, A Amir, R Vetter, J Hyde, ...
MSystems 3 (3), e00218-17 2018
Creating a 3D microbial and chemical snapshot of a human habitat.
CA Kapono, JT Morton, A Bouslimani, AV Melnik, K Orlinsky, TL Knaan, ...
Scientific reports 8 (1), 3669 2018
2017
A communal catalogue reveals Earth’s multiscale microbial diversity.
LR Thompson, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, ...
Nature 551 (7681), 457 2017
Critical assessment of metagenome interpretation—a benchmark of metagenomics software.
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ...
Nature methods 14 (11), 1063 2017
2016
Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease.
TR Sampson, JW Debelius, T Thron, S Janssen, GG Shastri, ZE Ilhan, ...
Cell 167 (6), 1469-1480. e12 2016
2015
Ambivalent covariance models.
S Janssen, R Giegerich
BMC Bioinformatics 16 (1), 178 2015
The RNA shapes studio.
S Janssen, R Giegerich
Bioinformatics 31 (3), 423-425 2015
2014
Kisses, ambivalent models and more: Contributions to the analysis of RNA secondary structure.
S Janssen
Universitätsbibliothek Bielefeld 2014
Abstract Shape Analysis of RNA.
S Janssen, R Giegerich
RNA Sequence, Structure, and Function: Computational and Bioinformatic … 2014
2013
Bellman’s GAP—a language and compiler for dynamic programming in sequence analysis.
G Sauthoff, M Möhl, S Janssen, R Giegerich
Bioinformatics 29 (5), 551-560 2013
2012
Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?
S Janssen, L Paulevé, Y Ponty, B Raman, M Zytnicki
Platinum Sponsor, 38 2012
2011
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
S Janssen, C Schudoma, G Steger, R Giegerich
BMC bioinformatics 12 (1), 429 2011
Bellman's GAP: a declarative language for dynamic programming.
G Sauthoff, S Janssen, R Giegerich
Proceedings of the 13th international ACM SIGPLAN symposium on Principles … 2011
Investigating the RFAM paradox: The pseudoknot explanation.
S Janssen, Y Ponty, B Raman, S Sheikh, JM Steyaert, P Clote
Fifth Indo-French Bioinformatics Meeting 2011
2010
Prediction of RNA secondary structure including kissing hairpin motifs.
C Theis, S Janssen, R Giegerich
International Workshop on Algorithms in Bioinformatics, 52-64 2010
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
JP Schlüter, J Reinkensmeier, S Daschkey, E Evguenieva-Hackenberg, S Janssen...
BMC genomics 11 (1), 245 2010
Faster computation of exact RNA shape probabilities.
S Janssen, R Giegerich
Bioinformatics 26 (5), 632-639 23 2010
Browsing rna structures by interactive sonification.
F Grond, S Janssen, S Schirmer, T Hermann
Proceedings of the 3rd Interactive Sonification Workshop 2010
2008
Shape based indexing for faster search of RNA family databases.
S Janssen, J Reeder, R Giegerich
BMC bioinformatics 9 (1), 131 2008
Suggested affiliation for future publications:
Algorithmic Bioinformatics, Justus Liebig University Giessen, Germany