References
2025
Touching Surfaces – Presence of microorganisms on antimicrobial metal surfaces on the International Space Station and in German schools.
CL Krämer, DW Müller, F Arndt, A Rehm, B Walkenfort, AS Ahmed, A Haben, A Schiele, A Auerhammer, M Hasenberg, AL Boschert, R Kautenburger, S Leuko, S Janssen, M Maurer, F Mücklich, K Siems
BMC Microbiology 25 (1), 631, 2025
Long-term TCDD oral exposure changes gut microbial glycosylation patterns in female but not male C57BL/6 mice.
D Reichert, S Janssen, A Rossi, C Esser
Archives of Toxicology, 2025
Multicenter exploration of microbial communities in hospital toilets reveals: antibiotic exposure in a nosocomial settings selects for Enterococcus over commensal taxa.
C Neidhöfer, M Neuenhoff, E Sib, A Rehm, LR Dias, B Neumann, J Steinmann, M Döhla, Y Kherabi, A Budimir, C Hajjar, R Khatib, K Axtmann, K Schwab, P Brossart, S Engelhart, NT Mutters, G Bierbaum, S Janssen, M Parčina
Antimicrobial Resistance & Infection Control 14 (1), 78, 2025
Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach.
N Broel, F Daumüller, A Ali, J Lemanschick, K Maibach, C Mewe, B Bunk, C Spröer, C Baschien, H Zorn, H Schlüter, M Rühl, S Janssen, M Gand
Microbiological Research, 128214, 2025
Immune training enhances anti-viral responses and improves outcomes in Pax5−/+ mice susceptible to chronic infection.
Z Lu, O Stencel, W Liu, E Vasileiou, HC Xu, P Pandey, P Stachura, A Elwy, A Tsombal, A Mai, F Auer, MNF Morcos, M Seidl, S Koziel, P Bruch, S Dietrich, S Elitzur, G Hartmann, KS Lang, S Janssen, U Fischer, S Bhatia, PA Lang, A Borkhardt, J Hauer, AA Pandyra
EMBO Molecular Medicine 17 (4), 696-721, 2025
Tolerance to land-use changes through natural modulations of the plant microbiome.
V Zieschank, A Muola, S Janssen, A Lach, RR Junker
The ISME Journal, wraf010, 2025
A gut instinct for childhood leukemia prevention: microbiome-targeting recommendations aimed at parents and caregivers.
E Kameri, VH Jepsen, P Stachura, N Rüchel, R Bhave, L Benitez, F Crispi, E Gratacos, N Dragano, S Janssen, A Borkhardt, AA Pandyra, G Kögler, U Fischer
Frontiers in Public Health 12, 2025
2024
TEMPTED: 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
Genome Biology 25 (1), 317, 2024
The host genotype actively shapes its microbiome across generations in laboratory mice.
L Benga, A Rehm, C Gougoula, P Westhoff, T Wachtmeister, WPM Benten, E Engelhardt, APM Weber, K Köhrer, M Sager, S Janssen
Microbiome 12 (1), 256, 2024
FLASH Bragg-Peak Irradiation With a Therapeutic Carbon Ion Beam: First In Vivo Results.
W Tinganelli, A Puspitasari-Kokko, O Sokol, A Helm, P Simoniello, C Schuy, S Lerchl, D Eckert, J Oppermann, A Rehm, S Janssen, D Engel, R Moeller, R Romano, F Horst, D Boscolo, C Fournier, M Durante, U Weber
International Journal of Radiation Oncology*Biology*Physics, 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, F Weber
Nature Communications 15 (1), 7602, 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, JL Metcalf, SJ Song, J Kanbar, S Miller-Montgomery, R Heaton, R Mckay, SP Patel, AD Swafford, T Korem, R Knight
Oncogene 43 (15), 1127, 2024
2023
Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents.
M Hanusch, X He, S Janssen, J Selke, W Trutschnig, RR Junker
Ecosystems 26 (8), 1819, 2023
Proglacial slopes are protected against erosion by trait diverse and dense plant communities associated with specific microbial communities.
L Ohler, S Haselberger, S Janssen, J Otto, S Kraushaar, RR Junker
Basic and Applied Ecology 71, 57, 2023
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, H Chang, A Rossi, C Esser, K Hochrath
Cytometry Part A 103 (5), 419, 2023
Sequence-structure-function relationships in the microbial protein universe.
LJ Koehler, P Szczerbiak, PD Renfrew, V Gligorijevic, D Berenberg, T Vatanen, BC Taylor, C Chandler, S Janssen, A Pataki, N Carriero, I Fisk, RJ Xavier, R Knight, R Bonneau, T Kosciolek
Nature Communications 14 (1), 2351, 2023
Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis.
K Siems, K Runzheimer, K Rebrosova, L Etzbach, A Auerhammer, A Rehm, O Schwengers, M Šiler, O Samek, F Růžička, R Moeller
Frontiers in Microbiology 14, 2023
Cytokine Hyperresponsiveness in Children With ETV6::RUNX1-positive Acute Lymphoblastic Leukemia After Challenge With Common Pathogens.
N Rüchel, M Oldenburg, S Janssen, AA 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 7 (2), 2023
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, vHD Heidler, L Kaser, F Arndt, C Neidhöfer, JP Mengel, M Parcina, A Lipski, T Hain, R Moeller
Frontiers in Microbiology 13, 2022
2021
Results from a pilot study on the oral microbiome in children and adolescents with chronic nonbacterial osteomyelitis.
M Zeus, S Janssen, H Laws, U Fischer, A Borkhardt, PT Oommen
Zeitschrift für Rheumatologie 82 (2), 123, 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
PLOS ONE 16 (5), e0250695, 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, M Gand
Biotechnology for Biofuels 14 (1), 74, 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 22 (1), 195, 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, G Armstrong, A Tripathi, JM Gauglitz, C Marotz, NL Matteson, C Martino, JG Sanders, AP Carrieri, SJ Song, AD Swafford, PC Dorrestein, KG Andersen, L Parida, H Kim, Y Vázquez-Baeza, R Knight
mSystems 6 (2), 10.1128/msystems.01216-20, 2021
The Microbiome in Childhood Acute Lymphoblastic Leukemia.
M Oldenburg, N Rüchel, S Janssen, A Borkhardt, KL Gössling
Cancers (Basel) 13 (19), 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 11 (1), 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, AA Pandyra, D Hein, KL Gössling, D Alonso-López, LRJ De, S Bhatia, FJ García-Criado, MB García-Cenador, APM Weber, K Köhrer, J Hauer, U Fischer, I Sánchez-García, A Borkhardt
Blood 136 (18), 2003, 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 111 (4), 884, 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, R Knight, P Wittung-Stafshede, V Gradinaru, M Chapman, SK Mazmanian
eLife 9, e53111, 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, C Bartenhagen, J Raboso-Gallego, A Casado-García, A Orfao, O Blanco, D Alonso-López, JDL Rivas, SGd Tena-Dávila, M Müschen, M Dugas, FJG Criado, MBG Cenador, C Vicente-Dueñas, J Hauer, AR Ramiro, I Sanchez-Garcia, A Borkhardt
Nature Communications 10 (1), 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, D McDonald, T Kosciolek, JB Yin, S Huang, N Salam, J Jiao, Z Wu, ZZ Xu, K Cantrell, Y Yang, E Sayyari, M Rabiee, JT Morton, S Podell, D Knights, W Li, C Huttenhower, N Segata, L Smarr, S Mirarab, R Knight
Nature Communications 10 (1), 5477, 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, H Alexander, EJ Alm, M Arumugam, F Asnicar, Y Bai, JE Bisanz, K Bittinger, A Brejnrod, CJ Brislawn, CT Brown, BJ Callahan, AM Caraballo-Rodríguez, J Chase, EK Cope, SR Da, C Diener, PC Dorrestein, GM Douglas, DM Durall, C Duvallet, CF Edwardson, M Ernst, M Estaki, J Fouquier, JM Gauglitz, SM Gibbons, DL Gibson, A Gonzalez, K Gorlick, J Guo, B Hillmann, S Holmes, H Holste, C Huttenhower, GA Huttley, S Janssen, AK Jarmusch, L Jiang, BD Kaehler, KB Kang, CR Keefe, P Keim, ST Kelley, D Knights, I Koester, T Kosciolek, J Kreps, MGI Langille, J Lee, R Ley, Y Liu, E Loftfield, C Lozupone, M Maher, C Marotz, BD Martin, D McDonald, LJ McIver, AV Melnik, JL Metcalf, SC Morgan, JT Morton, AT Naimey, JA Navas-Molina, LF Nothias, SB Orchanian, T Pearson, SL Peoples, D Petras, ML Preuss, E Pruesse, LB Rasmussen, A Rivers, MS Robeson, P Rosenthal, N Segata, M Shaffer, A Shiffer, R Sinha, SJ Song, JR Spear, AD Swafford, LR Thompson, PJ Torres, P Trinh, A Tripathi, PJ Turnbaugh, S Ul-Hasan, dHJJJ van, F Vargas, Y Vázquez-Baeza, E Vogtmann, HM von, WA Walters, Y Wan, M Wang, J Warren, KC Weber, CHD Williamson, AD Willis, ZZ Xu, JR Zaneveld, Y Zhang, Q Zhu, R Knight, JG Caporaso
Nature Biotechnology 37 (8), 852, 2019
The impact of skin care products on skin chemistry and microbiome dynamics.
A Bouslimani, SR da, T Kosciolek, S Janssen, C Callewaert, A Amir, K Dorrestein, AV Melnik, LS Zaramela, J Kim, G Humphrey, T Schwartz, K Sanders, C Brennan, T Luzzatto-Knaan, G Ackermann, D McDonald, K Zengler, R Knight, PC Dorrestein
BMC Biology 17 (1), 47, 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
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, S Peddada, A González, T Midtvedt, M Eggesbø
Microbiome 7 (1), 34, 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, AD Swafford, SB Orchanian, JG Sanders, J Shorenstein, H Holste, S Petrus, A Robbins-Pianka, CJ Brislawn, M Wang, JR Rideout, E Bolyen, M Dillon, JG Caporaso, PC Dorrestein, R Knight
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, AA Aksenov, B Behsaz, C Brennan, Y Chen, GL DeRight, PC Dorrestein, RR Dunn, AK Fahimipour, J Gaffney, JA Gilbert, G Gogul, JL Green, P Hugenholtz, G Humphrey, C Huttenhower, MA Jackson, S Janssen, DV Jeste, L Jiang, ST Kelley, D Knights, T Kosciolek, J Ladau, J Leach, C Marotz, D Meleshko, AV Melnik, JL Metcalf, H Mohimani, E Montassier, JA Navas-Molina, TT Nguyen, S Peddada, P Pevzner, KS Pollard, G Rahnavard, A Robbins-Pianka, N Sangwan, J Shorenstein, L Smarr, SJ Song, T Spector, AD Swafford, VG Thackray, LR Thompson, A Tripathi, Y Vázquez-Baeza, A Vrbanac, P Wischmeyer, E Wolfe, Q Zhu, R Knight
mSystems 3 (3), 10.1128/msystems.00031-18, 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, K Winker, DM Kado, ES Orwoll, MJ Manary, S Mirarab, R Knight
mSystems 3 (3), 10.1128/msystems.00021-18, 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, MM Doty, K Stillwell, J Benardini, JH Kim, EE Allen, K Venkateswaran, R Knight
mSystems 3 (3), 10.1128/msystems.00218-17, 2018
Creating a 3D microbial and chemical snapshot of a human habitat.
CA Kapono, JT Morton, A Bouslimani, AV Melnik, K Orlinsky, TL Knaan, N Garg, Y Vázquez-Baeza, I Protsyuk, S Janssen, Q Zhu, T Alexandrov, L Smarr, R Knight, PC Dorrestein
Scientific Reports 8 (1), 3669, 2018
2017
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software.
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, I Gregor, S Majda, J Fiedler, E Dahms, A Bremges, A Fritz, R Garrido-Oter, TS Jørgensen, N Shapiro, PD Blood, A Gurevich, Y Bai, D Turaev, MZ DeMaere, R Chikhi, N Nagarajan, C Quince, F Meyer, M Balvočiūtė, LH Hansen, SJ Sørensen, BKH Chia, B Denis, JL Froula, Z Wang, R Egan, KD Don, JJ Cook, C Deltel, M Beckstette, C Lemaitre, P Peterlongo, G Rizk, D Lavenier, Y Wu, SW Singer, C Jain, M Strous, H Klingenberg, P Meinicke, MD Barton, T Lingner, H Lin, Y Liao, GGZ Silva, DA Cuevas, RA Edwards, S Saha, VC Piro, BY Renard, M Pop, H Klenk, M Göker, NC Kyrpides, T Woyke, JA Vorholt, P Schulze-Lefert, EM Rubin, AE Darling, T Rattei, AC McHardy
Nature Methods 14 (11), 1063, 2017
A communal catalogue reveals Earth’s multiscale microbial diversity.
LR Thompson, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, RJ Prill, A Tripathi, SM Gibbons, G Ackermann, JA Navas-Molina, S Janssen, E Kopylova, Y Vázquez-Baeza, A González, JT Morton, S Mirarab, XZ Zech, L Jiang, MF Haroon, J Kanbar, Q Zhu, SS Jin, T Kosciolek, NA Bokulich, J Lefler, CJ Brislawn, G Humphrey, SM Owens, J Hampton-Marcell, D Berg-Lyons, V McKenzie, N Fierer, JA Fuhrman, A Clauset, RL Stevens, A Shade, KS Pollard, KD Goodwin, JK Jansson, JA Gilbert, R Knight
Nature 551 (7681), 457, 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, C Challis, CE Schretter, S Rocha, V Gradinaru, M Chesselet, A Keshavarzian, KM Shannon, R Krajmalnik-Brown, P Wittung-Stafshede, R Knight, SK Mazmanian
Cell 167 (6), 1469, 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, 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 Methods, 215, 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, 2013
2012
Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?.
S Janssen, L Paulevé, Y Ponty, B Raman, M Zytnicki
International Workshop on Bio-Design Automation, 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
Investigating the RFAM paradox: The pseudoknot explanation.
S Janssen, Y Ponty, B Raman, S Sheikh, J Steyaert, P Clote
Fifth Indo-French Bioinformatics Meeting, 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, 29–40, 2011
2010
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
J Schlüter, J Reinkensmeier, S Daschkey, E Evguenieva-Hackenberg, S Janssen, S Jänicke, JD Becker, R Giegerich, A Becker
BMC Genomics 11 (1), 245, 2010
Faster computation of exact RNA shape probabilities.
S Janssen, R Giegerich
Bioinformatics 26 (5), 632, 2010
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs.
C Theis, S Janssen, R Giegerich
International Workshop on Algorithms in Bioinformatics, 52, 2010
Browsing RNA Structures by Interactive Sonification.
F Grond, S Janssen, S Schirmer, T Hermann
Proceedings of the 3rd Interactive Sonification Workshop (Human Interaction with Auditory Displays), 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