L.B. Thingholm, M.C. Ruehlemann, M. Koch, B. Fuqua, G. Laucke, R. Boehm, C. Bang, E.A. Franzosa, M. Huebenthal, A. Rahnavard, F. Frost, J. Lloyd-Price, M. Schirmer, ..., C. Huttenhower, Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition [Cell Host & Microbe]

M. Schirmer, A. Garner, H. Vlamakis, R.J. Xavier, Microbial genes and pathways in inflammatory bowel disease [Nature Reviews Microbiology]

J. Lloyd-Price, C. Arze, A.N. Ananthakrishnan, M. Schirmer, J. Avila-Pacheco, ..., C. Huttenhower, Multi-omics of the Gut Microbial Ecosystem in Inflammatory Bowel Disease [Nature]

J.S. Hyams, S. Davis Thomas, N. Gotman, Y. Haberman, R. Karns, M. Schirmer, ..., L.A. Denson, Clinical and biological predictors of response to standardized pediatric colitis therapy (PROTECT): a multicentre inception cohort study [The Lancet]

Y. Haberman, M. Schirmer, P.J. Dexheimer, R. Karns, T. Braun, ..., L.A. Denson, Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis [Mucosal immunology]

N.A. Yudanin, F. Schmitz, A. Flamar, J.J.C. Thome, E.T. Wojno, J.B. Moeller, M. Schirmer, ..., D. Artis, Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity [Immunity]

Y. Haberman, R. Karns, P.J. Dexheimer, M. Schirmer, J. Somekh, ..., L.A. Denson, Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response [Nature Communications]


E.A. Franzosa, L.J. McIver, G. Rahnavard, L.R. Thompson, M. Schirmer, ..., C. Huttenhower, Species-level functional profiling of metagenomes and metatranscriptomes [Nature Methods]

M. Schirmer, L. Denson, H. Vlamakis, E.A. Franzosa, S.M. Thomas, ..., R.J. Xavier, Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course [Cell Host & Microbe]

M. Schirmer, E.A. Franzosa, J. Lloyd-Price, L.J. McIver, R. Schwager, ..., C. Huttenhower, Dynamics of metatranscription in the inflammatory bowel disease gut microbiome [Nature Microbiology]

M. Schirmer, V. Kumar, M.G Netea, R.J. Xavier, The causes and consequences of variation in human cytokine production in health [Current Opinion in Immunology]


S. Kugathasan, L.A. Denson, T.D. Walters, M. Kim, U.M. Marigorta, M. Schirmer, ..., M. Dubinsky, RISK Stratification Study Group, Predicting a complicated course for children newly diagnosed with Crohn's disease: a multicenter inception cohort study [The Lancet]


M. Schirmer, S.P. Smeekens, H. Vlamakis, M. Jaeger, M. Oosting, ... R.J. Xavier, Linking the human gut microbiome to inflammatory cytokine production capacity [Cell]

M.G Netea, L.A.B. Joosten, Y. Li, V. Kumar, M. Oosting, S. Smeekens, M. Jaeger, R. ter Horst, M. Schirmer, ..., C. Wijmenga, Understanding human immune function using the resources from the Human Functional Genomics Project [Nature Medicine]

A. Zhernakova, A. Kurilshikov, M.J. Bonder, E.F. Tigchelaar, M. Schirmer, ..., J. Fu, Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity [Science]

M. Schirmer, R. D’Amore, U.Z. Ijaz, N. Hall and C. Quince, Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data [BMC Bioinformatics]

M.J. Bonder, A. Kurilshikov, E.F. Tigchelaar, Z. Mujagic, F. Imhann, A.V. Vila, P. Deelen, T. Vatanen, M. Schirmer, ... A. Zhernakova, The effect of host genetics on the gut microbiome [Nature Genetics]

I. Gregor, J. Droege, M. Schirmer, C. Quince and A.C. McHardy, PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes [PeerJ]

R. D'Amore, U.Z. Ijaz, M. Schirmer, ..., N. Hall, A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling [BMC Genomics]


B. Khor, J. D. Gagnon, G. Goel, M. I. Roche, K. L. Conway. K. Tran, L. N. Aldrich, T. B. Sundberg, A. M. Paterson, S. Mordecai, D. Dombkowski, M. Schirmer, ..., R. J. Xavier, The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells [eLife]

J. M. Couto, U. Z. Ijaz, V. R. Phoenix, M. Schirmer and W. T. Sloan, Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2 tolerant NiFe membrane bound hydrogenases in lacustrine sediment [Current Microbiology]

M. Schirmer, U. Z. Ijaz, L. D’Amore, N. Hall and C. Quince, Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform [Nucleic Acid Research]

S. Haig, M. Schirmer, L. D'Amore, J. Gibbs, R. Davies, G. Collins and C. Quince, Stable-isotope probing and metagenomics reveal predation by protozoa drives E.coli removal in slow sand filters [ISME Journal]


J. Alneberg, B. S. Bjarnason, I. de Bruijn, M. Schirmer, J. Quick, ..., C. Quince, Binning metagenomic contigs by coverage and composition [Nature Methods]

M. Schirmer, W.T. Sloan and C. Quince, Benchmarking of viral haplotype reconstruction programs: an overview of the capacities and limitations of currently available programs [Briefings in Bioinformatics]