Publications

2019

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]

2018

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]

2017

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]

2016

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]

2015

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]

2014

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]