Publications

M. Schirmer, M. Stražar,  J. Avila-Pacheco,  D. F. Rojas-Tapias, E. M. Brown, ..., R. J. Xavier, Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course, [Cell Host & Microbe]

C. Pasin, C. R. Consiglio, J. S. Huisman, A.-M. G. de Lange, H. Peckham, E. Vallejo-Yagüe, I. A. Abela, U. Islander, N. Neuner-Jehle, M. Pujantell, O. Roth, M. Schirmer, ..., S. Bonhoeffer. Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications, [Royal Society Open Science]

T. Braun, K. E. Sosnovski, A. Amir, M. BenShoshan, K. L. VanDussen, R. Karns, N. Levhar, H. Abbas-Egbariya, R. Hadar, G. Efroni, D. Castel, C. Avivi, M. J. Rosen, A. M. Grifiths, T. D. Walters, D. R. Mack, B. M. Boyle, S. A. Ali, S. R. Moore, M. Schirmer, ..., Y. Haberman. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease, [JCI insight]

R. Luelf, K. Selg-Mann, T. Hoffmann, T. Zheng, M. Schirmer, M. Ehrmann, Carbohydrate Sources Influence the Microbiota and Flavour Profile of a Lupine-Based Moromi Fermentation, [Foods]

S. Ma, D. Shungin, H. Mallick, M. Schirmer, L.H. Nguyen, R. Kolde, E. Franzosa, H. Vlamakis, R. Xavier, C. Huttenhower, Population structure discovery in meta‑analyzed microbial communities and infammatory bowel disease using MMUPHin, [Genome Biology]

L. Hall and M. Schirmer, Current state and future of the microbiome field; why context matters, [Current Opinion in Microbiology]

D.F. Rojas-Tapias, E.M. Brown, E.R. Temple, M. Onyekaba, A.M.T. Mohamed, K. Duncan, M. Schirmer, …., R.J. Xavier, Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine, [Nature Microbiology]

S. Jin, D. Wetzel, M. Schirmer, Deciphering mechanisms and implications of bacterial translocation in human health and disease, [Current Opinion in Microbiology]

N. Vadaq, M. Schirmer, R.N. Tunjungputri, H. Vlamakis, C. Chiriac, E. Ardiansyah, M.H. Gasem, L. Joosten, P.G. de Groot, R.J. Xavier, M.G. Netea, A.JAM van der Ven, Q. de Mast, Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals, [Thrombosis and Haemostasis]

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]