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Publications


Journal Publications

2018
J.S. Hyams, S. Davis Thomas, N. Gotman, Y. Haberman, R. Karns, M. Schirmer, A. Mo, D.R. Mack, B. Boyle, A.M. Griffiths, N.S. Leleiko, C.G. Sauer, D.J. Keljo, J. Markowitz, S.S. Baker, J. Rosh, R.N. Baldassano, A. Patel, M. Pfefferkorn, A. Otley, M. Heyman, J. Noe, M. Oliva-Hemker, P.A. Rufo, J. Strople, D. Ziring, S.L. Guthery, B. Sudel, K. Benkov, P. Wali, D. Moulton, J. Evans, M.D. Kappelman, M.A. Marquis, F.A. Sylvester, M.H. Collins, S. Venkateswaran, M. Dubinsky, V. Tangpricha, K.L. Spada, B. Saul, J. Wang, J. Serrano, K. Hommel, U.M. Marigorta, G. Gibson, R.J. Xavier, S. Kugathasan, T. Walters, L.A. Denson. Clinical and biological predictors of response to standardized pediatric colitis therapy: a multicentre inception cohort study., The Lancet

2018
E.A. Franzosa, L.J. McIver, G. Rahnavard, L.R. Thompson, M. Schirmer, G. Weingart, K. Schwarzberg Lipson, R. Knight, J.G. Caporaso, N. Segata, C. Huttenhower. Functionally profiling metagenomes and metatranscriptomes at species-level resolution., Nature Methods

2018
M. Schirmer, L. Denson, H. Vlamakis, E.A. Franzosa, S.M. Thomas, N.M. Gotman, P. Rufo, S.S. Baker, C. Sauer, J. Markowitz, M. Pfefferkorn, M. Oliva-Hemker, J. Rosh, A. Otley, B. Boyle, D. Mack, R. Baldassano, D. Keljo, N. LeLeiko, M. Heyman, A. Griffiths, A. Patel, J. Noe, S. Kugathasan, T. Walters, C. Huttenhower, J. Hyams, R.J. Xavier. Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course., Cell Host & Microbe

2018
M. Schirmer, E.A. Franzosa, J. Lloyd-Price, L.J. McIver, R. Schwager, T. Poon, A.N. Ananthakrishnan, E. Andrews, G. Barron, K. Lake, M. Prasad, J. Sauk, B. Stevens, R.G. Wilson, J. Braun, L.A. Denson, S. Kugathasan, D.P.B. McGovern, H. Vlamakis, R.J. Xavier, C. Huttenhower. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome., Nature Microbiology

2017
S. Kugathasan, L.A. Denson, T.D. Walters, M. Kim, U.M. Marigorta, M. Schirmer, K. Mondal, C. Liu, A. Griffiths, J.D. Noe, W.V. Crandall, S. Snapper, S. Rabizadeh, J.R. Rosh, J.M. Shapiro, S. Guthery, D.R. Mack, R. Kellermayer, M.D. Kappelman, S. Steiner, D.E. Moulton, D. Keljo, S. Cohen, M. Oliva-Hemker, M.B. Heyman, A.R. Otley, S.S. Baker, J.S. Evans, B.S. Kirschner, A.S. Patel, D. Ziring, B.C. Trapnell, F.A. Sylvester, M.C. Stephens, R.N. Baldassano, J.F. Markowitz, J. Cho, R.J. Xavier, C. Huttenhower, B.J. Aronow, G. Gibson, J.S. Hyams, M.C. Dubinsky. Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study., The Lancet

2016
M. Schirmer, S.P. Smeekens, H. Vlamakis, M. Jaeger, M. Oosting, E.A. Franzosa, T. Jansen, L. Jacobs, M. Bonder, A. Kurilshikov, J. Fu, L.A.B. Joosten, A. Zhernakova, C. Huttenhower, C. Wijmenga, M.G. Netea, R.J. Xavier. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity., Cell

2016
M.G. Netea, L.A.B. Joosten, Y. Li, V. Kumar, M. Oosting, S. Smeekens, M. Jaeger, R. ter Horst, M. Schirmer, H. Vlamakis, R. Notebaart, N. Pavelka, R.R. Aguirre-Gamboa, M.A. Swertz, R.N. Tunjungputri, W. van de Heijden, E.A. Franzosa, A. Ng, D. Graham, K. Lassen, K. Schraa, R. Netea-Maier, J. Smit, Q. de Mast, F. van de Veerdonk, B.J. Kullberg, C. Tack, I. van de Munckhof, J. Rutten, J. van der Graaf, L. Franke, M. Hofker, I. Jonkers, M. Platteel, A. Maatman, J. Fu, A. Zhernakova, J.W.M. van der Meer, C.A. Dinarello, A. van der Ven, C. Huttenhouwer, H. Koenen, I. Joosten, R.J. Xavier, C. Wijmenga. Understanding human immune function using the resources from the Human Functional Genomics Project., Nature Medicine

2016
M. Bonder, A. Kurilshikov, E.F. Tigchelaar, Z. Mujagic, F. Imhann, A.V. Vila, P. Deelen, T. Vatanen, M. Schirmer, S.P. Smeekens, D.V. Zhernakova, S.A. Jankipersadsing, M. Jaeger, M. Oosting, M.C. Cenit, A.A. Masclee, M.A. Swertz, Y. Li, V. Kumar, L. Joosten, H. Harmsen, R.K. Weersma, L. Franke, M.H. Hofker, R.J. Xavier, D. Jonkers, M.G. Netea, C. Wijmenga, J. Fu, A. Zhernakova. The effect of host genetics on the gut microbiome., Nature Genetics

2016
A. Zhernakova, A. Kurilshikov, M.J. Bonder, E.F. Tigchelaar, M. Schirmer, T. Vatanen, Z. Mujagic, A.V. Vila, G. Falony, S. Vieira-Silva, J. Wang, F. Imhann, E. Brandsma, S.A. Jankipersadsing, M. Joossens, M.C. Cenit, P. Deelen, M.A. Swertz, LifeLines cohort study, R.K. Weersma, E.J.M. Feskens, M.G. Netea, D. Gevers, D. Jonkers, L. Franke, Y.S. Aulchenko, C. Huttenhower, J. Raes, M.H. Hofker, R.J. Xavier, C. Wijmenga and J. Fu. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity., Science

2016
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

2016
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

2016
R. D'Amore, U.Z. Ijaz, M. Schirmer, J.G. Kenny, R. Gregory, A.C. Darby, M. Shakya, M. Podar, C. Quince and N. Hall. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling., BMC Genomics

2015
J.M. Couto, U.Z. Ijaz, V.R. Phoenix, M. Schirmer, W.T. Sloan. Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment., Current Microbiology

2015
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

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, P.H. Tan, A.K. Bhan, R. Roychoudhuri, N.P. Restifo, J.J. O'Shea, B.D. Medoff, A.F. Shamji, S.L. Schreiber, A.H. Sharpe, S.Y. Shaw, R.J. Xavier. The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells., eLife

2015
M. Schirmer, U.Z. Ijaz, L. D'Amore, N. Hall, W.T. Sloan and C. Quince. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform., Nucleic Acids Research

2014
M. Schirmer. Algorithms for viral haplotype reconstruction and bacterial metagenomics: resolving fine-scale variation in next generation sequencing data., Thesis, University of Glasgow

2014
J. Alneberg, B.S. Bjarnason, I. de Bruijn, M. Schirmer, J. Quick, U.Z. Ijaz, L. Lahti, N.J. Loman, A.F. Andersson and C. Quince. Binning metagenomic contigs by coverage and composition., Nature Methods

2012
M. Schirmer, W.T. Sloan and C. Quince. Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes., Briefings in Bioinformatics
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