| Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases J Lloyd-Price, C Arze, AN Ananthakrishnan, M Schirmer, J Avila-Pacheco, ... Nature 569 (7758), 655-662, 2019 | 1899 | 2019 |
| Binning metagenomic contigs by coverage and composition J Alneberg, BS Bjarnason, I De Bruijn, M Schirmer, J Quick, UZ Ijaz, ... Nature methods 11 (11), 1144-1146, 2014 | 1811 | 2014 |
| Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity Science 352 (6285), 565-569, 2016 | 1704 | 2016 |
| Species-level functional profiling of metagenomes and metatranscriptomes EA Franzosa, LJ McIver, G Rahnavard, LR Thompson, M Schirmer, ... Nature methods 15 (11), 962-968, 2018 | 1269 | 2018 |
| Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity Cell 167 (4), 1125 - 1136.e8, 2016 | 1037 | 2016 |
| Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform M Schirmer, UZ Ijaz, R D'Amore, N Hall, WT Sloan, C Quince Nucleic acids research 43 (6), e37-e37, 2015 | 831 | 2015 |
| The effect of host genetics on the gut microbiome MJ Bonder, A Kurilshikov, EF Tigchelaar, Z Mujagic, F Imhann, AV Vila, ... Nature genetics 48 (11), 1407-1412, 2016 | 750 | 2016 |
| Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study S Kugathasan, LA Denson, TD Walters, MO Kim, UM Marigorta, ... The Lancet 389 (10080), 1710-1718, 2017 | 561 | 2017 |
| Microbial genes and pathways in inflammatory bowel disease M Schirmer, A Garner, H Vlamakis, RJ Xavier Nature Reviews Microbiology 17 (8), 497-511, 2019 | 539 | 2019 |
| Dynamics of metatranscription in the inflammatory bowel disease gut microbiome M Schirmer, EA Franzosa, J Lloyd-Price, LJ McIver, R Schwager, ... Nature microbiology 3 (3), 337-346, 2018 | 460 | 2018 |
| A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling R D’Amore, UZ Ijaz, M Schirmer, JG Kenny, R Gregory, AC Darby, ... BMC genomics 17, 1-20, 2016 | 429 | 2016 |
| Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data M Schirmer, R D’Amore, UZ Ijaz, N Hall, C Quince BMC bioinformatics 17, 1-15, 2016 | 390 | 2016 |
| Obese individuals with and without type 2 diabetes show different gut microbial functional capacity and composition LB Thingholm, MC Rühlemann, M Koch, B Fuqua, G Laucke, R Boehm, ... Cell host & microbe 26 (2), 252-264. e10, 2019 | 347 | 2019 |
| Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response Y Haberman, R Karns, PJ Dexheimer, M Schirmer, J Somekh, I Jurickova, ... Nature communications 10 (1), 38, 2019 | 254 | 2019 |
| Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course M Schirmer, L Denson, H Vlamakis, EA Franzosa, S Thomas, NM Gotman, ... Cell host & microbe 24 (4), 600-610. e4, 2018 | 222 | 2018 |
| Spatial and temporal mapping of human innate lymphoid cells reveals elements of tissue specificity NA Yudanin, F Schmitz, AL Flamar, JJC Thome, ET Wojno, JB Moeller, ... Immunity 50 (2), 505-519. e4, 2019 | 163 | 2019 |
| Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study JS Hyams, SD Thomas, N Gotman, Y Haberman, R Karns, M Schirmer, ... The Lancet 393 (10182), 1708-1720, 2019 | 145 | 2019 |
| CONCOCT: clustering contigs on coverage and composition J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, ... arXiv preprint arXiv:1312.4038, 2013 | 119 | 2013 |
| Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the human gut microbiome to inflammatory cytokine production capacity M Schirmer, SP Smeekens, H Vlamakis, M Jaeger, M Oosting, ... Cell 167 (4), 1125-1136, 2016 | 101 | 2016 |
| PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes I Gregor, J Dröge, M Schirmer, C Quince, AC McHardy PeerJ, 2016 | 96 | 2016 |
