Melanie Schirmer
Melanie Schirmer
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Cited by
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
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
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Science 352 (6285), 565-569, 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
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity
Cell 167 (4), 1125 - 1136.e8, 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
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
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
Microbial genes and pathways in inflammatory bowel disease
M Schirmer, A Garner, H Vlamakis, RJ Xavier
Nature Reviews Microbiology 17 (8), 497-511, 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
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
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
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
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
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
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
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
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
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
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
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