Published in PLoS One on February 21, 2017
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
Microbial influences in inflammatory bowel diseases. Gastroenterology (2008) 9.20
Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods (2012) 8.37
The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe (2014) 7.43
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One (2013) 7.23
PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics (2012) 7.10
Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol (2014) 4.74
Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut (2011) 3.36
Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J (2008) 2.96
Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm Bowel Dis (2009) 2.85
Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecol Lett (2013) 2.73
Decline in presumptively protective gut bacterial species and metabolites are paradoxically associated with disease improvement in pediatric Crohn's disease during enteral nutrition. Inflamm Bowel Dis (2014) 2.59
Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. Gastroenterology (2003) 2.57
Population-level analysis of gut microbiome variation. Science (2016) 1.74
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol (2009) 1.63
Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health? Curr Opin Clin Nutr Metab Care (2010) 1.27
Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition. Am J Gastroenterol (2015) 1.15
Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. Appl Environ Microbiol (2011) 1.15
Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities. Gut (2015) 1.02
Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn's disease and their unaffected siblings. Gut (2014) 0.94
Specific changes of gut commensal microbiota and TLRs during indomethacin-induced acute intestinal inflammation in rats. J Crohns Colitis (2014) 0.83
Increased antibody response to microbial antigens in patients with Crohn's disease and their unaffected first-degree relatives. Dig Liver Dis (2013) 0.79
Seqenv: linking sequences to environments through text mining. PeerJ (2016) 0.75
Treatment satisfaction, preferences and perception gaps between patients and physicians in the ulcerative colitis CARES study: A real world-based study. Dig Liver Dis (2016) 0.75
Intractable proctitis in a 46-year-old man. Clin Gastroenterol Hepatol (2014) 0.75
Long-Term Skeletal Disproportion in Childhood-Onset Crohn's Disease. Horm Res Paediatr (2017) 0.75