NIH Human Microbiome Project 2


The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease.
The Integrative HMP (iHMP) Research Network Consortium.
Cell Host & Microbe 2014. doi: 10.1016/j.chom.2014.08.014.
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Paneth Cell Phenotypes Define a Subtype of Pediatric Crohn's Disease Through Alterations in Host-Microbial Interactions.
Liu TC1, Gurram B, Baldridge M, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz M, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, Huttenhower C, McGovern D, Xavier R, Stappenbeck T, Salzman N.
Inflamm Bowel Dis 2016. doi: 10.1097/01.MIB.0000480097.23732.5e.
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High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.
Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C.
PLoS Comput Biol 2015. doi: 10.1371/journal.pcbi.1004557.
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The microbiome quality control project: baseline study design and future directions.
Sinha R, Abnet CC, White O, Knight R, Huttenhower C
Genome Biol 2015. doi: 10.1186/s13059-015-0841-8.
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.
Nat Methods 2015. doi: 10.1038/nmeth.3589.
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Compact graphical representation of phylogenetic data and metadata with GraPhlAn.
Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N.
PeerJ 2015. doi: 10.7717/peerj.1029.
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Identifying personal microbiomes using metagenomic codes.
Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C.
Proc Natl Acad Sci U S A 2015. doi: 10.1073/pnas.1423854112.
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Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C.
Nat Rev Microbiol 2015. doi: 10.1038/nrmicro3451.
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Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.
Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C.
Genome Biol 2015. doi: 10.1186/s13059-015-0637-x.
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Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.
Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC.
Cell Host Microbe 2015. doi: 10.1016/j.chom.2015.01.015.
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ConStrains identifies microbial strains in metagenomic datasets.
Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D.
Nat Biotechnol 2015. doi: 10.1038/nbt.3319.
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An integrative view of microbiome-host interactions in inflammatory bowel diseases.
Wlodarska M, Kostic AD, Xavier RJ.
Cell Host Microbe 2015. doi: 10.1016/j.chom.2015.04.008.
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Complex host genetics influence the microbiome in inflammatory bowel disease.
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P,Al-Ghalith GA,  Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ.
Genome Med 2014. doi: 10.1186/s13073-014-0107-1.
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Inflammatory Bowel Disease as a Model for Translating the Microbiome
Huttenhower C, Kostic AD, Xavier RJ.
Immunity 2014. doi:10.1016/j.immuni.2014.05.013
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Collaboration with Skip Virgin on Phage and IBD
Virgin, Skip. Xavier, Ramnik.