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Items: 1 to 20 of 115

1.

O-011 Paneth Cell Phenotypes Define a Subtype of Pediatric Crohn's Disease Through Alterations in Host-Microbial Interactions.

Liu TC, 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 Mar;22 Suppl 1:S4. doi: 10.1097/01.MIB.0000480097.23732.5e.

PMID:
26849729
2.

Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis.

Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, No D, Gobourne A, Littmann E, Huttenhower C, Pamer EG, Wolchok JD.

Nat Commun. 2016 Feb 2;7:10391. doi: 10.1038/ncomms10391.

PMID:
26837003
3.

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 Dec 18;11(12):e1004557. doi: 10.1371/journal.pcbi.1004557. eCollection 2015 Dec.

4.

The microbiome quality control project: baseline study design and future directions.

Sinha R, Abnet CC, White O, Knight R, Huttenhower C.

Genome Biol. 2015 Dec 9;16:276. doi: 10.1186/s13059-015-0841-8.

5.

Cross-biome comparison of microbial association networks.

Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J.

Front Microbiol. 2015 Oct 27;6:1200. doi: 10.3389/fmicb.2015.01200. eCollection 2015.

6.

Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).

Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB.

Stand Genomic Sci. 2015 Nov 14;10:101. doi: 10.1186/s40793-015-0099-5. eCollection 2015.

7.

American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome.

Semenkovich CF, Danska J, Darsow T, Dunne JL, Huttenhower C, Insel RA, McElvaine AT, Ratner RE, Shuldiner AR, Blaser MJ.

Diabetes. 2015 Dec;64(12):3967-77. doi: 10.2337/db15-0597. Epub 2015 Sep 29.

PMID:
26420863
8.

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 Oct;12(10):902-3. doi: 10.1038/nmeth.3589. No abstract available.

PMID:
26418763
9.

Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis.

Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, Giovannucci EL, Garraway LA, Freeman GJ, Dranoff G, Garrett WS, Huttenhower C, Meyerson M, Meyerhardt JA, Chan AT, Fuchs CS, Ogino S.

Gut. 2015 Aug 26. pii: gutjnl-2015-310101. doi: 10.1136/gutjnl-2015-310101. [Epub ahead of print]

PMID:
26311717
10.

Fusobacterium nucleatum and T Cells in Colorectal Carcinoma.

Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS, Ogino S.

JAMA Oncol. 2015 Aug;1(5):653-61. doi: 10.1001/jamaoncol.2015.1377.

PMID:
26181352
11.

A reproducible approach to high-throughput biological data acquisition and integration.

Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C.

PeerJ. 2015 Mar 31;3:e791. doi: 10.7717/peerj.791. eCollection 2015.

12.

Compact graphical representation of phylogenetic data and metadata with GraPhlAn.

Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N.

PeerJ. 2015 Jun 18;3:e1029. doi: 10.7717/peerj.1029. eCollection 2015.

13.

Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract.

Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, Padavattan N, Ismail N, Moodley A, Sabatini ME, Ghebremichael MS, Nusbaum C, Huttenhower C, Virgin HW, Ndung'u T, Dong KL, Walker BD, Fichorova RN, Kwon DS.

Immunity. 2015 May 19;42(5):965-76. doi: 10.1016/j.immuni.2015.04.019.

PMID:
25992865
14.

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 Jun 2;112(22):E2930-8. doi: 10.1073/pnas.1423854112. Epub 2015 May 11.

15.

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 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27. Review.

PMID:
25915636
16.

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 Apr 8;16:67. doi: 10.1186/s13059-015-0637-x.

17.

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 Mar 11;17(3):385-91. doi: 10.1016/j.chom.2015.01.015. Epub 2015 Feb 26.

PMID:
25732063
18.

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA.

J Clin Invest. 2015 Mar 2;125(3):1363. doi: 10.1172/JCI79657. Epub 2015 Mar 2. No abstract available.

19.

Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection.

Pelle KG, Oh K, Buchholz K, Narasimhan V, Joice R, Milner DA, Brancucci NM, Ma S, Voss TS, Ketman K, Seydel KB, Taylor TE, Barteneva NS, Huttenhower C, Marti M.

Genome Med. 2015 Feb 27;7(1):19. doi: 10.1186/s13073-015-0133-7. eCollection 2015.

20.

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 5.

PMID:
25662751
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