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Items: 7

1.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd; IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C.

Nature. 2019 May;569(7758):655-662. doi: 10.1038/s41586-019-1237-9. Epub 2019 May 29.

PMID:
31142855
2.

Species-level functional profiling of metagenomes and metatranscriptomes.

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C.

Nat Methods. 2018 Nov;15(11):962-968. doi: 10.1038/s41592-018-0176-y. Epub 2018 Oct 30.

3.

American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

4.

Host genetic variation and its microbiome interactions within the Human Microbiome Project.

Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C.

Genome Med. 2018 Jan 29;10(1):6. doi: 10.1186/s13073-018-0515-8.

5.

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Nov 9;551(7679):256. doi: 10.1038/nature24485. Epub 2017 Oct 12.

PMID:
29022944
6.

Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20. Erratum in: Nature. 2017 Oct 12;:.

7.

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.

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