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Items: 1 to 20 of 194

1.

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.

Nat Microbiol. 2019 Apr 10. doi: 10.1038/s41564-019-0442-5. [Epub ahead of print]

PMID:
30971771
2.

2017 NIH-wide workshop report on "The Human Microbiome: Emerging Themes at the Horizon of the 21st Century".

2017 NIH-wide microbiome workshop writing team.

Microbiome. 2019 Feb 26;7(1):32. doi: 10.1186/s40168-019-0627-4.

3.

Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):545. doi: 10.1038/s41564-019-0393-x.

PMID:
30723264
4.

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N.

Cell. 2019 Jan 24;176(3):649-662.e20. doi: 10.1016/j.cell.2019.01.001. Epub 2019 Jan 17.

5.

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor.

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L.

Am J Epidemiol. 2019 Jan 10. doi: 10.1093/aje/kwz006. [Epub ahead of print]

PMID:
30649166
6.

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA.

Nat Commun. 2019 Jan 3;10(1):38. doi: 10.1038/s41467-018-07841-3.

7.

Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors.

Fahimipour AK, Ben Mamaar S, McFarland AG, Blaustein RA, Chen J, Glawe AJ, Kline J, Green JL, Halden RU, Van Den Wymelenberg K, Huttenhower C, Hartmann EM.

mSystems. 2018 Dec 11;3(6). pii: e00200-18. doi: 10.1128/mSystems.00200-18. eCollection 2018 Nov-Dec.

8.

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):470-479. doi: 10.1038/s41564-018-0321-5. Epub 2018 Dec 17. Erratum in: Nat Microbiol. 2019 Feb 5;:.

PMID:
30559407
9.

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.

Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LA.

Mucosal Immunol. 2019 Mar;12(2):491-502. doi: 10.1038/s41385-018-0114-4. Epub 2018 Dec 12.

PMID:
30542108
10.

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.

Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4. Epub 2018 Dec 10. Erratum in: Nat Microbiol. 2019 Apr 10;:.

PMID:
30531976
11.

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017.

Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Hutchinson DLS, Le Marchand L, Li H, Orlich MJ, Shi J, Truelove A, Verma M, Vogtmann E, White O, Willett W, Zheng W, Mahabir S, Abnet C.

Microbiome. 2018 Nov 26;6(1):210. doi: 10.1186/s40168-018-0596-z.

12.

Low Tristetraprolin Expression Is Associated with Lethal Prostate Cancer.

Gerke T, Beltran H, Wang X, Lee GM, Sboner A, Karnes RJ, Klein EA, Davicioni E, Yousefi K, Ross AE, Börnigen D, Huttenhower C, Mucci LA, Trock BJ, Sweeney CJ.

Cancer Epidemiol Biomarkers Prev. 2019 Mar;28(3):584-590. doi: 10.1158/1055-9965.EPI-18-0667. Epub 2018 Nov 12.

PMID:
30420441
13.

Translating microbiome futures.

Taroncher-Oldenburg G, Jones S, Blaser M, Bonneau R, Christey P, Clemente JC, Elinav E, Ghedin E, Huttenhower C, Kelly D, Kyle D, Littman D, Maiti A, Maue A, Olle B, Segal L, van Hylckama Vlieg JET, Wang J.

Nat Biotechnol. 2018 Nov 9;36(11):1037-1042. doi: 10.1038/nbt.4287. No abstract available.

PMID:
30412201
14.

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.

PMID:
30377376
15.

Temporal development of the gut microbiome in early childhood from the TEDDY study.

Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF.

Nature. 2018 Oct;562(7728):583-588. doi: 10.1038/s41586-018-0617-x. Epub 2018 Oct 24.

PMID:
30356187
16.

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.

Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ.

Nature. 2018 Oct;562(7728):589-594. doi: 10.1038/s41586-018-0620-2. Epub 2018 Oct 24.

PMID:
30356183
17.

Daylight exposure modulates bacterial communities associated with household dust.

Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, Betancourt-Román CM, Brown GZ, Fretz M, Northcutt D, Siemens KN, Huttenhower C, Green JL, Van Den Wymelenberg K.

Microbiome. 2018 Oct 18;6(1):175. doi: 10.1186/s40168-018-0559-4.

18.

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.

Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ.

Cell Host Microbe. 2018 Oct 10;24(4):600-610.e4. doi: 10.1016/j.chom.2018.09.009.

PMID:
30308161
19.

Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.

Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L.

Genome Biol. 2018 Sep 25;19(1):142. doi: 10.1186/s13059-018-1511-4.

20.

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome.

Kosumi K, Hamada T, Koh H, Borowsky J, Bullman S, Twombly TS, Nevo D, Masugi Y, Liu L, da Silva A, Chen Y, Du C, Gu M, Li C, Li W, Liu H, Shi Y, Mima K, Song M, Nosho K, Nowak JA, Nishihara R, Baba H, Zhang X, Wu K, Wang M, Huttenhower C, Garrett WS, Meyerson ML, Lennerz JK, Giannakis M, Chan AT, Meyerhardt JA, Fuchs CS, Ogino S.

Am J Pathol. 2018 Dec;188(12):2839-2852. doi: 10.1016/j.ajpath.2018.08.015. Epub 2018 Sep 20.

PMID:
30243655

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