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Items: 1 to 50 of 92

1.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug 9. doi: 10.1038/s41587-019-0252-6. [Epub ahead of print]

PMID:
31399723
2.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Aug 9;:.

PMID:
31341288
3.

Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles.

Bokulich NA, Maldonado J, Kang DW, Krajmalnik-Brown R, Caporaso JG.

mSphere. 2019 Apr 10;4(2). pii: e00208-19. doi: 10.1128/mSphere.00208-19.

4.

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota.

Kang DW, Adams JB, Coleman DM, Pollard EL, Maldonado J, McDonough-Means S, Caporaso JG, Krajmalnik-Brown R.

Sci Rep. 2019 Apr 9;9(1):5821. doi: 10.1038/s41598-019-42183-0.

5.

Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins.

Stone NE, Nunnally AE, Jimenez V Jr, Cope EK, Sahl JW, Sheridan K, Hornstra HM, Vinocur J, Settles EW, Headley KC, Williamson CHD, Rideout JR, Bolyen E, Caporaso JG, Terriquez J, Monroy FP, Busch JD, Keim P, Wagner DM.

Anaerobe. 2019 Aug;58:53-72. doi: 10.1016/j.anaerobe.2019.03.017. Epub 2019 Apr 1. Review.

6.

An Introduction to Applied Bioinformatics: a free, open, and interactive text.

Bolyen E, Rideout JR, Chase J, Pitman TA, Shiffer A, Mercurio W, Dillon MR, Caporaso JG.

J Open Source Educ. 2018;1(5). pii: 27. doi: 10.21105/jose.00027. Epub 2018 Oct 2. No abstract available.

7.

Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.

Pearson T, Caporaso JG, Yellowhair M, Bokulich NA, Padi M, Roe DJ, Wertheim BC, Linhart M, Martinez JA, Bilagody C, Hornstra H, Alberts DS, Lance P, Thompson PA.

Cancer Med. 2019 Feb;8(2):617-628. doi: 10.1002/cam4.1965. Epub 2019 Jan 16.

8.

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data.

Bokulich NA, Dillon MR, Zhang Y, Rideout JR, Bolyen E, Li H, Albert PS, Caporaso JG.

mSystems. 2018 Nov 20;3(6). pii: e00219-18. doi: 10.1128/mSystems.00219-18. eCollection 2018 Nov-Dec.

9.

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.

10.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ.

Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

11.

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.

12.

Qiita: rapid, web-enabled microbiome meta-analysis.

Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R.

Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.

13.

Best practices for analysing microbiomes.

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC.

Nat Rev Microbiol. 2018 Jul;16(7):410-422. doi: 10.1038/s41579-018-0029-9. Review.

PMID:
29795328
14.

Current understanding of the human microbiome.

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R.

Nat Med. 2018 Apr 10;24(4):392-400. doi: 10.1038/nm.4517. Review.

PMID:
29634682
15.

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.

mSystems. 2017 Jun 20;2(3). pii: e00016-17. doi: 10.1128/mSystems.00016-17. eCollection 2017 May-Jun.

16.

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, Knight R, Gilbert JA, Quade J, Caporaso JG, Maier RM.

mSystems. 2017 May 30;2(3). pii: e00195-16. doi: 10.1128/mSystems.00195-16. eCollection 2017 May-Jun.

17.

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.

Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R.

Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.

18.

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.

mSystems. 2016 Oct 18;1(5). pii: e00062-16. eCollection 2016 Sep-Oct.

19.

Geography and Location Are the Primary Drivers of Office Microbiome Composition.

Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG.

mSystems. 2016 Apr 19;1(2). pii: e00022-16. eCollection 2016 Mar-Apr.

20.

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.

21.

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

Chase JH, Bolyen E, Rideout JR, Caporaso JG.

mSystems. 2015 Dec 22;1(1). pii: e00010-15. eCollection 2016 Jan-Feb.

22.

Open-Source Sequence Clustering Methods Improve the State Of the Art.

Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R.

mSystems. 2016 Feb 9;1(1). pii: e00003-15. eCollection 2016 Jan-Feb.

23.

Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.

Taylor DL, Walters WA, Lennon NJ, Bochicchio J, Krohn A, Caporaso JG, Pennanen T.

Appl Environ Microbiol. 2016 Nov 21;82(24):7217-7226. Print 2016 Dec 15.

24.

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG.

Gigascience. 2016 Jun 13;5:27. doi: 10.1186/s13742-016-0133-6.

25.

Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis.

Laubitz D, Harrison CA, Midura-Kiela MT, Ramalingam R, Larmonier CB, Chase JH, Caporaso JG, Besselsen DG, Ghishan FK, Kiela PR.

PLoS One. 2016 Apr 6;11(4):e0152044. doi: 10.1371/journal.pone.0152044. eCollection 2016.

26.

Phylogenetic organization of bacterial activity.

Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, Hayer M, McHugh TA, Marks JC, Price LB, Hungate BA.

ISME J. 2016 Sep;10(9):2336-40. doi: 10.1038/ismej.2016.28. Epub 2016 Mar 4.

27.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST.

Microbiome. 2016 Feb 24;4:11. doi: 10.1186/s40168-016-0153-6.

28.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.

Fuentes S, Barra B, Caporaso JG, Seeger M.

Appl Environ Microbiol. 2015 Nov 20;82(3):888-96. doi: 10.1128/AEM.02625-15. Print 2016 Feb 1.

29.

Quantitative microbial ecology through stable isotope probing.

Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, McHugh TA, Marks JC, Morrissey EM, Price LB.

Appl Environ Microbiol. 2015 Nov;81(21):7570-81. doi: 10.1128/AEM.02280-15. Epub 2015 Aug 21.

30.

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 Jul 31;3:34. doi: 10.1186/s40168-015-0098-1. eCollection 2015.

31.

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.

McFadden RM, Larmonier CB, Shehab KW, Midura-Kiela M, Ramalingam R, Harrison CA, Besselsen DG, Chase JH, Caporaso JG, Jobin C, Ghishan FK, Kiela PR.

Inflamm Bowel Dis. 2015 Nov;21(11):2483-94. doi: 10.1097/MIB.0000000000000522.

32.

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

Marzinelli EM, Campbell AH, Zozaya Valdes E, Vergés A, Nielsen S, Wernberg T, de Bettignies T, Bennett S, Caporaso JG, Thomas T, Steinberg PD.

Environ Microbiol. 2015 Oct;17(10):4078-88. doi: 10.1111/1462-2920.12972. Epub 2015 Aug 4.

PMID:
26148974
33.

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 May 20;3:20. doi: 10.1186/s40168-015-0081-x. eCollection 2015. Erratum in: Microbiome. 2015;3:34.

34.

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

Kang DW, DiBaise JK, Ilhan ZE, Crowell MD, Rideout JR, Caporaso JG, Rittmann BE, Krajmalnik-Brown R.

Anaerobe. 2015 Jun;33:33-41. doi: 10.1016/j.anaerobe.2015.01.005. Epub 2015 Jan 21.

PMID:
25617726
35.

A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples.

Rothrock MJ Jr, Hiett KL, Gamble J, Caudill AC, Cicconi-Hogan KM, Caporaso JG.

J Vis Exp. 2014 Dec 10;(94). doi: 10.3791/52161.

36.

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

Holscher HD, Caporaso JG, Hooda S, Brulc JM, Fahey GC Jr, Swanson KS.

Am J Clin Nutr. 2015 Jan;101(1):55-64. doi: 10.3945/ajcn.114.092064. Epub 2014 Nov 12.

PMID:
25527750
37.

Temporal variability is a personalized feature of the human microbiome.

Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N.

Genome Biol. 2014 Dec 3;15(12):531. doi: 10.1186/s13059-014-0531-y.

38.

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.

39.

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.

40.

Individual diet has sex-dependent effects on vertebrate gut microbiota.

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R.

Nat Commun. 2014 Jul 29;5:4500. doi: 10.1038/ncomms5500.

41.

Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE.

Cell. 2014 Jul 17;158(2):250-262. doi: 10.1016/j.cell.2014.06.037.

42.

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA.

MBio. 2014 Jul 15;5(4):e01371-14. doi: 10.1128/mBio.01371-14.

43.

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.

Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE.

Mol Ecol. 2014 Oct;23(19):4831-45. doi: 10.1111/mec.12846. Epub 2014 Jul 31.

44.

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R.

Ecol Lett. 2014 Aug;17(8):979-87. doi: 10.1111/ele.12301. Epub 2014 May 22.

45.

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.

Sahl JW, Caporaso JG, Rasko DA, Keim P.

PeerJ. 2014 Apr 1;2:e332. doi: 10.7717/peerj.332. eCollection 2014.

46.

The personal human oral microbiome obscures the effects of treatment on periodontal disease.

Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST.

PLoS One. 2014 Jan 29;9(1):e86708. doi: 10.1371/journal.pone.0086708. eCollection 2014.

47.

Advancing our understanding of the human microbiome using QIIME.

Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R.

Methods Enzymol. 2013;531:371-444. doi: 10.1016/B978-0-12-407863-5.00019-8.

48.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

49.

Meeting report: fungal its workshop (october 2012).

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.

50.

The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

Michelou VK, Caporaso JG, Knight R, Palumbi SR.

PLoS One. 2013 Jun 19;8(6):e67480. doi: 10.1371/journal.pone.0067480. Print 2013.

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