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Items: 17

1.

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 Apr 1. pii: S1075-9964(19)30064-2. doi: 10.1016/j.anaerobe.2019.03.017. [Epub ahead of print] Review.

2.

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.

3.

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile.

Chen LA, Hourigan SK, Grigoryan Z, Gao Z, Clemente JC, Rideout JR, Chirumamilla S, Rabidazeh S, Saeed S, Elson CO, Oliva-Hemker M, Blaser MJ, Sears CL.

J Pediatr Gastroenterol Nutr. 2019 Apr;68(4):502-508. doi: 10.1097/MPG.0000000000002210.

PMID:
30540709
4.

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.

5.

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.

6.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J.

Microbiome. 2018 May 17;6(1):90. doi: 10.1186/s40168-018-0470-z.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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
14.

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.

15.

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.

16.

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.

Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R.

J Allergy Clin Immunol. 2012 May;129(5):1204-8. doi: 10.1016/j.jaci.2012.03.010.

17.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG.

Gigascience. 2012 Jul 12;1(1):7. doi: 10.1186/2047-217X-1-7.

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