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Items: 1 to 50 of 122

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.

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.

4.

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.

5.

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
6.

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.

7.

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.

8.

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.

9.

Mock Code: A Code Blue Scenario Requested by and Developed for Registered Nurses.

Williams KL, Rideout J, Pritchett-Kelly S, McDonald M, Mullins-Richards P, Dubrowski A.

Cureus. 2016 Dec 23;8(12):e938. doi: 10.7759/cureus.938.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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
17.

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.

18.

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.

19.

Characterizing the learning curve of the VBLaST-PT(©) (Virtual Basic Laparoscopic Skill Trainer).

Zhang L, Sankaranarayanan G, Arikatla VS, Ahn W, Grosdemouge C, Rideout JM, Epstein SK, De S, Schwaitzberg SD, Jones DB, Cao CG.

Surg Endosc. 2013 Oct;27(10):3603-15. doi: 10.1007/s00464-013-2932-5. Epub 2013 Apr 10.

20.

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.

21.

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.

22.

Systematic health management: the time has come to do the right thing for each person.

Rideout J.

Am Health Drug Benefits. 2011 May;4(3):152-4. No abstract available.

23.

Landau model for the elastic properties of the ferroelastic crystal Rb(4)LiH(3)(SO(4))(4).

Quirion G, Wu W, Aktas O, Rideout J, Clouter MJ, Mróz B.

J Phys Condens Matter. 2009 Nov 11;21(45):455901. doi: 10.1088/0953-8984/21/45/455901. Epub 2009 Oct 21.

PMID:
21694021
24.

Bioactive triterpenes from Diospyros blancoi.

Ragasa CY, Puno MR, Sengson JM, Shen CC, Rideout JA, Raga DD.

Nat Prod Res. 2009;23(13):1252-8. doi: 10.1080/14786410902951054.

PMID:
19731144
25.

Secondary metabolites from Tectona philippinensis.

Ragasa CY, Lapina MC, Lee JJ, Mandia EH, Rideout JA.

Nat Prod Res. 2008 Jun 15;22(9):820-4. doi: 10.1080/14786410701640551.

PMID:
18569722
26.

Nonsymmetrical beta-carboline dimers from an Ascidian, Didemnum sp.

Kearns PS, Rideout JA.

J Nat Prod. 2008 Jul;71(7):1280-2. doi: 10.1021/np800077e. Epub 2008 Jun 12.

PMID:
18547113
27.

A new sesquiterpene from Artemisia vulgaris.

Ragasa CY, de Jesus JP, Apuada MJ, Rideout JA.

J Nat Med. 2008 Oct;62(4):461-3. doi: 10.1007/s11418-008-0253-0. Epub 2008 Apr 26.

PMID:
18438634
28.

Structure-activity relationships of dinucleotides: Potent and selective agonists of P2Y receptors.

Shaver SR, Rideout JL, Pendergast W, Douglass JG, Brown EG, Boyer JL, Patel RI, Redick CC, Jones AC, Picher M, Yerxa BR.

Purinergic Signal. 2005 Jun;1(2):183-91. doi: 10.1007/s11302-005-0648-2. Epub 2005 Mar 7.

29.

Chromomoric acid derivatives from Tectona philippinensis.

Ragasa CY, Tepora MM, Espinelli DH, Mandia EH, Rideout JA.

J Nat Prod. 2008 Apr;71(4):701-5. doi: 10.1021/np0704304. Epub 2008 Feb 16.

PMID:
18278870
30.

Iridoids from Gardenia jasminoides.

Ragasa CY, Pimenta LE, Rideout JA.

Nat Prod Res. 2007 Oct;21(12):1078-84.

PMID:
17852743
31.

The costs and effectiveness of different benefit designs for treating tobacco dependence: results from a randomized trial.

Halpin HA, McMenamin SB, Rideout J, Boyce-Smith G.

Inquiry. 2006 Spring;43(1):54-65.

PMID:
16838818
32.

Monoterpene lactones from the seeds of Nephelium lappaceum.

Ragasa CY, de Luna RD, Cruz WC Jr, Rideout JA.

J Nat Prod. 2005 Sep;68(9):1394-6.

PMID:
16180821
33.

Effect of an Internet-based system for doctor-patient communication on health care spending.

Baker L, Rideout J, Gertler P, Raube K.

J Am Med Inform Assoc. 2005 Sep-Oct;12(5):530-6. Epub 2005 May 19.

34.

Antifungal metabolites from Blumea balsamifera.

Ragasa CY, Co AL, Rideout JA.

Nat Prod Res. 2005 Apr;19(3):231-7.

PMID:
15702636
35.

Terpenoids and sterols from Lagerstroemia speciosa.

Ragasa CY, Ngo HT, Rideout JA.

J Asian Nat Prod Res. 2005 Feb;7(1):7-12.

PMID:
15621595
36.

New cycloartenol esters from Ixora coccinea.

Ragasa CY, Tiu F, Rideout JA.

Nat Prod Res. 2004 Aug;18(4):319-23.

PMID:
15214483
37.

Do health plans influence quality of care?

Baker LC, Hopkins D, Dixon R, Rideout J, Geppert J.

Int J Qual Health Care. 2004 Feb;16(1):19-30.

PMID:
15020557
38.

A new furanoid diterpene from Caesalpinia pulcherrima.

Ragasa CY, Ganzon J, Hofileña J, Tamboong B, Rideout JA.

Chem Pharm Bull (Tokyo). 2003 Oct;51(10):1208-10.

39.

New furanoid diterpenes from Caesalpinia pulcherrima.

Ragasa CY, Hofileña JG, Rideout JA.

J Nat Prod. 2002 Aug;65(8):1107-10.

PMID:
12193012
40.

Ionone derivatives from Alternanthera sessilis.

Ragasa CY, Tremor N, Rideout JA.

J Asian Nat Prod Res. 2002 Jun;4(2):109-15.

PMID:
12067155
41.

Bastadin 21, a novel isobastarane metabolite from the Great Barrier Reef marine sponge Ianthella quadrangulata.

Coll JC, Kearns PS, Rideout JA, Sankar V.

J Nat Prod. 2002 May;65(5):753-6.

PMID:
12027760
42.

An antifungal cadinanolide from Pseudoelephantopus spicatus.

Ragasa CY, Rideout JA.

Chem Pharm Bull (Tokyo). 2001 Oct;49(10):1359-61.

43.

A triterpene from Ficus pumila.

Ragasa CY, Juan E, Rideout JA.

J Asian Nat Prod Res. 1999;1(4):269-75.

PMID:
11523547
44.

Diastereomeric diterpenes from Coleus blumei.

Ragas CY, Templora VF, Rideout JA.

Chem Pharm Bull (Tokyo). 2001 Jul;49(7):927-9.

45.

Variations in treatment benefits influence smoking cessation: results of a randomised controlled trial.

Schauffler HH, McMenamin S, Olson K, Boyce-Smith G, Rideout JA, Kamil J.

Tob Control. 2001 Jun;10(2):175-80.

46.

Synthesis and P2Y receptor activity of a series of uridine dinucleoside 5'-polyphosphates.

Pendergast W, Yerxa BR, Douglass JG 3rd, Shaver SR, Dougherty RW, Redick CC, Sims IF, Rideout JL.

Bioorg Med Chem Lett. 2001 Jan 22;11(2):157-60.

PMID:
11206448
47.
48.

Organizational systems used by California capitated medical groups and independent practice associations to increase cancer screening.

Malin JL, Kahn K, Dulai G, Farmer MM, Rideout J, Simon LP, Ganz PA.

Cancer. 2000 Jun 15;88(12):2824-31.

PMID:
10870067
49.

Clerodane diterpenes from Tinospora rumphii.

Ragasa CY, Cruz MC, Gula R, Rideout JA.

J Nat Prod. 2000 Apr;63(4):509-11.

PMID:
10785426
50.

Benzimidazole 2'-isonucleosides: design, synthesis, and antiviral activity of 2-substituted-5,6-dichlorobenzimidazole 2'-isonucleosides.

Freeman GA, Selleseth DW, Rideout JL, Harvey RJ.

Nucleosides Nucleotides Nucleic Acids. 2000 Jan-Feb;19(1-2):155-74.

PMID:
10772707

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