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Items: 21

1.

Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome.

Berman HL, McLaren MR, Callahan BJ.

BJOG. 2019 Oct 9. doi: 10.1111/1471-0528.15978. [Epub ahead of print] Review.

PMID:
31597208
2.

Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers.

Foster DM, Jacob ME, Farmer KA, Callahan BJ, Theriot CM, Kathariou S, Cernicchiaro N, Prange T, Papich MG.

PLoS One. 2019 Oct 4;14(10):e0223378. doi: 10.1371/journal.pone.0223378. eCollection 2019.

3.

Consistent and correctable bias in metagenomic sequencing experiments.

McLaren MR, Willis AD, Callahan BJ.

Elife. 2019 Sep 10;8. pii: e46923. doi: 10.7554/eLife.46923.

4.

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 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
5.

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 Sep;37(9):1091.

PMID:
31341288
6.

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.

Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK.

Nucleic Acids Res. 2019 Oct 10;47(18):e103. doi: 10.1093/nar/gkz569.

7.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.

Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ.

Microbiome. 2018 Dec 17;6(1):226. doi: 10.1186/s40168-018-0605-2.

8.

Dosing Regimen of Enrofloxacin Impacts Intestinal Pharmacokinetics and the Fecal Microbiota in Steers.

Ferguson KM, Jacob ME, Theriot CM, Callahan BJ, Prange T, Papich MG, Foster DM.

Front Microbiol. 2018 Sep 19;9:2190. doi: 10.3389/fmicb.2018.02190. eCollection 2018.

9.

In Nature, There Is Only Diversity.

McLaren MR, Callahan BJ.

MBio. 2018 Jan 2;9(1). pii: e02149-17. doi: 10.1128/mBio.02149-17.

10.

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Callahan BJ, DiGiulio DB, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9966-9971. doi: 10.1073/pnas.1705899114. Epub 2017 Aug 28.

11.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.

Callahan BJ, McMurdie PJ, Holmes SP.

ISME J. 2017 Dec;11(12):2639-2643. doi: 10.1038/ismej.2017.119. Epub 2017 Jul 21.

12.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP.

Version 2. F1000Res. 2016 Jun 24 [revised 2016 Jan 1];5:1492. eCollection 2016.

13.

DADA2: High-resolution sample inference from Illumina amplicon data.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP.

Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23.

14.

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea.

Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA.

Nat Commun. 2016 Feb 3;7:10516. doi: 10.1038/ncomms10516.

15.

Temporal and spatial variation of the human microbiota during pregnancy.

DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11060-5. doi: 10.1073/pnas.1502875112. Epub 2015 Aug 17.

16.

Rapid evolution of adaptive niche construction in experimental microbial populations.

Callahan BJ, Fukami T, Fisher DS.

Evolution. 2014 Nov;68(11):3307-16. doi: 10.1111/evo.12512. Epub 2014 Sep 17.

PMID:
25138718
17.

Evolutionary dynamics and information hierarchies in biological systems.

Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM.

Ann N Y Acad Sci. 2013 Dec;1305:1-17. doi: 10.1111/nyas.12140. Epub 2013 May 20. Review.

PMID:
23691975
18.

Denoising PCR-amplified metagenome data.

Rosen MJ, Callahan BJ, Fisher DS, Holmes SP.

BMC Bioinformatics. 2012 Oct 31;13:283. doi: 10.1186/1471-2105-13-283.

19.

The length scale of selection in protein evolution.

Callahan BJ.

Fly (Austin). 2012 Jan-Mar;6(1):16-20. doi: 10.4161/fly.18305. Epub 2012 Jan 1.

PMID:
22198524
20.

Heterozygote advantage as a natural consequence of adaptation in diploids.

Sellis D, Callahan BJ, Petrov DA, Messer PW.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20666-71. doi: 10.1073/pnas.1114573108. Epub 2011 Dec 5.

21.

The afferent vagus and regulation of breathing in response to inhaled CO2 in awake newborn lambs.

Marsland DW, Callahan BJ, Shannon DC.

Biol Neonate. 1975;27(1-2):102-7.

PMID:
1148344

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