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Items: 1 to 50 of 158

1.

A great-ape view of the gut microbiome.

Nishida AH, Ochman H.

Nat Rev Genet. 2019 Apr;20(4):195-206. doi: 10.1038/s41576-018-0085-z. Review.

PMID:
30622302
2.

Factors driving effective population size and pan-genome evolution in bacteria.

Bobay LM, Ochman H.

BMC Evol Biol. 2018 Oct 12;18(1):153. doi: 10.1186/s12862-018-1272-4.

3.

Biological species in the viral world.

Bobay LM, Ochman H.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6040-6045. doi: 10.1073/pnas.1717593115. Epub 2018 May 21.

4.

ConSpeciFix: classifying prokaryotic species based on gene flow.

Bobay LM, Ellis BS, Ochman H.

Bioinformatics. 2018 Nov 1;34(21):3738-3740. doi: 10.1093/bioinformatics/bty400.

PMID:
29771275
5.

A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli.

Traverse CC, Ochman H.

G3 (Bethesda). 2018 Jul 2;8(7):2257-2264. doi: 10.1534/g3.118.200209.

6.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
7.

Local genic base composition impacts protein production and cellular fitness.

Quandt EM, Traverse CC, Ochman H.

PeerJ. 2018 Jan 16;6:e4286. doi: 10.7717/peerj.4286. eCollection 2018.

8.

Rates of gut microbiome divergence in mammals.

Nishida AH, Ochman H.

Mol Ecol. 2018 Apr;27(8):1884-1897. doi: 10.1111/mec.14473. Epub 2018 Jan 31.

9.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

10.

Impact of Recombination on the Base Composition of Bacteria and Archaea.

Bobay LM, Ochman H.

Mol Biol Evol. 2017 Oct 1;34(10):2627-2636. doi: 10.1093/molbev/msx189.

11.

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

Traverse CC, Ochman H.

MBio. 2017 Aug 29;8(4). pii: e01230-17. doi: 10.1128/mBio.01230-17.

12.

The Evolution of Bacterial Genome Architecture.

Bobay LM, Ochman H.

Front Genet. 2017 May 30;8:72. doi: 10.3389/fgene.2017.00072. eCollection 2017. Review.

13.

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome.

Raymann K, Moeller AH, Goodman AL, Ochman H.

mSphere. 2017 Feb 22;2(1). pii: e00026-17. doi: 10.1128/mSphere.00026-17. eCollection 2017 Jan-Feb.

14.

Biological species are universal across Life's domains.

Bobay LM, Ochman H.

Genome Biol Evol. 2017 Feb 10. doi: 10.1093/gbe/evx026. [Epub ahead of print] No abstract available.

15.

Cospeciation of gut microbiota with hominids.

Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, Pusey AE, Peeters M, Hahn BH, Ochman H.

Science. 2016 Jul 22;353(6297):380-2. doi: 10.1126/science.aaf3951.

16.

Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3639-44. doi: 10.1073/pnas.1525637113. Epub 2016 Mar 8.

17.

Realizing Microbial Evolution.

Ochman H.

Cold Spring Harb Perspect Biol. 2016 May 2;8(5). pii: a018101. doi: 10.1101/cshperspect.a018101. Review.

18.

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles.

Traverse CC, Ochman H.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3311-6. doi: 10.1073/pnas.1525329113. Epub 2016 Feb 16. Erratum in: Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4257-8.

19.

Social behavior shapes the chimpanzee pan-microbiome.

Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H.

Sci Adv. 2016 Jan 15;2(1):e1500997. doi: 10.1126/sciadv.1500997. eCollection 2016 Jan.

20.

Assessing the Unseen Bacterial Diversity in Microbial Communities.

Caro-Quintero A, Ochman H.

Genome Biol Evol. 2015 Nov 27;7(12):3416-25. doi: 10.1093/gbe/evv234.

21.

Impermanence of bacterial clones.

Bobay LM, Traverse CC, Ochman H.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8893-900. doi: 10.1073/pnas.1501724112.

22.

Effects of Genic Base Composition on Growth Rate in G+C-rich Genomes.

Kelkar YD, Phillips DS, Ochman H.

G3 (Bethesda). 2015 Apr 20;5(6):1247-52. doi: 10.1534/g3.115.016824. Erratum in: G3 (Bethesda). 2015 Dec;5(12):2921.

23.

Where next for microbiome research?

Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H.

PLoS Biol. 2015 Jan 20;13(1):e1002050. doi: 10.1371/journal.pbio.1002050. eCollection 2015 Jan.

24.

Genome rearrangements can make and break small RNA genes.

Raghavan R, Kacharia FR, Millar JA, Sislak CD, Ochman H.

Genome Biol Evol. 2015 Jan 18;7(2):557-66. doi: 10.1093/gbe/evv009.

25.

Stability of the gorilla microbiome despite simian immunodeficiency virus infection.

Moeller AH, Peeters M, Ayouba A, Ngole EM, Esteban A, Hahn BH, Ochman H.

Mol Ecol. 2015 Feb;24(3):690-7. doi: 10.1111/mec.13057. Epub 2015 Jan 19.

26.

Rapid changes in the gut microbiome during human evolution.

Moeller AH, Li Y, Mpoudi Ngole E, Ahuka-Mundeke S, Lonsdorf EV, Pusey AE, Peeters M, Hahn BH, Ochman H.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16431-5. doi: 10.1073/pnas.1419136111. Epub 2014 Nov 3.

27.

Microbiomes are true to type.

Moeller AH, Ochman H.

Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9372-3. doi: 10.1073/pnas.1408654111. Epub 2014 Jun 17. No abstract available.

28.

Disentangling associated genomes.

Sloan DB, Bennett GM, Engel P, Williams D, Ochman H.

Methods Enzymol. 2013;531:445-64. doi: 10.1016/B978-0-12-407863-5.00020-4.

PMID:
24060132
29.

SIV-induced instability of the chimpanzee gut microbiome.

Moeller AH, Shilts M, Li Y, Rudicell RS, Lonsdorf EV, Pusey AE, Wilson ML, Hahn BH, Ochman H.

Cell Host Microbe. 2013 Sep 11;14(3):340-5. doi: 10.1016/j.chom.2013.08.005.

30.

Factors that drive variation among gut microbial communities.

Moeller AH, Ochman H.

Gut Microbes. 2013 Sep-Oct;4(5):403-8. doi: 10.4161/gmic.26039. Epub 2013 Aug 9.

31.

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.

Williams D, Trimble WL, Shilts M, Meyer F, Ochman H.

BMC Genomics. 2013 Aug 8;14:537. doi: 10.1186/1471-2164-14-537.

32.

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities.

Moeller AH, Peeters M, Ndjango JB, Li Y, Hahn BH, Ochman H.

Genome Res. 2013 Oct;23(10):1715-20. doi: 10.1101/gr.154773.113. Epub 2013 Jun 26.

33.

Chimpanzees and humans harbour compositionally similar gut enterotypes.

Moeller AH, Degnan PH, Pusey AE, Wilson ML, Hahn BH, Ochman H.

Nat Commun. 2012;3:1179. doi: 10.1038/ncomms2159.

34.

Genome reduction promotes increase in protein functional complexity in bacteria.

Kelkar YD, Ochman H.

Genetics. 2013 Jan;193(1):303-7. doi: 10.1534/genetics.112.145656. Epub 2012 Oct 31.

35.

A selective force favoring increased G+C content in bacterial genes.

Raghavan R, Kelkar YD, Ochman H.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14504-7. doi: 10.1073/pnas.1205683109. Epub 2012 Aug 20.

36.

Antisense transcription is pervasive but rarely conserved in enteric bacteria.

Raghavan R, Sloan DB, Ochman H.

MBio. 2012 Aug 7;3(4). pii: e00156-12. doi: 10.1128/mBio.00156-12. Print 2012.

37.

Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park.

Degnan PH, Pusey AE, Lonsdorf EV, Goodall J, Wroblewski EE, Wilson ML, Rudicell RS, Hahn BH, Ochman H.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):13034-9. doi: 10.1073/pnas.1110994109. Epub 2012 Jul 23.

38.

Causes and consequences of genome expansion in fungi.

Kelkar YD, Ochman H.

Genome Biol Evol. 2012;4(1):13-23. doi: 10.1093/gbe/evr124. Epub 2011 Nov 24.

39.

Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera.

Degnan PH, Ochman H, Moran NA.

PLoS Genet. 2011 Sep;7(9):e1002252. doi: 10.1371/journal.pgen.1002252. Epub 2011 Sep 1.

40.

Illumina-based analysis of microbial community diversity.

Degnan PH, Ochman H.

ISME J. 2012 Jan;6(1):183-94. doi: 10.1038/ismej.2011.74. Epub 2011 Jun 16.

41.

Genome-wide detection of novel regulatory RNAs in E. coli.

Raghavan R, Groisman EA, Ochman H.

Genome Res. 2011 Sep;21(9):1487-97. doi: 10.1101/gr.119370.110. Epub 2011 Jun 10.

42.
43.

Evolutionary relationships of wild hominids recapitulated by gut microbial communities.

Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, Hugenholtz P.

PLoS Biol. 2010 Nov 16;8(11):e1000546. doi: 10.1371/journal.pbio.1000546.

44.

The extinction dynamics of bacterial pseudogenes.

Kuo CH, Ochman H.

PLoS Genet. 2010 Aug 5;6(8). pii: e1001050. doi: 10.1371/journal.pgen.1001050.

45.

Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.

Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP.

Genome Biol Evol. 2010 Jan 6;2:53-66. doi: 10.1093/gbe/evp057.

46.

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P.

ISME J. 2010 May;4(5):642-7. doi: 10.1038/ismej.2009.153. Epub 2010 Jan 21.

PMID:
20090784
47.

Systems biology. Excavating the functional landscape of bacterial cells.

Ochman H, Raghavan R.

Science. 2009 Nov 27;326(5957):1200-1. doi: 10.1126/science.1183757. No abstract available.

PMID:
19965458
48.

Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome.

Jarvik T, Smillie C, Groisman EA, Ochman H.

J Bacteriol. 2010 Jan;192(2):560-7. doi: 10.1128/JB.01233-09. Epub 2009 Nov 6.

49.

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria.

Kuo CH, Ochman H.

Biol Direct. 2009 Sep 29;4:35. doi: 10.1186/1745-6150-4-35.

50.

A single genetic locus in the phytopathogen Pantoea stewartii enables gut colonization and pathogenicity in an insect host.

Stavrinides J, No A, Ochman H.

Environ Microbiol. 2010 Jan;12(1):147-55. doi: 10.1111/j.1462-2920.2009.02056.x. Epub 2009 Sep 24.

PMID:
19788413

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