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Items: 1 to 50 of 134

1.

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster.

Rudman SM, Greenblum S, Hughes RC, Rajpurohit S, Kiratli O, Lowder DB, Lemmon SG, Petrov DA, Chaston JM, Schmidt P.

Proc Natl Acad Sci U S A. 2019 Sep 16. pii: 201907787. doi: 10.1073/pnas.1907787116. [Epub ahead of print]

PMID:
31527278
2.

Empowering conservation practice with efficient and economical genotyping from poor quality samples.

Natesh M, Taylor RW, Truelove NK, Hadly EA, Palumbi SR, Petrov DA, Ramakrishnan U.

Methods Ecol Evol. 2019 Jun;10(6):853-859. doi: 10.1111/2041-210X.13173. Epub 2019 Apr 10.

3.

Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces.

Feder AF, Pennings PS, Hermisson J, Petrov DA.

G3 (Bethesda). 2019 Aug 28. pii: g3.400605.2019. doi: 10.1534/g3.119.400605. [Epub ahead of print]

4.

Magnetic segregation effect in liquid crystals doped with carbon nanotubes.

Petrov DA, Skokov PK, Zakhlevnykh AN, Makarov DV.

Beilstein J Nanotechnol. 2019 Jul 22;10:1464-1474. doi: 10.3762/bjnano.10.145. eCollection 2019.

5.

Exploiting selection at linked sites to infer the rate and strength of adaptation.

Uricchio LH, Petrov DA, Enard D.

Nat Ecol Evol. 2019 Jun;3(6):977-984. doi: 10.1038/s41559-019-0890-6. Epub 2019 May 6.

PMID:
31061475
6.

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.

Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J.

PLoS Genet. 2019 Feb 12;15(2):e1007900. doi: 10.1371/journal.pgen.1007900. eCollection 2019 Feb.

7.

Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila.

Combs PA, Krupp JJ, Khosla NM, Bua D, Petrov DA, Levine JD, Fraser HB.

Curr Biol. 2018 Dec 17;28(24):3969-3975.e3. doi: 10.1016/j.cub.2018.10.036. Epub 2018 Nov 29.

PMID:
30503619
8.

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans.

Enard D, Petrov DA.

Cell. 2018 Oct 4;175(2):360-371.e13. doi: 10.1016/j.cell.2018.08.034.

PMID:
30290142
9.

Spatiotemporal dynamics and genome-wide association genome-wide association analysis of desiccation tolerance in Drosophila melanogaster.

Rajpurohit S, Gefen E, Bergland AO, Petrov DA, Gibbs AG, Schmidt PS.

Mol Ecol. 2018 Sep;27(17):3525-3540. doi: 10.1111/mec.14814. Epub 2018 Aug 13.

10.

Inferior Vena Cava Filter Strut Penetration into the Vertebral Column: A Case of 10-Year Clinical Follow Up.

Petrov DA, Chauhan A, Fitzpatrick S, Altman DT, Casagranda B.

Curr Probl Diagn Radiol. 2018 Apr 18. pii: S0363-0188(18)30091-4. doi: 10.1067/j.cpradiol.2018.04.006. [Epub ahead of print]

PMID:
29773455
11.

Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos.

McCoy RC, Newnham LJ, Ottolini CS, Hoffmann ER, Chatzimeletiou K, Cornejo OE, Zhan Q, Zaninovic N, Rosenwaks Z, Petrov DA, Demko ZP, Sigurjonsson S, Handyside AH.

Hum Mol Genet. 2018 Jul 15;27(14):2573-2585. doi: 10.1093/hmg/ddy147.

12.

Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice.

Rogers ZN, McFarland CD, Winters IP, Seoane JA, Brady JJ, Yoon S, Curtis C, Petrov DA, Winslow MM.

Nat Genet. 2018 Apr;50(4):483-486. doi: 10.1038/s41588-018-0083-2. Epub 2018 Apr 2.

13.

Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions.

Li Y, Venkataram S, Agarwala A, Dunn B, Petrov DA, Sherlock G, Fisher DS.

Curr Biol. 2018 Feb 19;28(4):515-525.e6. doi: 10.1016/j.cub.2018.01.009. Epub 2018 Feb 8.

14.

Magnetic field induced orientational transitions in liquid crystals doped with carbon nanotubes.

Petrov DA, Skokov PK, Zakhlevnykh AN.

Beilstein J Nanotechnol. 2017 Dec 29;8:2807-2817. doi: 10.3762/bjnano.8.280. eCollection 2017.

15.

Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster.

Behrman EL, Howick VM, Kapun M, Staubach F, Bergland AO, Petrov DA, Lazzaro BP, Schmidt PS.

Proc Biol Sci. 2018 Jan 10;285(1870). pii: 20172599. doi: 10.1098/rspb.2017.2599.

16.

Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity.

Winters IP, Chiou SH, Paulk NK, McFarland CD, Lalgudi PV, Ma RK, Lisowski L, Connolly AJ, Petrov DA, Kay MA, Winslow MM.

Nat Commun. 2017 Dec 12;8(1):2053. doi: 10.1038/s41467-017-01519-y.

17.

Perioperative Internal Iliac Artery Balloon Occlusion, In the Setting of Placenta Accreta and Its Variants: The Role of the Interventional Radiologist.

Petrov DA, Karlberg B, Singh K, Hartman M, Mittal PK.

Curr Probl Diagn Radiol. 2018 Nov;47(6):445-451. doi: 10.1067/j.cpradiol.2017.10.010. Epub 2017 Nov 10. Review.

PMID:
29224889
18.

Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift.

Wittmann MJ, Bergland AO, Feldman MW, Schmidt PS, Petrov DA.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9932-E9941. doi: 10.1073/pnas.1702994114. Epub 2017 Oct 30.

19.

Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations.

Assaf ZJ, Tilk S, Park J, Siegal ML, Petrov DA.

Genome Res. 2017 Dec;27(12):1988-2000. doi: 10.1101/gr.219956.116. Epub 2017 Oct 27.

20.

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites.

Ebel ER, Telis N, Venkataram S, Petrov DA, Enard D.

PLoS Genet. 2017 Sep 28;13(9):e1007023. doi: 10.1371/journal.pgen.1007023. eCollection 2017 Sep.

21.

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host.

Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z.

PLoS Pathog. 2017 May 25;13(5):e1006358. doi: 10.1371/journal.ppat.1006358. eCollection 2017 May.

22.

Soft Selective Sweeps in Evolutionary Rescue.

Wilson BA, Pennings PS, Petrov DA.

Genetics. 2017 Apr;205(4):1573-1586. doi: 10.1534/genetics.116.191478. Epub 2017 Feb 17.

23.

Seeking Goldilocks During Evolution of Drug Resistance.

Sherlock G, Petrov DA.

PLoS Biol. 2017 Feb 3;15(2):e2001872. doi: 10.1371/journal.pbio.2001872. eCollection 2017 Feb.

24.

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2017 Jan 19;6. pii: e24879. doi: 10.7554/eLife.24879. No abstract available.

25.

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum.

Zhu YO, Sherlock G, Petrov DA.

PLoS Genet. 2017 Jan 3;13(1):e1006455. doi: 10.1371/journal.pgen.1006455. eCollection 2017 Jan.

26.

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.

Venkataram S, Dunn B, Li Y, Agarwala A, Chang J, Ebel ER, Geiler-Samerotte K, Hérissant L, Blundell JR, Levy SF, Fisher DS, Sherlock G, Petrov DA.

Cell. 2016 Sep 8;166(6):1585-1596.e22. doi: 10.1016/j.cell.2016.08.002. Epub 2016 Sep 1.

27.

An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates.

Lou DI, Kim ET, Meyerson NR, Pancholi NJ, Mohni KN, Enard D, Petrov DA, Weller SK, Weitzman MD, Sawyer SL.

Cell Host Microbe. 2016 Aug 10;20(2):178-88. doi: 10.1016/j.chom.2016.07.003.

28.

Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation.

Zhu YO, Sherlock G, Petrov DA.

G3 (Bethesda). 2016 Aug 9;6(8):2421-34. doi: 10.1534/g3.116.029397.

29.

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.

Sellis D, Kvitek DJ, Dunn B, Sherlock G, Petrov DA.

Genetics. 2016 Jul;203(3):1401-13. doi: 10.1534/genetics.115.185165. Epub 2016 May 18.

30.

Viruses are a dominant driver of protein adaptation in mammals.

Enard D, Cai L, Gwennap C, Petrov DA.

Elife. 2016 May 17;5. pii: e12469. doi: 10.7554/eLife.12469.

31.

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster.

Garud NR, Petrov DA.

Genetics. 2016 Jun;203(2):863-80. doi: 10.1534/genetics.115.184002. Epub 2016 Apr 20.

32.

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2016 Feb 15;5. pii: e10670. doi: 10.7554/eLife.10670. Erratum in: Elife. 2017 Jan 19;6:.

33.

Effects of maternal age on euploidy rates in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening.

Demko ZP, Simon AL, McCoy RC, Petrov DA, Rabinowitz M.

Fertil Steril. 2016 May;105(5):1307-1313. doi: 10.1016/j.fertnstert.2016.01.025. Epub 2016 Feb 8.

34.

Global Transcriptional Profiling of Diapause and Climatic Adaptation in Drosophila melanogaster.

Zhao X, Bergland AO, Behrman EL, Gregory BD, Petrov DA, Schmidt PS.

Mol Biol Evol. 2016 Mar;33(3):707-20. doi: 10.1093/molbev/msv263. Epub 2015 Nov 13.

35.

Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster.

Machado HE, Bergland AO, O'Brien KR, Behrman EL, Schmidt PS, Petrov DA.

Mol Ecol. 2016 Feb;25(3):723-40. doi: 10.1111/mec.13446. Epub 2016 Jan 18.

36.

Evidence of Selection against Complex Mitotic-Origin Aneuploidy during Preimplantation Development.

McCoy RC, Demko ZP, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Petrov DA.

PLoS Genet. 2015 Oct 22;11(10):e1005601. doi: 10.1371/journal.pgen.1005601. eCollection 2015 Oct.

37.

Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance.

Moreno-Gamez S, Hill AL, Rosenbloom DI, Petrov DA, Nowak MA, Pennings PS.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2874-83. doi: 10.1073/pnas.1424184112. Epub 2015 May 18.

38.

Obstruction of adaptation in diploids by recessive, strongly deleterious alleles.

Assaf ZJ, Petrov DA, Blundell JR.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):E2658-66. doi: 10.1073/pnas.1424949112. Epub 2015 May 4.

39.

Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos.

McCoy RC, Demko Z, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Fraser HB, Petrov DA.

Science. 2015 Apr 10;348(6231):235-8. doi: 10.1126/science.aaa3337.

40.

Quantitative evolutionary dynamics using high-resolution lineage tracking.

Levy SF, Blundell JR, Venkataram S, Petrov DA, Fisher DS, Sherlock G.

Nature. 2015 Mar 12;519(7542):181-6. doi: 10.1038/nature14279. Epub 2015 Feb 25.

41.

Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps.

Garud NR, Messer PW, Buzbas EO, Petrov DA.

PLoS Genet. 2015 Feb 23;11(2):e1005004. doi: 10.1371/journal.pgen.1005004. eCollection 2015 Feb.

42.

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.

Fiston-Lavier AS, Barrón MG, Petrov DA, González J.

Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.

43.

Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila.

Bergland AO, Behrman EL, O'Brien KR, Schmidt PS, Petrov DA.

PLoS Genet. 2014 Nov 6;10(11):e1004775. doi: 10.1371/journal.pgen.1004775. eCollection 2014 Nov.

44.

Population genomics of transposable elements in Drosophila.

Barrón MG, Fiston-Lavier AS, Petrov DA, González J.

Annu Rev Genet. 2014;48:561-81. doi: 10.1146/annurev-genet-120213-092359. Epub 2014 Oct 1. Review.

PMID:
25292358
45.

Reply to Chen and Zhang: On interpreting genome-wide trends from yeast mutation accumulation data.

Zhu YO, Siegal ML, Hall DW, Petrov DA.

Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4063. doi: 10.1073/pnas.1413861111. Epub 2014 Sep 12. No abstract available.

46.

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.

McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS.

PLoS One. 2014 Sep 4;9(9):e106689. doi: 10.1371/journal.pone.0106689. eCollection 2014.

47.

Soft selective sweeps in complex demographic scenarios.

Wilson BA, Petrov DA, Messer PW.

Genetics. 2014 Oct;198(2):669-84. doi: 10.1534/genetics.114.165571. Epub 2014 Jul 24.

48.

Precise estimates of mutation rate and spectrum in yeast.

Zhu YO, Siegal ML, Hall DW, Petrov DA.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2310-8. doi: 10.1073/pnas.1323011111. Epub 2014 May 20.

49.

Comparative population genomics: power and principles for the inference of functionality.

Lawrie DS, Petrov DA.

Trends Genet. 2014 Apr;30(4):133-9. doi: 10.1016/j.tig.2014.02.002. Epub 2014 Mar 20. Review.

50.

Genome-wide signals of positive selection in human evolution.

Enard D, Messer PW, Petrov DA.

Genome Res. 2014 Jun;24(6):885-95. doi: 10.1101/gr.164822.113. Epub 2014 Mar 11.

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