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Items: 1 to 50 of 65

1.

Fine-mapping cis-regulatory variants in diverse human populations.

Tehranchi A, Hie B, Dacre M, Kaplow I, Pettie K, Combs P, Fraser HB.

Elife. 2019 Jan 16;8. pii: e39595. doi: 10.7554/eLife.39595.

2.

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
3.

Improving Estimates of Compensatory cis-trans Regulatory Divergence.

Fraser HB.

Trends Genet. 2019 Jan;35(1):88. doi: 10.1016/j.tig.2018.10.003. Epub 2018 Nov 30. No abstract available.

PMID:
30509787
4.

Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes.

Martin T, Fraser HB.

Nat Commun. 2018 Nov 23;9(1):4963. doi: 10.1038/s41467-018-07436-y.

5.

Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes.

York RA, Patil C, Abdilleh K, Johnson ZV, Conte MA, Genner MJ, McGrath PT, Fraser HB, Fernald RD, Streelman JT.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11081-E11090. doi: 10.1073/pnas.1810140115. Epub 2018 Nov 5.

6.

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.

Combs PA, Fraser HB.

PLoS Genet. 2018 Nov 1;14(11):e1007631. doi: 10.1371/journal.pgen.1007631. eCollection 2018 Nov.

7.

Improving Estimates of Compensatory cis-trans Regulatory Divergence.

Fraser HB.

Trends Genet. 2019 Jan;35(1):3-5. doi: 10.1016/j.tig.2018.09.003. Epub 2018 Sep 27. Review. Erratum in: Trends Genet. 2018 Nov 30;:.

PMID:
30270122
8.

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing.

Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, Fraser HB.

Cell. 2018 Oct 4;175(2):544-557.e16. doi: 10.1016/j.cell.2018.08.057. Epub 2018 Sep 20.

PMID:
30245013
9.

Worldwide patterns of human epigenetic variation.

Carja O, MacIsaac JL, Mah SM, Henn BM, Kobor MS, Feldman MW, Fraser HB.

Nat Ecol Evol. 2017 Oct;1(10):1577-1583. doi: 10.1038/s41559-017-0299-z. Epub 2017 Aug 28.

PMID:
29185505
10.

High-resolution mapping of cis-regulatory variation in budding yeast.

Kita R, Venkataram S, Zhou Y, Fraser HB.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10736-E10744. doi: 10.1073/pnas.1717421114. Epub 2017 Nov 28.

11.

Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids.

Artieri CG, Naor A, Turgeman-Grott I, Zhou Y, York R, Gophna U, Fraser HB.

Sci Rep. 2017 Jun 21;7(1):3986. doi: 10.1038/s41598-017-04278-4.

12.

Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin.

Kita R, Fraser HB.

PLoS Genet. 2016 Oct 19;12(10):e1006382. doi: 10.1371/journal.pgen.1006382. eCollection 2016 Oct.

13.

Genetic variation in MHC proteins is associated with T cell receptor expression biases.

Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, Pritchard JK.

Nat Genet. 2016 Sep;48(9):995-1002. doi: 10.1038/ng.3625. Epub 2016 Aug 1.

14.

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk.

Tehranchi AK, Myrthil M, Martin T, Hie BL, Golan D, Fraser HB.

Cell. 2016 Apr 21;165(3):730-41. doi: 10.1016/j.cell.2016.03.041. Epub 2016 Apr 14.

15.

Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.

Naranjo S, Smith JD, Artieri CG, Zhang M, Zhou Y, Palmer ME, Fraser HB.

PLoS Genet. 2015 Dec 29;11(12):e1005751. doi: 10.1371/journal.pgen.1005751. eCollection 2015 Dec.

16.

Disentangling Sources of Selection on Exonic Transcriptional Enhancers.

Agoglia RM, Fraser HB.

Mol Biol Evol. 2016 Feb;33(2):585-90. doi: 10.1093/molbev/msv234. Epub 2015 Oct 24.

17.

A pooling-based approach to mapping genetic variants associated with DNA methylation.

Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, Fraser HB.

Genome Res. 2015 Jun;25(6):907-17. doi: 10.1101/gr.183749.114. Epub 2015 Apr 24.

18.

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.

19.

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse.

Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, Fraser HB.

Nat Genet. 2015 May;47(5):544-9. doi: 10.1038/ng.3274. Epub 2015 Apr 13.

20.

Discordance of DNA methylation variance between two accessible human tissues.

Jiang R, Jones MJ, Chen E, Neumann SM, Fraser HB, Miller GE, Kobor MS.

Sci Rep. 2015 Feb 9;5:8257. doi: 10.1038/srep08257.

21.

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation.

Artieri CG, Fraser HB.

Genome Res. 2014 Dec;24(12):2011-21. doi: 10.1101/gr.175893.114. Epub 2014 Oct 7.

22.

Transcript length mediates developmental timing of gene expression across Drosophila.

Artieri CG, Fraser HB.

Mol Biol Evol. 2014 Nov;31(11):2879-89. doi: 10.1093/molbev/msu226. Epub 2014 Jul 28.

23.

Evolution at two levels of gene expression in yeast.

Artieri CG, Fraser HB.

Genome Res. 2014 Mar;24(3):411-21. doi: 10.1101/gr.165522.113. Epub 2013 Dec 6.

25.

The molecular mechanism of a cis-regulatory adaptation in yeast.

Chang J, Zhou Y, Hu X, Lam L, Henry C, Green EM, Kita R, Kobor MS, Fraser HB.

PLoS Genet. 2013;9(9):e1003813. doi: 10.1371/journal.pgen.1003813. Epub 2013 Sep 19.

26.

A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers.

Smith JD, McManus KF, Fraser HB.

Mol Biol Evol. 2013 Nov;30(11):2509-18. doi: 10.1093/molbev/mst134. Epub 2013 Jul 30.

27.

Ancient cis-regulatory constraints and the evolution of genome architecture.

Irimia M, Maeso I, Roy SW, Fraser HB.

Trends Genet. 2013 Sep;29(9):521-8. doi: 10.1016/j.tig.2013.05.008. Epub 2013 Jun 18. Review.

PMID:
23791467
28.

Reply to Suderman et al.: Importance of accounting for blood cell composition in epigenetic studies.

Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, Kobor MS.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):E1247. No abstract available.

29.

Gene expression drives local adaptation in humans.

Fraser HB.

Genome Res. 2013 Jul;23(7):1089-96. doi: 10.1101/gr.152710.112. Epub 2013 Mar 28.

30.

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.

Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, Bessa J.

BMC Genomics. 2012 Dec 19;13:713. doi: 10.1186/1471-2164-13-713.

31.

Factors underlying variable DNA methylation in a human community cohort.

Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, Kobor MS.

Proc Natl Acad Sci U S A. 2012 Oct 16;109 Suppl 2:17253-60. doi: 10.1073/pnas.1121249109. Epub 2012 Oct 8.

32.

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.

Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB.

Genome Res. 2012 Dec;22(12):2356-67. doi: 10.1101/gr.139725.112. Epub 2012 Jun 21.

33.

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity.

Fraser HB, Levy S, Chavan A, Shah HB, Perez JC, Zhou Y, Siegal ML, Sinha H.

Genome Res. 2012 Oct;22(10):1930-9. doi: 10.1101/gr.134080.111. Epub 2012 May 29.

34.

Population-specificity of human DNA methylation.

Fraser HB, Lam LL, Neumann SM, Kobor MS.

Genome Biol. 2012 Feb 9;13(2):R8. doi: 10.1186/gb-2012-13-2-r8.

35.

Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.

Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE.

PLoS One. 2011;6(7):e20090. doi: 10.1371/journal.pone.0020090. Epub 2011 Jul 5.

37.

Systematic detection of polygenic cis-regulatory evolution.

Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, Schadt EE.

PLoS Genet. 2011 Mar;7(3):e1002023. doi: 10.1371/journal.pgen.1002023. Epub 2011 Mar 31.

38.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE.

BMC Genomics. 2010 Aug 13;11:473. doi: 10.1186/1471-2164-11-473.

39.

Evidence for widespread adaptive evolution of gene expression in budding yeast.

Fraser HB, Moses AM, Schadt EE.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2977-82. doi: 10.1073/pnas.0912245107. Epub 2010 Jan 28.

40.

The quantitative genetics of phenotypic robustness.

Fraser HB, Schadt EE.

PLoS One. 2010 Jan 8;5(1):e8635. doi: 10.1371/journal.pone.0008635.

41.

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9. doi: 10.1073/pnas.0812841106. Epub 2009 Feb 10.

42.

Common polymorphic transcript variation in human disease.

Fraser HB, Xie X.

Genome Res. 2009 Apr;19(4):567-75. doi: 10.1101/gr.083477.108. Epub 2009 Feb 2.

43.
44.

Confirmation of organized modularity in the yeast interactome.

Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, Vidal M.

PLoS Biol. 2007 Jun;5(6):e153. No abstract available.

45.

Assessing the determinants of evolutionary rates in the presence of noise.

Plotkin JB, Fraser HB.

Mol Biol Evol. 2007 May;24(5):1113-21. Epub 2007 Mar 7.

PMID:
17347158
46.

Codon usage and selection on proteins.

Plotkin JB, Dushoff J, Desai MM, Fraser HB.

J Mol Evol. 2006 Nov;63(5):635-53. Epub 2006 Oct 14.

PMID:
17043750
47.

Coevolution, modularity and human disease.

Fraser HB.

Curr Opin Genet Dev. 2006 Dec;16(6):637-44. Epub 2006 Sep 26. Review.

PMID:
17005391
48.

Estimating selection pressures from limited comparative data.

Plotkin JB, Dushoff J, Desai MM, Fraser HB.

Mol Biol Evol. 2006 Aug;23(8):1457-9. Epub 2006 Jun 5.

PMID:
16754640
49.

Aging and gene expression in the primate brain.

Fraser HB, Khaitovich P, Plotkin JB, Pääbo S, Eisen MB.

PLoS Biol. 2005 Sep;3(9):e274. Epub 2005 Aug 2.

50.

Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae.

Lynch PJ, Fraser HB, Sevastopoulos E, Rine J, Rusche LN.

Mol Cell Biol. 2005 Jul;25(14):5920-32.

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