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Items: 1 to 50 of 132

1.

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
2.

Post-translational buffering leads to convergent protein expression levels between primates.

Wang SH, Hsiao CJ, Khan Z, Pritchard JK.

Genome Biol. 2018 Jun 27;19(1):83. doi: 10.1186/s13059-018-1451-z.

3.

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes.

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y.

Elife. 2018 May 8;7. pii: e33480. doi: 10.7554/eLife.33480.

4.

Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment.

Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, Pritchard JK, Nakauchi H.

Cell Stem Cell. 2018 Apr 5;22(4):600-607.e4. doi: 10.1016/j.stem.2018.03.013.

5.

Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila.

Sparvoli D, Richardson E, Osakada H, Lan X, Iwamoto M, Bowman GR, Kontur C, Bourland WA, Lynn DH, Pritchard JK, Haraguchi T, Dacks JB, Turkewitz AP.

Curr Biol. 2018 Mar 5;28(5):697-710.e13. doi: 10.1016/j.cub.2018.01.047. Epub 2018 Feb 22.

PMID:
29478853
6.

Annotation-free quantification of RNA splicing using LeafCutter.

Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK.

Nat Genet. 2018 Jan;50(1):151-158. doi: 10.1038/s41588-017-0004-9. Epub 2017 Dec 11.

7.

Impact of regulatory variation across human iPSCs and differentiated cells.

Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y.

Genome Res. 2018 Jan;28(1):122-131. doi: 10.1101/gr.224436.117. Epub 2017 Dec 5.

8.

Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates.

Harpak A, Lan X, Gao Z, Pritchard JK.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12779-12784. doi: 10.1073/pnas.1708151114. Epub 2017 Nov 14.

9.

Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression.

Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK.

Am J Hum Genet. 2017 Nov 2;101(5):686-699. doi: 10.1016/j.ajhg.2017.09.009. Epub 2017 Oct 26.

10.

Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.

Sharon E, Shi H, Kharbanda S, Koh W, Martin LR, Khush KK, Valantine H, Pritchard JK, De Vlaminck I.

PLoS Comput Biol. 2017 Aug 3;13(8):e1005629. doi: 10.1371/journal.pcbi.1005629. eCollection 2017 Aug.

11.

An Expanded View of Complex Traits: From Polygenic to Omnigenic.

Boyle EA, Li YI, Pritchard JK.

Cell. 2017 Jun 15;169(7):1177-1186. doi: 10.1016/j.cell.2017.05.038. Review.

12.

Rapid evolution of the human mutation spectrum.

Harris K, Pritchard JK.

Elife. 2017 Apr 25;6. pii: e24284. doi: 10.7554/eLife.24284.

13.

Tracing the peopling of the world through genomics.

Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E.

Nature. 2017 Jan 18;541(7637):302-310. doi: 10.1038/nature21347. Review.

14.

Batch effects and the effective design of single-cell gene expression studies.

Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y.

Sci Rep. 2017 Jan 3;7:39921. doi: 10.1038/srep39921.

15.

Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans.

Harpak A, Bhaskar A, Pritchard JK.

PLoS Genet. 2016 Dec 15;12(12):e1006489. doi: 10.1371/journal.pgen.1006489. eCollection 2016 Dec.

16.

A Bibliometric History of the Journal GENETICS.

Telis N, Lehmann BV, Feldman MW, Pritchard JK.

Genetics. 2016 Dec;204(4):1337-1342. Epub 2016 Dec 7. No abstract available.

17.

Detection of human adaptation during the past 2000 years.

Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK.

Science. 2016 Nov 11;354(6313):760-764. Epub 2016 Oct 13.

18.

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY.

Nat Genet. 2016 Oct;48(10):1193-203. doi: 10.1038/ng.3646. Epub 2016 Aug 15.

19.

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.

20.

Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice.

Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA.

Nat Genet. 2016 Aug;48(8):919-26. doi: 10.1038/ng.3609. Epub 2016 Jul 4.

21.

Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila.

Kontur C, Kumar S, Lan X, Pritchard JK, Turkewitz AP.

G3 (Bethesda). 2016 Aug 9;6(8):2505-16. doi: 10.1534/g3.116.028878.

22.

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK.

Elife. 2016 May 27;5. pii: e13328. doi: 10.7554/eLife.13328.

23.

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.

Lan X, Pritchard JK.

Science. 2016 May 20;352(6288):1009-13. doi: 10.1126/science.aad8411.

24.

RNA splicing is a primary link between genetic variation and disease.

Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK.

Science. 2016 Apr 29;352(6285):600-4. doi: 10.1126/science.aad9417. Epub 2016 Apr 28.

25.

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs.

Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y.

PLoS Genet. 2016 Jan 26;12(1):e1005793. doi: 10.1371/journal.pgen.1005793. eCollection 2016 Jan.

26.

Abundant contribution of short tandem repeats to gene expression variation in humans.

Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y.

Nat Genet. 2016 Jan;48(1):22-9. doi: 10.1038/ng.3461. Epub 2015 Dec 7.

27.

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M.

PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030. eCollection 2015.

28.

WASP: allele-specific software for robust molecular quantitative trait locus discovery.

van de Geijn B, McVicker G, Gilad Y, Pritchard JK.

Nat Methods. 2015 Nov;12(11):1061-3. doi: 10.1038/nmeth.3582. Epub 2015 Sep 14.

29.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M.

Cell. 2015 Aug 27;162(5):1051-65. doi: 10.1016/j.cell.2015.07.048. Epub 2015 Aug 20.

30.

Icing on the Cake: The Role of Research in Practitioner Training.

Pritchard JK, Wine B.

Behav Anal Pract. 2015 Aug 11;8(2):140-141. doi: 10.1007/s40617-015-0074-z. eCollection 2015 Oct.

31.

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature.

Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y.

PLoS Genet. 2015 May 7;11(5):e1005216. doi: 10.1371/journal.pgen.1005216. eCollection 2015 May.

32.

Genomic variation. Impact of regulatory variation from RNA to protein.

Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y.

Science. 2015 Feb 6;347(6222):664-7. doi: 10.1126/science.1260793. Epub 2014 Dec 18.

33.

The genetic and mechanistic basis for variation in gene regulation.

Pai AA, Pritchard JK, Gilad Y.

PLoS Genet. 2015 Jan 8;11(1):e1004857. doi: 10.1371/journal.pgen.1004857. eCollection 2015 Jan.

34.

Epigenetic modifications are associated with inter-species gene expression variation in primates.

Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y.

Genome Biol. 2014;15(12):547.

35.

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels.

Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y.

PLoS Genet. 2014 Sep 18;10(9):e1004663. doi: 10.1371/journal.pgen.1004663. eCollection 2014 Sep.

36.

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines.

Çalışkan M, Pritchard JK, Ober C, Gilad Y.

PLoS One. 2014 Sep 5;9(9):e107166. doi: 10.1371/journal.pone.0107166. eCollection 2014.

37.

fastSTRUCTURE: variational inference of population structure in large SNP data sets.

Raj A, Stephens M, Pritchard JK.

Genetics. 2014 Jun;197(2):573-89. doi: 10.1534/genetics.114.164350. Epub 2014 Apr 2.

38.

The functional consequences of variation in transcription factor binding.

Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y.

PLoS Genet. 2014 Mar 6;10(3):e1004226. doi: 10.1371/journal.pgen.1004226. eCollection 2014 Mar.

39.

Admixture facilitates genetic adaptations to high altitude in Tibet.

Jeong C, Alkorta-Aranburu G, Basnyat B, Neupane M, Witonsky DB, Pritchard JK, Beall CM, Di Rienzo A.

Nat Commun. 2014;5:3281. doi: 10.1038/ncomms4281.

40.

The deleterious mutation load is insensitive to recent population history.

Simons YB, Turchin MC, Pritchard JK, Sella G.

Nat Genet. 2014 Mar;46(3):220-4. doi: 10.1038/ng.2896. Epub 2014 Feb 9.

41.

The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation.

Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN.

BMC Genomics. 2014 Feb 1;15:92. doi: 10.1186/1471-2164-15-92.

42.

Archaic humans: Four makes a party.

Birney E, Pritchard JK.

Nature. 2014 Jan 2;505(7481):32-4. doi: 10.1038/nature12847. Epub 2013 Dec 18. No abstract available.

PMID:
24352230
43.

Identification of genetic variants that affect histone modifications in human cells.

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK.

Science. 2013 Nov 8;342(6159):747-9. doi: 10.1126/science.1242429. Epub 2013 Oct 17.

44.

Primate transcript and protein expression levels evolve under compensatory selection pressures.

Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y.

Science. 2013 Nov 29;342(6162):1100-4. doi: 10.1126/science.1242379. Epub 2013 Oct 17.

45.

Skills™.

Pritchard JK.

Behav Anal Pract. 2013 Spring;6(1):96-100.

46.

The genetic architecture of adaptations to high altitude in Ethiopia.

Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A.

PLoS Genet. 2012;8(12):e1003110. doi: 10.1371/journal.pgen.1003110. Epub 2012 Dec 6.

47.

Controls of nucleosome positioning in the human genome.

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK.

PLoS Genet. 2012;8(11):e1003036. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15.

48.

Inference of population splits and mixtures from genome-wide allele frequency data.

Pickrell JK, Pritchard JK.

PLoS Genet. 2012;8(11):e1002967. doi: 10.1371/journal.pgen.1002967. Epub 2012 Nov 15.

49.

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y.

PLoS Genet. 2012;8(10):e1003000. doi: 10.1371/journal.pgen.1003000. Epub 2012 Oct 11.

50.

Genomics: ENCODE explained.

Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E.

Nature. 2012 Sep 6;489(7414):52-5. doi: 10.1038/489052a. No abstract available.

PMID:
22955614

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