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Items: 31

1.

Profiling the genome-wide landscape of tandem repeat expansions.

Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M.

Nucleic Acids Res. 2019 Jun 13. pii: gkz501. doi: 10.1093/nar/gkz501. [Epub ahead of print]

PMID:
31194863
2.

A reference haplotype panel for genome-wide imputation of short tandem repeats.

Saini S, Mitra I, Mousavi N, Fotsing SF, Gymrek M.

Nat Commun. 2018 Oct 23;9(1):4397. doi: 10.1038/s41467-018-06694-0.

3.

Targeted genotyping of variable number tandem repeats with adVNTR.

Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V.

Genome Res. 2018 Nov;28(11):1709-1719. doi: 10.1101/gr.235119.118. Epub 2018 Oct 23.

4.

Quantitative analysis of population-scale family trees with millions of relatives.

Kaplanis J, Gordon A, Shor T, Weissbrod O, Geiger D, Wahl M, Gershovits M, Markus B, Sheikh M, Gymrek M, Bhatia G, MacArthur DG, Price AL, Erlich Y.

Science. 2018 Apr 13;360(6385):171-175. doi: 10.1126/science.aam9309. Epub 2018 Mar 1.

PMID:
29496957
5.

Interpreting short tandem repeat variations in humans using mutational constraint.

Gymrek M, Willems T, Reich D, Erlich Y.

Nat Genet. 2017 Oct;49(10):1495-1501. doi: 10.1038/ng.3952. Epub 2017 Sep 11.

6.

Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms.

Rusu V, Hoch E, Mercader JM, Tenen DE, Gymrek M, Hartigan CR, DeRan M, von Grotthuss M, Fontanillas P, Spooner A, Guzman G, Deik AA, Pierce KA, Dennis C, Clish CB, Carr SA, Wagner BK, Schenone M, Ng MCY, Chen BH; MEDIA Consortium; SIGMA T2D Consortium, Centeno-Cruz F, Zerrweck C, Orozco L, Altshuler DM, Schreiber SL, Florez JC, Jacobs SBR, Lander ES.

Cell. 2017 Jun 29;170(1):199-212.e20. doi: 10.1016/j.cell.2017.06.011.

7.

Genome-wide profiling of heritable and de novo STR variations.

Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y.

Nat Methods. 2017 Jun;14(6):590-592. doi: 10.1038/nmeth.4267. Epub 2017 Apr 24.

8.

A genomic view of short tandem repeats.

Gymrek M.

Curr Opin Genet Dev. 2017 Jun;44:9-16. doi: 10.1016/j.gde.2017.01.012. Epub 2017 Feb 16. Review.

PMID:
28213161
9.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D.

Nature. 2016 Oct 13;538(7624):201-206. doi: 10.1038/nature18964. Epub 2016 Sep 21.

10.

Recommendations for open data science.

Gymrek M, Farjoun Y.

Gigascience. 2016 May 18;5:22. doi: 10.1186/s13742-016-0127-4. eCollection 2016.

11.

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.

Willems T, Gymrek M, Poznik GD, Tyler-Smith C; 1000 Genomes Project Chromosome Y Group, Erlich Y.

Am J Hum Genet. 2016 May 5;98(5):919-933. doi: 10.1016/j.ajhg.2016.04.001. Epub 2016 Apr 25.

12.

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE; 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.

Nat Genet. 2016 Jun;48(6):593-9. doi: 10.1038/ng.3559. Epub 2016 Apr 25. Review.

13.

Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ.

Nucleic Acids Res. 2016 May 5;44(8):3750-62. doi: 10.1093/nar/gkw219. Epub 2016 Apr 7.

14.

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.

15.

EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma.

Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN.

Cancer Cell. 2014 Nov 10;26(5):668-681. doi: 10.1016/j.ccell.2014.10.004. Epub 2014 Oct 30.

16.

PyBamView: a browser-based application for viewing short read alignments.

Gymrek M.

Bioinformatics. 2014 Dec 1;30(23):3405-7. doi: 10.1093/bioinformatics/btu565. Epub 2014 Aug 21.

PMID:
25147359
17.

The landscape of human STR variation.

Willems T, Gymrek M, Highnam G; 1000 Genomes Project Consortium, Mittelman D, Erlich Y.

Genome Res. 2014 Nov;24(11):1894-904. doi: 10.1101/gr.177774.114. Epub 2014 Aug 18.

18.

OTX2 duplication is implicated in hemifacial microsomia.

Zielinski D, Markus B, Sheikh M, Gymrek M, Chu C, Zaks M, Srinivasan B, Hoffman JD, Aizenbud D, Erlich Y.

PLoS One. 2014 May 9;9(5):e96788. doi: 10.1371/journal.pone.0096788. eCollection 2014.

19.

LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.

Breker M, Gymrek M, Moldavski O, Schuldiner M.

Nucleic Acids Res. 2014 Jan;42(Database issue):D726-30. doi: 10.1093/nar/gkt933. Epub 2013 Oct 22.

20.

Profiling short tandem repeats from short reads.

Gymrek M, Erlich Y.

Methods Mol Biol. 2013;1038:113-35. doi: 10.1007/978-1-62703-514-9_7.

PMID:
23872972
21.

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses.

Breker M, Gymrek M, Schuldiner M.

J Cell Biol. 2013 Mar 18;200(6):839-50. doi: 10.1083/jcb.201301120. Erratum in: J Cell Biol. 2013 Apr 15;201(2):353.

22.

Identifying personal genomes by surname inference.

Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y.

Science. 2013 Jan 18;339(6117):321-4. doi: 10.1126/science.1229566.

23.

Back to the family: a renewed approach to rare variant studies.

Zielinski D, Gymrek M, Erlich Y.

Genome Med. 2012 Dec 19;4(12):97. doi: 10.1186/gm398. eCollection 2012.

24.

The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism.

Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R.

Cell. 2012 Dec 7;151(6):1185-99. doi: 10.1016/j.cell.2012.10.047.

25.

Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis.

Nadler-Holly M, Breker M, Gruber R, Azia A, Gymrek M, Eisenstein M, Willison KR, Schuldiner M, Horovitz A.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18833-8. doi: 10.1073/pnas.1209277109. Epub 2012 Oct 29.

26.

lobSTR: A short tandem repeat profiler for personal genomes.

Gymrek M, Golan D, Rosset S, Erlich Y.

Genome Res. 2012 Jun;22(6):1154-62. doi: 10.1101/gr.135780.111. Epub 2012 Apr 20.

27.

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE.

Cell. 2011 Dec 23;147(7):1628-39. doi: 10.1016/j.cell.2011.09.057.

28.

Using DNA sequencers as stethoscopes.

Gymrek M, Erlich Y.

Genome Med. 2011 Nov 21;3(11):73. doi: 10.1186/gm289.

29.

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.

Mol Cell Proteomics. 2010 Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206. Epub 2010 Jul 14.

30.

Digital transcriptome profiling from attomole-level RNA samples.

Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM.

Genome Res. 2010 Apr;20(4):519-25. doi: 10.1101/gr.102129.109. Epub 2010 Feb 4.

31.

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.

Nat Methods. 2010 Jan;7(1):47-9. doi: 10.1038/nmeth.1404. Epub 2009 Nov 29.

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