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    Melissa Gymrek

    TitleAssistant Professor
    SchoolUniversity of California, San Diego
    DepartmentComputer Science and Engineering
    Address9500 Gilman Drive #0639
    CA La Jolla 92093
    Phone858-246-0895
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Gymrek M, Willems T, Reich D, Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017 Sep 11. PMID: 28892063.
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      2. 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. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms. Cell. 2017 Jun 29; 170(1):199-212.e20. PMID: 28666119.
        View in: PubMed
      3. Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y. Genome-wide profiling of heritable and de novo STR variations. Nat Methods. 2017 Jun; 14(6):590-592. PMID: 28436466.
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      4. Gymrek M. A genomic view of short tandem repeats. Curr Opin Genet Dev. 2017 Feb 14; 44:9-16. PMID: 28213161.
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      5. 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. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Sep 21; 538(7624):201-206. PMID: 27654912.
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      6. Gymrek M, Farjoun Y. Recommendations for open data science. Gigascience. 2016; 5:22. PMID: 27195107.
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      7. 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. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016 Jun; 48(6):593-9. PMID: 27111036.
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      8. Willems T, Gymrek M, Poznik GD, Tyler-Smith C. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet. 2016 May 5; 98(5):919-33. PMID: 27126583.
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      9. Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Res. 2016 May 5; 44(8):3750-62. PMID: 27060133.
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      10. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y. Abundant contribution of short tandem repeats to gene expression variation in humans. Nat Genet. 2016 Jan; 48(1):22-9. PMID: 26642241.
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      11. Gymrek M. PyBamView: a browser-based application for viewing short read alignments. Bioinformatics. 2014 Dec 1; 30(23):3405-7. PMID: 25147359.
        View in: PubMed
      12. Willems T, Gymrek M, Highnam G. The landscape of human STR variation. Genome Res. 2014 Nov; 24(11):1894-904. PMID: 25135957; PMCID: PMC4216929.
      13. Zielinski D, Markus B, Sheikh M, Gymrek M, Chu C, Zaks M, Srinivasan B, Hoffman JD, Aizenbud D, Erlich Y. OTX2 duplication is implicated in hemifacial microsomia. PLoS One. 2014; 9(5):e96788. PMID: 24816892; PMCID: PMC4016008.
      14. Breker M, Gymrek M, Moldavski O, Schuldiner M. 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. Nucleic Acids Res. 2014 Jan; 42(Database issue):D726-30. PMID: 24150937; PMCID: PMC3965041.
      15. Breker M, Gymrek M, Schuldiner M. A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. J Cell Biol. 2013 Mar 18; 200(6):839-50. PMID: 23509072; PMCID: PMC3601363.
      16. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y. Identifying personal genomes by surname inference. Science. 2013 Jan 18; 339(6117):321-4. PMID: 23329047.
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      17. Gymrek M, Erlich Y. Profiling short tandem repeats from short reads. Methods Mol Biol. 2013; 1038:113-35. PMID: 23872972.
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      18. Zielinski D, Gymrek M, Erlich Y. Back to the family: a renewed approach to rare variant studies. Genome Med. 2012; 4(12):97. PMID: 23253160; PMCID: PMC3580437.
      19. 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. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 7; 151(6):1185-99. PMID: 23217706; NIHMSID: NIHMS421628.
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      20. Nadler-Holly M, Breker M, Gruber R, Azia A, Gymrek M, Eisenstein M, Willison KR, Schuldiner M, Horovitz A. Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis. Proc Natl Acad Sci U S A. 2012 Nov 13; 109(46):18833-8. PMID: 23112166; PMCID: PMC3503220.
      21. Gymrek M, Golan D, Rosset S, Erlich Y. lobSTR: A short tandem repeat profiler for personal genomes. Genome Res. 2012 Jun; 22(6):1154-62. PMID: 22522390; PMCID: PMC3371701.
      22. 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. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. PMID: 22196736; NIHMSID: NIHMS355789.
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      23. Gymrek M, Erlich Y. Using DNA sequencers as stethoscopes. Genome Med. 2011; 3(11):73. PMID: 22103962; PMCID: PMC3308028.
      24. Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics. 2010 Nov; 9(11):2558-70. PMID: 20631208; PMCID: PMC2984232.
      25. Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010 Apr; 20(4):519-25. PMID: 20133332; PMCID: PMC2847755.
      26. Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan; 7(1):47-9. PMID: 19946276; NIHMSID: NIHMS194275.
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