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Melissa Gymrek

Title(s)Assistant Professor, Medicine
SchoolHealth Sciences
Phone858-246-0895
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    Collapse Research 
    Collapse Research Activities and Funding
    Refining Mendelian disease analysis via detection of clinically relevant repeat variants
    NIH/NHGRI R01HG010149Sep 14, 2018 - Jun 30, 2022
    Role: Principal Investigator
    Interrogating regulatory variants by multiplexed genome editing
    NIH/NHGRI R21HG010070Aug 9, 2018 - Jul 31, 2020
    Role: Principal Investigator
    Systematic identification and interpretation of repetitive variants underlying schizophrenia
    NIH DP5OD024577Sep 1, 2017 - Aug 31, 2022
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    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. Breuss MW, Antaki D, George RD, Kleiber M, James KN, Ball LL, Hong O, Mitra I, Yang X, Wirth SA, Gu J, Garcia CAB, Gujral M, Brandler WM, Musaev D, Nguyen A, McEvoy-Venneri J, Knox R, Sticca E, Botello MCC, Uribe Fenner J, Pérez MC, Arranz M, Moffitt AB, Wang Z, Hervás A, Devinsky O, Gymrek M, Sebat J, Gleeson JG. Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med. 2019 Dec 23. PMID: 31873310.
      View in: PubMed
    2. Fotsing SF, Margoliash J, Wang C, Saini S, Yanicky R, Shleizer-Burko S, Goren A, Gymrek M. The impact of short tandem repeat variation on gene expression. Nat Genet. 2019 11; 51(11):1652-1659. PMID: 31676866.
      View in: PubMed
    3. Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TGP. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun. 2019 09 11; 10(1):4128. PMID: 31511524.
      View in: PubMed
    4. Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M. Profiling the genome-wide landscape of tandem repeat expansions. Nucleic Acids Res. 2019 09 05; 47(15):e90. PMID: 31194863.
      View in: PubMed
    5. Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res. 2018 11; 28(11):1709-1719. PMID: 30352806.
      View in: PubMed
    6. Saini S, Mitra I, Mousavi N, Fotsing SF, Gymrek M. A reference haplotype panel for genome-wide imputation of short tandem repeats. Nat Commun. 2018 10 23; 9(1):4397. PMID: 30353011.
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    7. 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. Quantitative analysis of population-scale family trees with millions of relatives. Science. 2018 04 13; 360(6385):171-175. PMID: 29496957.
      View in: PubMed
    8. Gymrek M, Willems T, Reich D, Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017 Oct; 49(10):1495-1501. PMID: 28892063.
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    9. 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, Centeno-Cruz F, Zerrweck C, Orozco L, Altshuler DM, Schreiber SL, Florez JC, Jacobs SBR, Lander ES. 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
    10. 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.
      View in: PubMed
    11. Gymrek M. A genomic view of short tandem repeats. Curr Opin Genet Dev. 2017 Jun; 44:9-16. PMID: 28213161.
      View in: PubMed
    12. 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 Oct 13; 538(7624):201-206. PMID: 27654912.
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    13. Gymrek M, Farjoun Y. Recommendations for open data science. Gigascience. 2016; 5:22. PMID: 27195107.
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    14. 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, Bustamante CD, Tyler-Smith C. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016 06; 48(6):593-9. PMID: 27111036.
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    15. Willems T, Gymrek M, Poznik GD, Tyler-Smith C, Erlich Y. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet. 2016 05 05; 98(5):919-933. PMID: 27126583.
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    16. 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 05 05; 44(8):3750-62. PMID: 27060133.
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    17. 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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    18. 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. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 2014 Nov 10; 26(5):668-681. PMID: 25453903.
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    19. Gymrek M. PyBamView: a browser-based application for viewing short read alignments. Bioinformatics. 2014 Dec 01; 30(23):3405-7. PMID: 25147359.
      View in: PubMed
    20. Willems T, Gymrek M, Highnam G, Mittelman D, Erlich Y. The landscape of human STR variation. Genome Res. 2014 Nov; 24(11):1894-904. PMID: 25135957.
      View in: PubMed
    21. 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.
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    22. 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.
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    23. 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.
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    24. 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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    25. Gymrek M, Erlich Y. Profiling short tandem repeats from short reads. Methods Mol Biol. 2013; 1038:113-35. PMID: 23872972.
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    26. 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.
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    27. 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 07; 151(6):1185-99. PMID: 23217706.
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    28. 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.
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    29. 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.
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    30. 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.
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    31. Gymrek M, Erlich Y. Using DNA sequencers as stethoscopes. Genome Med. 2011 Nov 21; 3(11):73. PMID: 22103962.
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    32. 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.
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    33. 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.
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    34. 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.
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