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Melissa Gymrek

Title(s)Assistant Professor, Computer Science and Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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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 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics. 2020 Aug 17. Mousavi N, Margoliash J, Pusarla N, Saini S, Yanicky R, Gymrek M. PMID: 32805020.
      View in: PubMed   Mentions:    Fields:    
    2. Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med. 2020 01; 26(1):143-150. 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. PMID: 31873310.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    3. The impact of short tandem repeat variation on gene expression. Nat Genet. 2019 11; 51(11):1652-1659. Fotsing SF, Margoliash J, Wang C, Saini S, Yanicky R, Shleizer-Burko S, Goren A, Gymrek M. PMID: 31676866.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    4. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun. 2019 09 11; 10(1):4128. 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. PMID: 31511524.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    5. Profiling the genome-wide landscape of tandem repeat expansions. Nucleic Acids Res. 2019 09 05; 47(15):e90. Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M. PMID: 31194863.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    6. A reference haplotype panel for genome-wide imputation of short tandem repeats. Nat Commun. 2018 10 23; 9(1):4397. Saini S, Mitra I, Mousavi N, Fotsing SF, Gymrek M. PMID: 30353011.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    7. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res. 2018 11; 28(11):1709-1719. Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. PMID: 30352806.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    8. Quantitative analysis of population-scale family trees with millions of relatives. Science. 2018 04 13; 360(6385):171-175. 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. PMID: 29496957.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    9. Journal of Open Source Software (JOSS): design and first-year review. PeerJ Prepr. 2018; 4:e147. Smith AM, Niemeyer KE, Katz DS, Barba LA, Githinji G, Gymrek M, Huff KD, Madan CR, Mayes AC, Moerman KM, Prins P, Ram K, Rokem A, Teal TK, Guimera RV, Vanderplas JT. PMID: 32704456.
      View in: PubMed   Mentions:
    10. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017 Oct; 49(10):1495-1501. Gymrek M, Willems T, Reich D, Erlich Y. PMID: 28892063.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    11. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms. Cell. 2017 Jun 29; 170(1):199-212.e20. 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. PMID: 28666119.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    12. Genome-wide profiling of heritable and de novo STR variations. Nat Methods. 2017 Jun; 14(6):590-592. Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y. PMID: 28436466.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    13. A genomic view of short tandem repeats. Curr Opin Genet Dev. 2017 Jun; 44:9-16. Gymrek M. PMID: 28213161.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    14. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13; 538(7624):201-206. 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. PMID: 27654912.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansAnimals
    15. Recommendations for open data science. Gigascience. 2016; 5:22. Gymrek M, Farjoun Y. PMID: 27195107.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    16. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet. 2016 05 05; 98(5):919-933. Willems T, Gymrek M, Poznik GD, Tyler-Smith C, Erlich Y. PMID: 27126583.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    17. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016 06; 48(6):593-9. 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. PMID: 27111036.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    18. 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. Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ. PMID: 27060133.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    19. Abundant contribution of short tandem repeats to gene expression variation in humans. Nat Genet. 2016 Jan; 48(1):22-9. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y. PMID: 26642241.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    20. 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. 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. PMID: 25453903.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimalsCells
    21. PyBamView: a browser-based application for viewing short read alignments. Bioinformatics. 2014 Dec 01; 30(23):3405-7. Gymrek M. PMID: 25147359.
      View in: PubMed   Mentions: 1     Fields:    
    22. The landscape of human STR variation. Genome Res. 2014 Nov; 24(11):1894-904. Willems T, Gymrek M, Highnam G, Mittelman D, Erlich Y. PMID: 25135957.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    23. OTX2 duplication is implicated in hemifacial microsomia. PLoS One. 2014; 9(5):e96788. Zielinski D, Markus B, Sheikh M, Gymrek M, Chu C, Zaks M, Srinivasan B, Hoffman JD, Aizenbud D, Erlich Y. PMID: 24816892.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    24. 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. Breker M, Gymrek M, Moldavski O, Schuldiner M. PMID: 24150937.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    25. A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. J Cell Biol. 2013 Mar 18; 200(6):839-50. Breker M, Gymrek M, Schuldiner M. PMID: 23509072.
      View in: PubMed   Mentions: 68     Fields:    Translation:Animals
    26. Identifying personal genomes by surname inference. Science. 2013 Jan 18; 339(6117):321-4. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y. PMID: 23329047.
      View in: PubMed   Mentions: 245     Fields:    Translation:HumansCellsPHPublic Health
    27. Profiling short tandem repeats from short reads. Methods Mol Biol. 2013; 1038:113-35. Gymrek M, Erlich Y. PMID: 23872972.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    28. Back to the family: a renewed approach to rare variant studies. Genome Med. 2012; 4(12):97. Zielinski D, Gymrek M, Erlich Y. PMID: 23253160.
      View in: PubMed   Mentions: 1     Fields:    
    29. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 07; 151(6):1185-99. 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. PMID: 23217706.
      View in: PubMed   Mentions: 212     Fields:    Translation:HumansAnimalsCells
    30. 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. Nadler-Holly M, Breker M, Gruber R, Azia A, Gymrek M, Eisenstein M, Willison KR, Schuldiner M, Horovitz A. PMID: 23112166.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    31. lobSTR: A short tandem repeat profiler for personal genomes. Genome Res. 2012 Jun; 22(6):1154-62. Gymrek M, Golan D, Rosset S, Erlich Y. PMID: 22522390.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansCells
    32. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. 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. PMID: 22196736.
      View in: PubMed   Mentions: 166     Fields:    Translation:HumansCells
    33. Using DNA sequencers as stethoscopes. Genome Med. 2011 Nov 21; 3(11):73. Gymrek M, Erlich Y. PMID: 22103962.
      View in: PubMed   Mentions: 1     Fields:    
    34. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics. 2010 Nov; 9(11):2558-70. Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM. PMID: 20631208.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    35. Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010 Apr; 20(4):519-25. Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. PMID: 20133332.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    36. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan; 7(1):47-9. Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. PMID: 19946276.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
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