Melissa Gymrek

Title(s)Associate Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Genetic & Social Determinants of Health: Center for Admixture Science and Technology
    NIH RM1HG011558Sep 22, 2021 - Jun 30, 2026
    Role: Co-Principal Investigator
    Characterization of Tandem Repeat and Structural Variants Contributing to Addictive Behaviors in Mice and Rats
    NIH U01DA051234May 1, 2021 - Feb 28, 2026
    Role: Co-Principal Investigator
    Systematic characterization of tandem repeat variants contributing to complex traits
    NIH R01HG010885Sep 17, 2020 - Jul 31, 2024
    Role: Principal Investigator
    Refining Mendelian disease analysis via detection of clinically relevant repeat variants
    NIH R01HG010149Sep 14, 2018 - Jun 30, 2022
    Role: Principal Investigator
    Interrogating regulatory variants by multiplexed genome editing
    NIH 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

    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. 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. Haptools: a toolkit for admixture and haplotype analysis. Bioinformatics. 2023 Feb 27. Massarat AR, Lamkin M, Reeve C, Williams AL, D'Antonio M, Gymrek M. PMID: 36847450.
      View in: PubMed   Mentions:    Fields:    
    2. Deep learning predicts the impact of regulatory variants on cell-type-specific enhancers in the brain. Bioinform Adv. 2023; 3(1):vbad002. Zheng A, Shen Z, Glass CK, Gymrek M. PMID: 36726730; PMCID: PMC9887460.
      View in: PubMed   Mentions:
    3. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep. 2022 12 06; 41(10):111761. Orth MF, Surdez D, Faehling T, Ehlers AC, Marchetto A, Grosset?te S, Volckmann R, Zwijnenburg DA, Gerke JS, Zaidi S, Alonso J, Sastre A, Baulande S, Sill M, Cidre-Aranaz F, Ohmura S, Kirchner T, Hauck SM, Reischl E, Gymrek M, Pfister SM, Strauch K, Koster J, Delattre O, Gr?newald TGP. PMID: 36476851.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    4. Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol. 2023 Feb; 36(2):321-336. Verbiest M, Maksimov M, Jin Y, Anisimova M, Gymrek M, Bilgin Sonay T. PMID: 36289560.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    5. HMOX1 Genetic Polymorphisms Display Ancestral Diversity and May Be Linked to Hypertensive Disorders in Pregnancy. Reprod Sci. 2022 Dec; 29(12):3465-3476. Sun T, Cruz GI, Mousavi N, Maric I, Brewer A, Wong RJ, Aghaeepour N, Sayed N, Wu JC, Stevenson DK, Leonard SA, Gymrek M, Winn VD. PMID: 35697922; PMCID: PMC9734242.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    6. SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains. Cell Genom. 2022 Mar 09; 2(3). Mortazavi M, Ren Y, Saini S, Antaki D, St Pierre CL, Williams A, Sohni A, Wilkinson MF, Gymrek M, Sebat J, Palmer AA. PMID: 35720252; PMCID: PMC9205302.
      View in: PubMed   Mentions: 3  
    7. Missing heritability may be hiding in repeats. Science. 2021 Sep 24; 373(6562):1440-1441. Gymrek M, Goren A. PMID: 34554784.
      View in: PubMed   Mentions: 1     Fields:    
    8. Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Sci Adv. 2021 06; 7(25). Hoeksema MA, Shen Z, Holtman IR, Zheng A, Spann NJ, Cobo I, Gymrek M, Glass CK. PMID: 34134993; PMCID: PMC8208725.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    9. TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics. 2021 05 05; 37(5):731-733. Mousavi N, Margoliash J, Pusarla N, Saini S, Yanicky R, Gymrek M. PMID: 32805020; PMCID: PMC8097685.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    10. A flexible ChIP-sequencing simulation toolkit. BMC Bioinformatics. 2021 Apr 20; 22(1):201. Zheng A, Lamkin M, Qiu Y, Ren K, Goren A, Gymrek M. PMID: 33879052; PMCID: PMC8056602.
      View in: PubMed   Mentions: 1     Fields:    
    11. Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants. Cell Rep Med. 2021 04 20; 2(4):100250. Pinsach-Abuin ML, Del Olmo B, P?rez-Agustin A, Mates J, Allegue C, Iglesias A, Ma Q, Merkurjev D, Konovalov S, Zhang J, Sheikh F, Telenti A, Brugada J, Brugada R, Gymrek M, di Iulio J, Garcia-Bassets I, Pagans S. PMID: 33948580; PMCID: PMC8080235.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    12. Variable number tandem repeats mediate the expression of proximal genes. Nat Commun. 2021 04 06; 12(1):2075. Bakhtiari M, Park J, Ding YC, Shleizer-Burko S, Neuhausen SL, Halld?rsson BV, Stef?nsson K, Gymrek M, Bafna V. PMID: 33824302; PMCID: PMC8024321.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    13. Deep neural networks identify sequence context features predictive of transcription factor binding. Nat Mach Intell. 2021 Feb; 3(2):172-180. Zheng A, Lamkin M, Zhao H, Wu C, Su H, Gymrek M. PMID: 33796819; PMCID: PMC8009085.
      View in: PubMed   Mentions: 14  
    14. Patterns of de novo tandem repeat mutations and their role in autism. Nature. 2021 01; 589(7841):246-250. Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M. PMID: 33442040; PMCID: PMC7810352.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    15. 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, P?rez MC, Arranz M, Moffitt AB, Wang Z, Herv?s A, Devinsky O, Gymrek M, Sebat J, Gleeson JG. PMID: 31873310; PMCID: PMC7032648.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    16. 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; PMCID: PMC6917484.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    17. 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, H?lting TLB, Grosset?te S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-P?rez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Gr?newald TGP. PMID: 31511524; PMCID: PMC6739408.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    18. 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; PMCID: PMC6735967.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    19. 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; PMCID: PMC6211647.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    20. 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; PMCID: PMC6199332.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    21. 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; PMCID: PMC6593158.
      View in: PubMed   Mentions: 56     Fields:    Translation:Humans
    22. 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; PMCID: PMC7340488.
      View in: PubMed   Mentions: 5  
    23. 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; PMCID: PMC5679271.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    24. 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, MEDIA Consortium, SIGMA T2D Consortium, Centeno-Cruz F, Zerrweck C, Orozco L, Altshuler DM, Schreiber SL, Florez JC, Jacobs SBR, Lander ES. PMID: 28666119; PMCID: PMC5562285.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    25. 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; PMCID: PMC5482724.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansCells
    26. A genomic view of short tandem repeats. Curr Opin Genet Dev. 2017 Jun; 44:9-16. Gymrek M. PMID: 28213161.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    27. 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, P??bo S, Kelso J, Patterson N, Reich D. PMID: 27654912; PMCID: PMC5161557.
      View in: PubMed   Mentions: 487     Fields:    Translation:HumansAnimals
    28. Recommendations for open data science. Gigascience. 2016; 5:22. Gymrek M, Farjoun Y. PMID: 27195107; PMCID: PMC4870738.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    29. 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, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C. PMID: 27111036; PMCID: PMC4884158.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansCells
    30. 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, 1000 Genomes Project Chromosome Y Group, Erlich Y. PMID: 27126583; PMCID: PMC4863667.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    31. 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; PMCID: PMC4857002.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    32. 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; PMCID: PMC4909355.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansCells
    33. 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, Suv? 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; PMCID: PMC4492343.
      View in: PubMed   Mentions: 192     Fields:    Translation:HumansAnimalsCells
    34. 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: 3     Fields:    
    35. The landscape of human STR variation. Genome Res. 2014 Nov; 24(11):1894-904. Willems T, Gymrek M, Highnam G, 1000 Genomes Project Consortium, Mittelman D, Erlich Y. PMID: 25135957; PMCID: PMC4216929.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansCells
    36. 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; PMCID: PMC4016008.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    37. 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; PMCID: PMC3965041.
      View in: PubMed   Mentions: 40     Fields:    Translation:Animals
    38. 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; PMCID: PMC3601363.
      View in: PubMed   Mentions: 106     Fields:    Translation:Animals
    39. 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: 336     Fields:    Translation:HumansCellsPHPublic Health
    40. 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
    41. 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; PMCID: PMC3580437.
      View in: PubMed   Mentions: 2     Fields:    
    42. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 07; 151(6):1185-99. Sebasti?n 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; PMCID: PMC3526953.
      View in: PubMed   Mentions: 321     Fields:    Translation:HumansAnimalsCells
    43. 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; PMCID: PMC3503220.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    44. 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; PMCID: PMC3371701.
      View in: PubMed   Mentions: 136     Fields:    Translation:HumansCells
    45. 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; PMCID: PMC3312319.
      View in: PubMed   Mentions: 201     Fields:    Translation:HumansCells
    46. Using DNA sequencers as stethoscopes. Genome Med. 2011 Nov 21; 3(11):73. Gymrek M, Erlich Y. PMID: 22103962; PMCID: PMC3308028.
      View in: PubMed   Mentions: 1     Fields:    
    47. 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; PMCID: PMC2984232.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    48. 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; PMCID: PMC2847755.
      View in: PubMed   Mentions: 38     Fields:    Translation:AnimalsCells
    49. 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; PMCID: PMC2862482.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansAnimalsCells
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