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Raluca Gordan PhD

TitleProfessor
InstitutionUMass Chan Medical School
DepartmentGenomics and Computational Biology
AddressUMass Chan Medical School
368 Plantation Street, AS4.1077
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentGenomics and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiophysical Chemical and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology


    Collapse Biography 
    Collapse education and training
    Duke University, Durham, NC, United StatesPHD

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordan R, Adar S. The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency. Nucleic Acids Res. 2025 Feb 08; 53(4). PMID: 39933696.
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    2. Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordan R, Adar S. The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency. Nucleic Acids Res. 2025 Feb 08; 53(4). PMID: 39970291.
      Citations:    
    3. Snyder LF, O'Brien EM, Zhao J, Liang J, Bruce BJ, Zhang Y, Zhu W, Cassier TJ, Schnicker NJ, Zhou X, Gord?n R, He BZ. Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions Affecting Activation and Autoinhibition. bioRxiv. 2025 Jan 02. PMID: 39253425.
      Citations:    
    4. King DE, Beard EE, Satusky MJ, Ryde IT, George A, Johnson C, Dolan EL, Zhang Y, Zhu W, Wilkins H, Corden E, Murphy SK, Erie D, Gordan R, Meyer JN. TFAM as a sensor of UVC-induced mitochondrial DNA damage. bioRxiv. 2024 Nov 01. PMID: 39484377.
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    5. Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gord?n R, Llin?s M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2024 Sep 23; 52(17):10161-10179. PMID: 38966997.
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    6. Deciphering the impact of genomic variation on function. Nature. 2024 Sep; 633(8028):47-57. PMID: 39232149.
      Citations:    
    7. Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gord?n R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proc Natl Acad Sci U S A. 2024 Jan 23; 121(4):e2310854121. PMID: 38241433.
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    8. Martin V, Zhuang F, Zhang Y, Pinheiro K, Gord?n R. High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins. Nucleic Acids Res. 2023 Nov 27; 51(21):11600-11612. PMID: 37889068.
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    9. Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gord?n R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science. 2023 09 22; 381(6664):eadd1250. PMID: 37733848.
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    10. Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. Computational design of sequence-specific DNA-binding proteins. bioRxiv. 2023 Sep 21. PMID: 37790440.
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    11. Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gord?n R, Afek A. UV irradiation remodels the specificity landscape of transcription factors. Proc Natl Acad Sci U S A. 2023 03 14; 120(11):e2217422120. PMID: 36888663.
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    12. Zhao J, Martin V, Gord?n R. Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer. Res Comput Mol Biol. 2022 May; 13278:36-51. PMID: 36507923.
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    13. Sun T, Ding CC, Zhang Y, Zhang Y, Lin CC, Wu J, Setayeshpour Y, Coggins S, Shepard C, Macias E, Kim B, Zhou P, Gord?n R, Chi JT. MESH1 knockdown triggers proliferation arrest through TAZ repression. Cell Death Dis. 2022 03 10; 13(3):221. PMID: 35273140.
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    14. Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gord?n R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener. 2021 08 24; 16(1):58. PMID: 34429139.
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    15. Zhang Y, Ho TD, Buchler NE, Gord?n R. Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Res. 2021 Jul; 31(7):1216-1229. PMID: 33975875.
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    16. Liu M, Boot A, Ng AWT, Gord?n R, Rozen SG. Mutational processes in cancer preferentially affect binding of particular transcription factors. Sci Rep. 2021 02 08; 11(1):3339. PMID: 33558557.
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    17. Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gord?n R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. 2020 11; 587(7833):291-296. PMID: 33087930.
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    18. Ilic S, Cohen S, Afek A, Gordan R, Lukatsky DB, Akabayov B. DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling. J Vis Exp. 2019 10 08; (152). PMID: 31657797.
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    19. Martin V, Zhao J, Afek A, Mielko Z, Gord?n R. QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic Acids Res. 2019 07 02; 47(W1):W127-W135. PMID: 31114870.
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    20. Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E. Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine. Biochim Biophys Acta Gen Subj. 2019 09; 1863(9):1343-1350. PMID: 31170499.
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    21. Innocenti F, Jiang C, Sibley AB, Etheridge AS, Hatch AJ, Denning S, Niedzwiecki D, Shterev ID, Lin J, Furukawa Y, Kubo M, Kindler HL, Auman JT, Venook AP, Hurwitz HI, McLeod HL, Ratain MJ, Gordan R, Nixon AB, Owzar K. Genetic variation determines VEGF-A plasma levels in cancer patients. Sci Rep. 2018 11 05; 8(1):16332. PMID: 30397360.
      Citations:    
    22. Innocenti F, Owzar K, Jiang C, Etheridge AS, Gord?n R, Sibley AB, Mulkey F, Niedzwiecki D, Glubb D, Neel N, Talamonti MS, Bentrem DJ, Seiser E, Yeh JJ, Van Loon K, McLeod H, Ratain MJ, Kindler HL, Venook AP, Nakamura Y, Kubo M, Petersen GM, Bamlet WR, McWilliams RR. The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation. PLoS One. 2018; 13(8):e0202272. PMID: 30107003.
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    23. Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R. Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In?Vivo Binding. Cell Syst. 2018 Apr 25; 6(4):470-483.e8. PMID: 29605182.
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    24. Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B. DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase. iScience. 2018 Apr 27; 2:141-147. PMID: 30428370.
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    25. Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gord?n R. Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Nucleic Acids Res. 2017 Nov 16; 45(20):11684-11699. PMID: 28977539.
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    26. Joh DY, Hucknall AM, Wei Q, Mason KA, Lund ML, Fontes CM, Hill RT, Blair R, Zimmers Z, Achar RK, Tseng D, Gordan R, Freemark M, Ozcan A, Chilkoti A. Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood. Proc Natl Acad Sci U S A. 2017 08 22; 114(34):E7054-E7062. PMID: 28784765.
      Citations:    
    27. Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, Nellore V, Kongpetch S, Ng AWT, Ng LM, Choo SP, Myint SS, Thanan R, Nagarajan S, Lim WK, Ng CCY, Boot A, Liu M, Ong CK, Rajasegaran V, Lie S, Lim AST, Lim TH, Tan J, Loh JL, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PK, Chung AYF, Ooi LLPJ, Lim KH, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov LB, Gord?n R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P. Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Cancer Discov. 2017 10; 7(10):1116-1135. PMID: 28667006.
      Citations:    
    28. Zhao J, Li D, Seo J, Allen AS, Gord?n R. Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Res Comput Mol Biol. 2017 May; 10229:336-352. PMID: 28691125.
      Citations:    
    29. Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gord?n R, Yao G, You L. Expression level is a key determinant of E2F1-mediated cell fate. Cell Death Differ. 2017 04; 24(4):626-637. PMID: 28211871.
      Citations:    
    30. Schipper JL, Gord?n RM. Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources. Cold Spring Harb Protoc. 2016 11 01; 2016(11). PMID: 27803259.
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    31. Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gord?n R, Megraw M, Brady SM, Benfey PN. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev Cell. 2016 12 05; 39(5):585-596. PMID: 27923776.
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    32. Medina EM, Turner JJ, Gord?n R, Skotheim JM, Buchler NE. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. Elife. 2016 05 10; 5. PMID: 27162172.
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    33. Frank CL, Manandhar D, Gord?n R, Crawford GE. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics Chromatin. 2016; 9:15. PMID: 27087856.
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    34. Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gord?n R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 2016 Mar 25; 351(6280):1450-1454. PMID: 27013732.
      Citations:    
    35. Afek A, Cohen H, Barber-Zucker S, Gord?n R, Lukatsky DB. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PLoS Comput Biol. 2015 Aug; 11(8):e1004429. PMID: 26285121.
      Citations:    
    36. Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gord?n R, Rohs R. Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4654-9. PMID: 25775564.
      Citations:    
    37. Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gord?n R, Wray GA, Silver DL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol. 2015 Mar 16; 25(6):772-779. PMID: 25702574.
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    38. Afek A, Schipper JL, Horton J, Gord?n R, Lukatsky DB. Protein-DNA binding in the absence of specific base-pair recognition. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17140-5. PMID: 25313048.
      Citations:    
    39. Slattery M, Zhou T, Yang L, Dantas Machado AC, Gord?n R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci. 2014 Sep; 39(9):381-99. PMID: 25129887.
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    40. Munteanu A, Ohler U, Gord?n R. COUGER--co-factors associated with uniquely-bound genomic regions. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W461-7. PMID: 24861628.
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    41. Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gord?n R, Price DH. Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biol. 2014; 15(10):482. PMID: 25287278.
      Citations:    
    42. Siggers T, Gord?n R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res. 2014 Feb; 42(4):2099-111. PMID: 24243859.
      Citations:    
    43. Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gord?n R, Rohs R. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014 Jan; 42(Database issue):D148-55. PMID: 24214955.
      Citations:    
    44. Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gord?n R. Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics. 2013 Jul 01; 29(13):i117-25. PMID: 23812975.
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    45. Gord?n R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep. 2013 Apr 25; 3(4):1093-104. PMID: 23562153.
      Citations:    
    46. Gord?n R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pac Symp Biocomput. 2012; 299-310. PMID: 22174285.
      Citations:    
    47. Gord?n R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 2011 Dec 21; 12(12):R125. PMID: 22189060.
      Citations:    
    48. Miller HB, Robinson TJ, Gord?n R, Hartemink AJ, Garcia-Blanco MA. Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. RNA. 2011 Apr; 17(4):665-74. PMID: 21282347.
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