Gordân Lab

Our work

Publications

dCas proteins and epigenome editing Transcription factor-induced DNA mutagenesis Quantitative regulatory genomics

Star (*) denotes co-corresponding authors. Plus (+) denotes co-first authors.

Preprints

  1. Zhu W+, Tian M+, Duan Y, Reisman SJ, Miller SE, Corden E, ter Weele M, Song L, Blount J, Safi A, Schreiber J, Gersbach CA, Crawford GE*, Gordân R*. Quantitative profiling of intrinsic dCas9-DNA recognition reveals key determinants of guide RNA performance. bioRxiv (2026). doi: 10.64898/2026.08.10.743836
  2. Reisman SJ, Zhu W, Miller SE, Halabi D, Sangvai N, Crawford GE*, Gordân R*, Gersbach CA*. Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming. bioRxiv (2026). doi: 10.64898/2026.02.01.703129
  3. Bounds LR, Barrera A, ter Weele M, Liu A, Wu E, Li S, Venukuttan R, Rai R, Mu W, Iglesias N, Giusti-Rodríguez P, Reddy TE, Li Y, Gordân R, Allen AS, Love MI, Sullivan PF*, Crawford GE*, Gersbach CA*. Functional Annotation of the Major Histocompatibility Complex Locus. bioRxiv (2026). doi: 10.64898/2026.02.01.703124
  4. Hoyt SH, Reddy TE, Gordân R, Allen AS, Majoros WH. Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference. bioRxiv (2026). doi: 10.64898/2026.03.28.714974

Peer-reviewed publications

  1. Wasserman H, Chi B, Bohm K, Duan M, Sahay H, Safi A, Crawford G, Mao P, Wyrick J, Pufall M, Gordân R. High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution. Nature Communications. In press (2026). doi: 10.1038/s41467-026-75115-4
  2. King DE, Beard EE, Satusky MJ, George A, Ryde I, Johnson C, Dolan EL, Zhang Y, Zhu W, Wilkins H, Corden E, Murphy SK, Erie D*, Gordân R*, Meyer JN*. UV irradiation alters TFAM binding specificity and compaction of DNA. eLife 14:RP108862 (2026).
  3. Zhu W, Zhang Y, Sahay H, Wasserman H, Afek A, Williams J, Shaltz S, Johnson C, MacAlpine DM, Weninger K, Erie D, Jinks-Robertson S*, Gordân R*. DNA mutagenesis driven by transcription factor competition with mismatch repair. Cell 188(20):5735–5747 (2025).
  4. Glasscock CJ+, Pecoraro R+, McHugh L+, 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, Gordân R, Stoddard BL, DiMaio F, Baker D. Computational design of sequence-specific DNA-binding proteins. Nature Structural & Molecular Biology 32(11):2252–2262 (2025).
  5. Snyder LF, O’Brien EM, Zhao J, Liang J, Zhang Y, Zhu W, Cassier TJ, Schnicker NJ, Zhou X, Gordân R, He BZ. Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions Affecting Activation and Autoinhibition. Nature Communications 16(1):5340 (2025).
  6. Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordân R, Adar S. The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency. Nucleic Acids Research 53(4):gkaf048 (2025).
  7. IGVF Consortium. Deciphering the impact of genomic variation on function. Nature 633:47–57 (2024).
  8. Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence context and chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Research gkae585 (2024).
  9. Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gordân R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proceedings of the National Academy of Sciences 121(4):e2310854121 (2024).
  10. Martin V, Zhuang F, Zhang Y, Pinheiro K, Gordân R. High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins. Nucleic Acids Research 51(21):11600–11612 (2023).
  11. Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 381(6664):eadd1250 (2023).
  12. Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gordân R*, Afek A*. UV irradiation remodels the specificity landscape of transcription factors. Proceedings of the National Academy of Sciences 120(11):e2217422120 (2023).
  13. Zhao J+, Martin V+, Gordân R. Transcription factor-centric approach to identify non-recurring putative regulatory drivers in cancer. Research in Computational Molecular Biology (RECOMB) 13278:36–51 (2022).
  14. Sun T, Ding CC, Zhang Y, Zhang Y, Lin CC, Wu J, Setayeshpour Y, Coggins S, Shepard C, Macias E, Kim B, Zhou P, Gordân R, Chi JT. MESH1 knockdown triggers proliferation arrest through TAZ repression. Cell Death and Disease 13(3):221 (2022).
  15. Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gordân 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. Molecular Neurodegeneration 16(1):58 (2021).
  16. Zhang Y, Ho T, Gordân R. Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Research 31(7):1216–1229 (2021).
  17. Liu M, Boot A, Ng AWT, Gordân R, Rozen SG. Mutational Processes in Cancer Preferentially Affect Binding of Particular Transcription Factors. Scientific Reports 11:3339 (2021).
  18. 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*, Gordân R*. DNA mismatches reveal widespread conformational penalties in protein-DNA recognition. Nature 587(7833):291–296 (2020).
  19. Martin V+, Zhao J+, Afek A, Mielko Z, Gordân R. QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic Acids Research 47:W127–W135 (2019).
  20. Ilic S, Cohen S, Afek A, Gordân R, Lukatsky DB, Akabayov B. DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling. JoVE 152, doi: 10.3791/59737 (2019).
  21. Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordân R, Arbely E. Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine. Biochimica et Biophysica Acta – General Subjects 1863(9):1343–1350 (2019).
  22. Shen N, Zhao J, Schipper J, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordân R. Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding. Cell Systems 6(4):470–483 (2018).
  23. Afek A, Tagliafierro L, Glenn OC, Lukatsky DB, Gordân R*, Chiba-Falek O*. Deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neurogenetics 19(3):135–144 (2018).
  24. Afek A, Ilic S, Horton J, Lukatsky DB*, Gordân R*, Akabayov B*. DNA sequence context controls the binding and processivity of the T7 DNA primase. iScience 2:141–147 (2018).
  25. 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, Gordân R, Nixon AB, Owzar K. Genetic variation determines VEGF-A plasma levels in cancer patients. Scientific Reports 8(1):16332 (2018).
  26. Innocenti F, Owzar K, Jiang C, Etheridge AS, Gordân 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 13(8):e0202272 (2018).
  27. Manandhar D+, Song L+, Kabadi A, Kwon J, Edsall L, Ehrlich M, Tsumagari K, Gersbach C, Crawford C*, Gordân R*. Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Nucleic Acids Research 45(20):11684–11699 (2017).
  28. Joh DY, Hucknall AM, Wei Q, Mason KA, Lund ML, Fontes CM, Hill RT, Blair R, Zimmers Z, Achar RK, Tseng D, Gordân R, Freemark M, Ozcan A, Chilkoti A. Inkjet Printed Point-of-Care Immunoassay on a Nanoscale Polymer Brush Enables Sub-Picomolar Detection of Analytes in Blood. Proceedings of the National Academy of Sciences 114(34):E7054–E7062 (2017).
  29. 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 PKH, Chung AYF, Lucien L, Ooi PJ, Lim KH, Dima S, Duda DG, Popescu I, Broet O, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov L, Gordân R*, Rozen SG*, Shibata T*, Pairojkul C*, Teh BT*, Tan P*. Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Cancer Discovery 7(10):1116–1135 (2017).
  30. Zhao J+, Li D+, Seo J, Allen AS, Gordân R. Quantifying the impact of non-coding variants on transcription factor-DNA binding. Research in Computational Molecular Biology 2017 (RECOMB17), Lecture Notes in Computer Science 10229:336–352 (2017).
  31. Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gordân R, Yao G, You L. Expression level is a key determinant of E2F1-mediated cell fate. Cell Death and Differentiation 24(4):626–637 (2017).
  32. Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gordân R, Megraw M, Brady SM, Benfey PN. Establishment of expression in the SHORTROOT-SCARECROW transcriptional cascade through opposing activities of both activators and repressors. Developmental Cell 39(5):585–596 (2016).
  33. Medina EM, Turner JJ, Gordân R, Skotheim JM, Buchler NE. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. eLife 5:e09492 (2016).
  34. Frank CL, Manandhar D, Gordân R, Crawford GE. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics and Chromatin 9:15 (2016).
  35. Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân 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 351(6280):1450–1454 (2016).
  36. Schipper JL, Gordân R. Transcription factor-DNA binding motifs in Saccharomyces cerevisiae: Tools and resources. In Budding Yeast: A Laboratory Manual. Cold Spring Harbor Protocol 2016(11):pdb.top080622 (2016).
  37. Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky D. Nonconsensus protein binding to repetitive DNA sequence elements significantly affects eukaryotic genomes. PLOS Computational Biology 11(8):e1004429 (2015).
  38. Zhou T+, Shen N+, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R*, Rohs R*. Quantitative modeling of transcription factor binding specificities using DNA shape. Proceedings of the National Academy of Sciences 112(15):4654–4659 (2015).
  39. Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gordân R, Wray GA, Silver DL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Current Biology 25(6):772–779 (2015).
  40. Afek A, Schipper JL, Horton J, Gordân R*, Lukatsky D*. Protein-DNA binding in the absence of specific base-pair recognition. Proceedings of the National Academy of Sciences 111(48):17140–17145 (2014).
  41. Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH. Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biology 15:482 (2014).
  42. Munteanu A, Ohler U, Gordân R. COUGER – CO-factors associated with Uniquely-bound GEnomic Regions. Nucleic Acids Research 42(W1):W461–W467 (2014).
  43. Slattery M*, Zhou T, Yang L, Dantas-Machado AC, Gordân R*, Rohs R*. Absence of a simple code: how transcription factors read the genome. Trends in Biochemical Sciences 39(9):381–399 (2014).
  44. Siggers T*, Gordân R*. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Research 42:2099–2111 (2014).
  45. Yang L, Dror I, Zhou T, Mathelier A, Wasserman W, Gordân R, Rohs R. TFBSshape: a motif-based database for DNA shape features of transcription factor binding sites. Nucleic Acids Research 42(1):D148–D155 (2013).
  46. Mordelet F, Hartemink AJ, Engelhardt BE, Gordân R. Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics 29:i117–i125 (2013).
  47. Munteanu A, Gordân R. Distinguishing between genomic regions bound by paralogous transcription factors. Research in Computational Molecular Biology (RECOMB2013), Lecture Notes in Computer Science 7821:145 (2013).
  48. Gordân R, Shen N, Dror I, Zhou T, Rohs R*, Bulyk ML*. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Reports 3:1093–1104 (2013).
  49. Gordân R+, Murphy K+, 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 Biology 12(12):R125 (2012).
  50. Gordân R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pacific Symposium on Biocomputing 2012:299–310 (2011).
  51. Miller HB, Robinson TJ, Gordân R, Hartemink AJ, Garcia-Blanco MA. Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. RNA 17(4):665–674 (2011).
  52. Gordân R+, Narlikar L+, Hartemink AJ. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Research 38(6):e90 (2010).
  53. MacAlpine HK+, Gordân R+, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Research 20(2):201–211 (2010).
  54. Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research 19(11):2090–2100 (2009).
  55. Gordân R+, Narlikar L+, Hartemink AJ. A fast, alignment-free, conservation-based method for transcription factor binding site discovery. Research in Computational Molecular Biology (RECOMB08), Lecture Notes in Bioinformatics 4955:98–111 (2008).
  56. Gordân R, Hartemink AJ. Using DNA duplex stability information to discover transcription factor binding sites. Pacific Symposium on Biocomputing 13:453–464 (2008).
  57. Narlikar L+, Gordân R+, Hartemink AJ. A nucleosome-guided map of transcription factor binding sites in yeast. PLOS Computational Biology 3(11):e215 (2007).
  58. Narlikar L+, Gordân R+, Hartemink AJ. Nucleosome occupancy information improves de novo motif discovery. Research in Computational Molecular Biology (RECOMB07), Lecture Notes in Bioinformatics 4453:107–121 (2007).
  59. Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Intelligent Systems in Molecular Biology 2006 (ISMB06), Bioinformatics 22(14):e384–e392 (2006).