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Publications of Raluca M. Gordan    :chronological  alphabetical  combined  bibtex listing:

Journal articles or Book chapters PUBLISHED

  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, vol. 53 no. 4 (February, 2025) [doi]  [abs]
  2. Duan, M; Song, S; Wasserman, H; Lee, P-H; 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., Proc Natl Acad Sci U S A, vol. 121 no. 4 (January, 2024), pp. e2310854121 [doi]  [abs]
  3. 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 Res, vol. 51 no. 21 (November, 2023), pp. 11600-11612 [doi]  [abs]
  4. Horton, CA; Alexandari, AM; Hayes, MGB; Marklund, E; Schaepe, JM; Aditham, AK; Shah, N; Suzuki, PH; 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, vol. 381 no. 6664 (September, 2023), pp. eadd1250 [doi]  [abs]
  5. 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 (September, 2023) [doi]  [abs]
  6. 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., Proc Natl Acad Sci U S A, vol. 120 no. 11 (March, 2023), pp. e2217422120 [doi]  [abs]
  7. Sun, T; Ding, C-KC; Zhang, Y; Zhang, Y; Lin, C-C; Wu, J; Setayeshpour, Y; Coggins, S; Shepard, C; Macias, E; Kim, B; Zhou, P; Gordân, R; Chi, J-T, MESH1 knockdown triggers proliferation arrest through TAZ repression., Cell Death Dis, vol. 13 no. 3 (March, 2022), pp. 221 [doi]  [abs]
  8. Zhao, J; Martin, V; Gordân, R, Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13278 LNBI (January, 2022), pp. 36-51, ISBN 9783031047480 [doi]  [abs]
  9. 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., Mol Neurodegener, vol. 16 no. 1 (August, 2021), pp. 58 [doi]  [abs]
  10. Zhang, Y; Ho, TD; Buchler, NE; Gordân, R, Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions., Genome Res, vol. 31 no. 7 (July, 2021), pp. 1216-1229 [doi]  [abs]
  11. Liu, M; Boot, A; Ng, AWT; Gordân, R; Rozen, SG, Mutational processes in cancer preferentially affect binding of particular transcription factors., Sci Rep, vol. 11 no. 1 (February, 2021), pp. 3339 [doi]  [abs]
  12. 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 conformational penalties in protein-DNA recognition., Nature, vol. 587 no. 7833 (November, 2020), pp. 291-296 [doi]  [abs]
  13. 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 no. 152 (October, 2019) [doi]  [abs]
  14. 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, vol. 1863 no. 9 (September, 2019), pp. 1343-1350 [doi]  [abs]
  15. 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 Res, vol. 47 no. W1 (July, 2019), pp. W127-W135 [doi]  [abs]
  16. Afek, A; Shi, H; Rangadurai, A; Al-Hashimi, HM; Gordan, RM, Mismatched base pairs locally distort DNA structure, leading to increased DNA-binding by transcription factor proteins, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 37 (May, 2019), pp. 80-81, TAYLOR & FRANCIS INC
  17. 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, vol. 8 no. 1 (November, 2018), pp. 16332 [doi]  [abs]
  18. Afek, A; Tagliafierro, L; Glenn, OC; Lukatsky, DB; Gordan, R; Chiba-Falek, O, Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene., Neurogenetics, vol. 19 no. 3 (August, 2018), pp. 135-144 [doi]  [abs]
  19. 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, vol. 13 no. 8 (August, 2018), pp. e0202284-e0202284, Public Library of Science (PLoS) [doi]  [abs]
  20. 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, vol. 2 (April, 2018), pp. 141-147 [doi]  [abs]
  21. 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, vol. 6 no. 4 (April, 2018), pp. 470-483.e8 [doi]  [abs]
  22. Manandhar, D; Song, L; Kabadi, A; Kwon, JB; Edsall, LE; Ehrlich, M; Tsumagari, K; Gersbach, CA; Crawford, GE; Gordân, R, Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies., Nucleic Acids Res, vol. 45 no. 20 (November, 2017), pp. 11684-11699 [doi]  [abs]
  23. 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-H; Chung, AYF; Ooi, LLPJ; Lim, KH; Dima, S; Duda, DG; Popescu, I; Broet, P; Hsieh, S-Y; Yu, M-C; Scarpa, A; Lai, J; Luo, D-X; Carvalho, AL; Vettore, AL; Rhee, H; Park, YN; Alexandrov, LB; Gordân, R; Rozen, SG; Shibata, T; Pairojkul, C; Teh, BT; Tan, P, Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma., Cancer Discov, vol. 7 no. 10 (October, 2017), pp. 1116-1135 [doi]  [abs]
  24. Correction for Joh et al., 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, vol. 114 no. 39 (September, 2017), pp. E8315 [doi]
  25. 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, vol. 114 no. 34 (August, 2017), pp. E7054-E7062 [doi]  [abs]
  26. Zhao, J; Li, D; Seo, J; Allen, AS; Gordân, R, Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding., Res Comput Mol Biol, vol. 10229 (May, 2017), pp. 336-352, ISBN 9783319569697 [doi]  [abs]
  27. 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 Differ, vol. 24 no. 4 (April, 2017), pp. 626-637 [doi]  [abs]
  28. 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., Dev Cell, vol. 39 no. 5 (December, 2016), pp. 585-596 [doi]  [abs]
  29. Schipper, JL; Gordân, RM, Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources., Cold Spring Harb Protoc, vol. 2016 no. 11 (November, 2016), pp. pdb.top080622 [doi]  [abs]
  30. Medina, EM; Turner, JJ; Gordân, R; Skotheim, JM; Buchler, NE, Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi., Elife, vol. 5 no. MAY2016 (May, 2016) [repository], [doi]  [abs]
  31. 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, vol. 351 no. 6280 (March, 2016), pp. 1450-1454 [doi]  [abs]
  32. Frank, CL; Manandhar, D; Gordân, R; Crawford, GE, HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells., Epigenetics Chromatin, vol. 9 (2016), pp. 15 [doi]  [abs]
  33. Afek, A; Cohen, H; Barber-Zucker, S; Gordân, R; Lukatsky, DB, Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes., edited by Ioshikhes, I, PLoS computational biology, vol. 11 no. 8 (August, 2015), pp. e1004429 [doi]  [abs]
  34. 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., Proc Natl Acad Sci U S A, vol. 112 no. 15 (April, 2015), pp. 4654-4659, ISSN 0027-8424 [doi]  [abs]
  35. Boyd, JL; Skove, SL; Rouanet, JP; Pilaz, L-J; Bepler, T; Gordân, R; Wray, GA; Silver, DL, Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex., Curr Biol, vol. 25 no. 6 (March, 2015), pp. 772-779, ISSN 0960-9822 [repository], [doi]  [abs]
  36. Afek, A; Schipper, JL; Horton, J; Gordân, R; Lukatsky, DB, Protein-DNA binding in the absence of specific base-pair recognition., Proc Natl Acad Sci U S A, vol. 111 no. 48 (December, 2014), pp. 17140-17145, ISSN 0027-8424 [doi]  [abs]
  37. 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 Biochem Sci, vol. 39 no. 9 (September, 2014), pp. 381-399, ISSN 0968-0004 [doi]  [abs]
  38. Munteanu, A; Ohler, U; Gordân, R, COUGER--co-factors associated with uniquely-bound genomic regions., Nucleic Acids Res, vol. 42 no. Web Server issue (July, 2014), pp. W461-W467, ISSN 0305-1048 [doi]  [abs]
  39. Siggers, T; Gordân, R, Protein-DNA binding: complexities and multi-protein codes., Nucleic Acids Res, vol. 42 no. 4 (February, 2014), pp. 2099-2111, ISSN 0305-1048 [doi]  [abs]
  40. Yang, L; Zhou, T; Dror, I; Mathelier, A; Wasserman, WW; Gordân, R; Rohs, R, TFBSshape: a motif database for DNA shape features of transcription factor binding sites., Nucleic Acids Res, vol. 42 no. Database issue (January, 2014), pp. D148-D155, ISSN 0305-1048 [doi]  [abs]
  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 Biol, vol. 15 no. 10 (2014), pp. 482 [doi]  [abs]
  42. Mordelet, F; Horton, J; Hartemink, AJ; Engelhardt, BE; Gordân, R, Stability selection for regression-based models of transcription factor-DNA binding specificity., Bioinformatics, vol. 29 no. 13 (July, 2013), pp. i117-i125 [23812975], [doi]  [abs]
  43. Gordân, 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, vol. 3 no. 4 (April, 2013), pp. 1093-1104, ISSN 2211-1247 [doi]  [abs]
  44. Munteanu, A; Gordân, R, Distinguishing between genomic regions bound by paralogous transcription factors, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7821 LNBI (April, 2013), pp. 145-157, Springer Berlin Heidelberg, ISSN 0302-9743 [doi]  [abs]
  45. Gordân, R; Pyne, S; Bulyk, ML, Identification of cell cycle-regulated, putative hyphal genes in Candida albicans., Pac Symp Biocomput (2012), pp. 299-310, ISSN 2335-6936  [abs]
  46. Gordân, 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, vol. 12 no. 12 (December, 2011), pp. R125, ISSN 1474-7596 [doi]  [abs]
  47. 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, vol. 17 no. 4 (April, 2011), pp. 665-674 [21282347], [doi]  [abs]
  48. Gordân, R; Narlikar, L; Hartemink, AJ, Finding regulatory DNA motifs using alignment-free evolutionary conservation information., Nucleic Acids Res, vol. 38 no. 6 (April, 2010), pp. e90 [20047961], [doi]  [abs]
  49. MacAlpine, HK; Gordân, R; Powell, SK; Hartemink, AJ; MacAlpine, DM, Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading., Genome Res, vol. 20 no. 2 (February, 2010), pp. 201-211 [19996087], [doi]  [abs]
  50. Gordân, R; Narlikar, L; Hartemink, AJ, Finding regulatory DNA motifs using alignment-free evolutionary conservation information, Nucleic Acids Research, vol. 38 no. 6 (January, 2010), pp. e90.1-e90.12, ISSN 0305-1048 [doi]  [abs]
  51. Gordân, R; Hartemink, AJ; Bulyk, ML, Distinguishing direct versus indirect transcription factor-DNA interactions., Genome Res, vol. 19 no. 11 (November, 2009), pp. 2090-2100 [19652015], [doi]  [abs]
  52. Gordân, R; Hartemink, AJ, Using DNA duplex stability information for transcription factor binding site discovery., Pac Symp Biocomput (2008), pp. 453-464, ISSN 2335-6936 [18229707]  [abs]
  53. Gordân, R; Narlikar, L; Hartemink, AJ, A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery., edited by Vingron, M; Wong, L, RECOMB, vol. 4955 (2008), pp. 98-111, Springer, ISSN 0302-9743, ISBN 978-3-540-78838-6 [doi]  [abs]
  54. Narlikar, L; Gordân, R; Hartemink, AJ, A nucleosome-guided map of transcription factor binding sites in yeast., PLoS Comput Biol, vol. 3 no. 11 (November, 2007), pp. e215 [17997593], [doi]  [abs]
  55. Narlikar, L; Gordân, R; Hartemink, AJ, Nucleosome Occupancy Information Improves de novo Motif Discovery., edited by Speed, TP; Huang, H, RECOMB, vol. 4453 (2007), pp. 107-121, Springer, ISSN 0302-9743, ISBN 3-540-71680-7 [doi]  [abs]
  56. Narlikar, L; Gordân, R; Ohler, U; Hartemink, AJ, Informative priors based on transcription factor structural class improve de novo motif discovery., Bioinformatics, vol. 22 no. 14 (July, 2006), pp. e384-e392 [16873497], [doi]  [abs]
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