Publications

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1. Zhang Y, Ho TD, Buchler NE, Gordan R (2021) Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Research, Published in Advance May 11, 2021

   • All raw and processed data available in GEO, SuperSeries GSE163512

2. Liu M, Boot A, Ng AWT, Gordan R, Rozen SG (2021) Mutational processes in cancer preferentially affect binding of particular transcription factors. Scientific Reports 11(1):3339.

3. 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, Gordan R (2020) DNA mismatches reveal conformational penalties in protein–DNA recognition. Nature Advanced online access (* co-corresponding authors)

   • All raw and processed data available in GEO, SuperSeries GSE156375
   • Check out the New and Views by Kale Kundert & James S. Fraser: DNA-binding proteins meet their mismatch
   • Recommended by Faculty Opinions / Biological Physics
   • Recommended by Faculty Opinions / Bioinformatics, Biomedical Informatics & Computational Biology

4. Martin V*, Zhao J*, Afek A, Mielko Z, Gordan R (2019) QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic Acids Research 47(W1):W127-W135 (* co-first authors)

   • The QBiC-Pred web server: qbic.genome.duke.edu
   • All raw and processed data available in GEO, SuperSeries GSE130837

5. Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R,  Arbely E (2019) Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine. Biochimica et Biophysica Acta – General Subjects 1863(9):1343-1350

6. Shen N, Zhao J, Schipper J, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R (2018) Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding. Cell Systems 6(4):470-483

   • Selected for the RSG Recommended Reading List 2018 by the ISCB Regulatory and Systems Genomics community
   • All models and predictions are available through our iMADS web server
   • All raw and processed data available in GEO, SuperSeries GSE97794

7. Afek A, Tagliafierro L, Glenn OC, Lukatsky DB, Gordan R*, Chiba-Falek O* (2018) Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neurogenetics 19(3): 135-144.

8. Afek A, Ilic S, Horton J, Lukatsky DB*, Gordan R*, Akabayov B* (2018) DNA sequence context controls the binding and processivity of the T7 DNA primase. iScience 2:141-147.

9. Manandhar D+, Song L+, Kabadi A, Kwon J, Edsall L, Ehrlich M, Tsumagari K, Gersbach C, Crawford C*, Gordan R* (2017) Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. NAR 45(20):11684-11699.

10. 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 (2017) Inkjet Printed Point-of-Care Immunoassay on a Nanoscale Polymer Brush Enables Sub-Picomolar Detection of Analytes in Blood. PNAS 114(34):E7054-E7062.

11. 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* (2017) Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.  Cancer Discovery 7(10):1116-1135 (+ co-first authors, * co-corresponding authors)

12. Zhao J*, Li D*, Seo J, Allen AS, Gordân R (2017) 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. (* co-first authors)

13. Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gordân R, Yao G, You L (2017) Expression level is a key determinant of E2F1-mediated cell fate. Cell Death and Differentiation 24(4):626-637.

14. 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 (2016) Establishment of expression in the SHORTROOT-SCARECROW transcriptional cascade through opposing activities of both activators and repressors. Developmental Cell 39(5):585-596.

15. Schipper JL, Gordân R (2016)  Transcription factor-DNA binding motifs in Saccharomyces cerevisiae: Tools and resources. In Budding Yeast: A Laboratory Manual. Cold Spring Harbor Protocols 2016(11):pdb.top080622.

16. Medina EM, Turner JJ, Gordân R, Skotheim JM, Buchler NE (2016) Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. Elife 5. pii: e09492.

17. Frank CL, Manandhar D, Gordân R, Crawford GE (2016) HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics and Chromatin. 9:15.

18. 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 (2016) Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 351(6280):1450-4.

19. Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky D (2015) Nonconsensus protein binding to repetitive DNA sequence elements significantly affects eukaryotic genomes. PLOS Computational Biology 11(8):e1004429

20. Zhou T+, Shen N+, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R*, Rohs R* (2015) Quantitative modeling of transcription factor binding specificities using DNA shape. PNAS 112(15):4654–4659 (+ co-first authors, * co-corresponding authors)

    • Highlighted in PNAS Commentary by Teresa Przytycka and David Levens: Shapely DNA attracts the right partner
    • Recommended by F1000 Structural Biology 

21. Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gordân R, Wray GA, Silver, DL (2015) Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Current Biology 25(6):772–779.

22. Afek A, Schipper JL, Horton J, Gordân R*, Lukatsky D* (2014) Protein-DNA binding in the absence of specific base-pair recognition. PNAS 111(48):17140–17145. (* co-corresponding authors)

    • Highlighted in PNAS Commentary by Peter H. von Hippel: Increased subtlety of transcription factor binding increases complexity of genome regulation 

23. Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH (2014) Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biology 15:482.

24. Slattery M*, Zhou T, Yang L, Dantas Machado AC, Gordân R*, Rohs R* (2014) Absence of a simple code: how transcription factors read the genome. Trends in Biochemical Sciences 39(9):381–399. (* co-corresponding authors)

25. Munteanu A, Ohler U, Gordân R (2014) COUGER – CO-factors associated with Uniquely-bound GEnomic Regions. Nucleic Acids Research. 42(W1):W461–W467.

    • Website: couger.oit.duke.edu 

26. Siggers T*, Gordân R* (2014) Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Research 42(4):2099–111. (* co-corresponding authors)

27. Yang L, Zhou T, Dror I, Mathelier A, Wasserman W, Gordân R, Rohs R (2014) TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Research 42:D148–55.

    • Selected as an NAR Breakthrough Article
    • Winner of the 2014 Top Ten Paper Award in Regulatory and Systems Genomics 

28. Mordelet F, Horton J, Hartemink A, Engelhardt B, Gordân R (2013) Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics 29(13):i117–i125.

29. Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML (2013) Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Reports 3(4):1093–1104.

    • Winner of the 2013 Top Ten Paper Award in Regulatory and Systems Genomics
    • Selected as Highlights Presentation at Recomb 2014 

30. Munteanu A, Gordân R (2013) “Distinguishing between genomic regions bound by paralogous transcription factors.” Research in Computational Molecular Biology 2013 (RECOMB13). 7821:145. [Supp. Info.] [Data] [COUGER software]

31. Gordân R, Pyne S, Bulyk ML (2012) Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pacific Symposium on Biocomputing, 2012:299–310.

32. Gordân R*, Murphy K*, McCord RP, Zhu C, Vedenko A, Bulyk ML (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biology, 12(12):R125.

    • Highly accessed 

33. Miller HB, Robinson TJ, Gordân R, Hartemink AJ, & Garcia-Blanco MA (2011) Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. RNA, 17(4):665–674.

34. Gordân R*, Narlikar L*, Hartemink AJ (2010) Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Research, 38(6):e90. (* equal contribution)

35. MacAlpine HK*, Gordân R*, Powell SK, Hartemink AJ, MacAlpine DM (2009) Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Research, 20(2):201–211. (* equal contribution)

36. Gordân R, Hartemink AJ, & Bulyk ML (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research, 19(11):2090–2100.

37. Gordân R*, Narlikar L.*, Hartemink AJ (2008) A fast, alignment-free, conservation-based method for transcription factor binding site discovery. Research in Computational Molecular Biology 2008 (RECOMB08). Lecture Notes in Bioinformatics, eds. 4955, pp. 98–111. (* equal contribution) [Supp. Info.]

38. Gordân R, Hartemink AJ (2008) Using DNA Duplex Stability Information to Discover Transcription Factor Binding Sites. Pacific Symposium on Biocomputing 2008 (PSB08), 13:453–464. [Supp. Info.]

39. Narlikar L*, Gordân R*, Hartemink AJ (2007) A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. PLOS Computational Biology, 3(11):e215. (* equal contribution).

40. Narlikar L*, Gordân R.*, Hartemink AJ (2007) Nucleosome occupancy information improves de novo motif discovery. Research in Computational Molecular Biology 2007 (RECOMB07). Lecture Notes in Bioinformatics, eds. 4453, April 2007. pp. 107–121. (* equal contribution) [Supp. Info.]

41. Narlikar L, Gordân R, Ohler U, Hartemink AJ (2006) Informative Priors Based on Transcription Factor Structural Class Improve de novo Motif Discovery. Intelligent Systems in Molecular Biology 2006 (ISMB06), Bioinformatics, 22. pp. e384–e392. [Supp. Info.] [Code] [Input Data]