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Items: 1 to 50 of 51

1.

Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.

Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E.

Biochim Biophys Acta Gen Subj. 2019 Sep;1863(9):1343-1350. doi: 10.1016/j.bbagen.2019.05.019. Epub 2019 Jun 3.

PMID:
31170499
2.

QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.

Martin V, Zhao J, Afek A, Mielko Z, Gordân R.

Nucleic Acids Res. 2019 Jul 2;47(W1):W127-W135. doi: 10.1093/nar/gkz363.

3.

DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase.

Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B.

iScience. 2018 Apr 27;2:141-147. doi: 10.1016/j.isci.2018.03.019. Epub 2018 Mar 27.

4.

Genetic variation determines VEGF-A plasma levels in cancer patients.

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.

Sci Rep. 2018 Nov 5;8(1):16332. doi: 10.1038/s41598-018-34506-4.

5.

Electroactive graphene composite scaffolds for cardiac tissue engineering.

Hitscherich P, Aphale A, Gordan R, Whitaker R, Singh P, Xie LH, Patra P, Lee EJ.

J Biomed Mater Res A. 2018 Nov;106(11):2923-2933. doi: 10.1002/jbm.a.36481. Epub 2018 Oct 16.

PMID:
30325093
6.

The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation.

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.

PLoS One. 2018 Aug 14;13(8):e0202272. doi: 10.1371/journal.pone.0202272. eCollection 2018.

7.

Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene.

Afek A, Tagliafierro L, Glenn OC, Lukatsky DB, Gordan R, Chiba-Falek O.

Neurogenetics. 2018 Aug;19(3):135-144. doi: 10.1007/s10048-018-0546-8. Epub 2018 May 5.

8.

Involvement of cytosolic and mitochondrial iron in iron overload cardiomyopathy: an update.

Gordan R, Wongjaikam S, Gwathmey JK, Chattipakorn N, Chattipakorn SC, Xie LH.

Heart Fail Rev. 2018 Sep;23(5):801-816. doi: 10.1007/s10741-018-9700-5. Review.

9.

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.

Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R.

Cell Syst. 2018 Apr 25;6(4):470-483.e8. doi: 10.1016/j.cels.2018.02.009. Epub 2018 Mar 28.

10.

Newly Identified NO-Sensor Guanylyl Cyclase/Connexin 43 Association Is Involved in Cardiac Electrical Function.

Crassous PA, Shu P, Huang C, Gordan R, Brouckaert P, Lampe PD, Xie LH, Beuve A.

J Am Heart Assoc. 2017 Dec 21;6(12). pii: e006397. doi: 10.1161/JAHA.117.006397.

11.

Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.

Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gordân R.

Nucleic Acids Res. 2017 Nov 16;45(20):11684-11699. doi: 10.1093/nar/gkx773.

12.

Effect of densely ionizing radiation on cardiomyocyte differentiation from human-induced pluripotent stem cells.

Baljinnyam E, Venkatesh S, Gordan R, Mareedu S, Zhang J, Xie LH, Azzam EI, Suzuki CK, Fraidenraich D.

Physiol Rep. 2017 Aug;5(15). pii: e13308. doi: 10.14814/phy2.13308.

13.

Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood.

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.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):E7054-E7062. doi: 10.1073/pnas.1703200114. Epub 2017 Aug 7. Erratum in: Proc Natl Acad Sci U S A. 2017 Sep 18;:.

14.

Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.

Zhao J, Li D, Seo J, Allen AS, Gordân R.

Res Comput Mol Biol. 2017 May;10229:336-352. doi: 10.1007/978-3-319-56970-3_21. Epub 2017 Apr 12.

15.

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

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, Gordân R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P.

Cancer Discov. 2017 Oct;7(10):1116-1135. doi: 10.1158/2159-8290.CD-17-0368. Epub 2017 Jun 30.

16.

Expression level is a key determinant of E2F1-mediated cell fate.

Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gordân R, Yao G, You L.

Cell Death Differ. 2017 Apr;24(4):626-637. doi: 10.1038/cdd.2017.12. Epub 2017 Feb 17.

17.

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

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.

Dev Cell. 2016 Dec 5;39(5):585-596. doi: 10.1016/j.devcel.2016.09.031. Epub 2016 Oct 27.

18.

Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.

Schipper JL, Gordân RM.

Cold Spring Harb Protoc. 2016 Nov 1;2016(11). doi: 10.1101/pdb.top080622.

PMID:
27803259
19.

Involvement of mitochondrial permeability transition pore (mPTP) in cardiac arrhythmias: Evidence from cyclophilin D knockout mice.

Gordan R, Fefelova N, Gwathmey JK, Xie LH.

Cell Calcium. 2016 Dec;60(6):363-372. doi: 10.1016/j.ceca.2016.09.001. Epub 2016 Sep 2.

20.

Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.

Medina EM, Turner JJ, Gordân R, Skotheim JM, Buchler NE.

Elife. 2016 May 10;5. pii: e09492. doi: 10.7554/eLife.09492.

21.

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.

Frank CL, Manandhar D, Gordân R, Crawford GE.

Epigenetics Chromatin. 2016 Apr 16;9:15. doi: 10.1186/s13072-016-0065-5. eCollection 2016.

22.

Survey of variation in human transcription factors reveals prevalent DNA binding changes.

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.

Science. 2016 Mar 25;351(6280):1450-1454. doi: 10.1126/science.aad2257. Epub 2016 Mar 24.

23.

The effect of PVDF-TrFE scaffolds on stem cell derived cardiovascular cells.

Hitscherich P, Wu S, Gordan R, Xie LH, Arinzeh T, Lee EJ.

Biotechnol Bioeng. 2016 Jul;113(7):1577-85. doi: 10.1002/bit.25918. Epub 2016 Jan 28.

PMID:
26705272
24.

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky DB.

PLoS Comput Biol. 2015 Aug 18;11(8):e1004429. doi: 10.1371/journal.pcbi.1004429. eCollection 2015 Aug.

25.

Autonomic and endocrine control of cardiovascular function.

Gordan R, Gwathmey JK, Xie LH.

World J Cardiol. 2015 Apr 26;7(4):204-14. doi: 10.4330/wjc.v7.i4.204. Review.

26.

Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9.

27.

Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.

Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gordân R, Wray GA, Silver DL.

Curr Biol. 2015 Mar 16;25(6):772-779. doi: 10.1016/j.cub.2015.01.041. Epub 2015 Feb 19.

28.

Overexpression of adenylyl cyclase type 5 (AC5) confers a proarrhythmic substrate to the heart.

Zhao Z, Babu GJ, Wen H, Fefelova N, Gordan R, Sui X, Yan L, Vatner DE, Vatner SF, Xie LH.

Am J Physiol Heart Circ Physiol. 2015 Feb 1;308(3):H240-9. doi: 10.1152/ajpheart.00630.2014. Epub 2014 Dec 5.

29.

Protein-DNA binding in the absence of specific base-pair recognition.

Afek A, Schipper JL, Horton J, Gordân R, Lukatsky DB.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17140-5. doi: 10.1073/pnas.1410569111. Epub 2014 Oct 13.

30.

Sequence specificity incompletely defines the genome-wide occupancy of Myc.

Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH.

Genome Biol. 2014;15(10):482.

31.

Absence of a simple code: how transcription factors read the genome.

Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R.

Trends Biochem Sci. 2014 Sep;39(9):381-99. doi: 10.1016/j.tibs.2014.07.002. Epub 2014 Aug 14. Review.

32.

Primary effect of reactive oxygen species on electrical remodeling of the heart.

Gordan R, Xie LH.

Circ J. 2014;78(8):1834-6. Epub 2014 Jul 9. No abstract available.

33.

COUGER--co-factors associated with uniquely-bound genomic regions.

Munteanu A, Ohler U, Gordân R.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W461-7. doi: 10.1093/nar/gku435. Epub 2014 May 26.

34.

Modulation of intracellular calcium waves and triggered activities by mitochondrial ca flux in mouse cardiomyocytes.

Zhao Z, Gordan R, Wen H, Fefelova N, Zang WJ, Xie LH.

PLoS One. 2013 Nov 7;8(11):e80574. doi: 10.1371/journal.pone.0080574. eCollection 2013.

35.

Protein-DNA binding: complexities and multi-protein codes.

Siggers T, Gordân R.

Nucleic Acids Res. 2014 Feb;42(4):2099-111. doi: 10.1093/nar/gkt1112. Epub 2013 Nov 16. Review.

36.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R.

Nucleic Acids Res. 2014 Jan;42(Database issue):D148-55. doi: 10.1093/nar/gkt1087. Epub 2013 Nov 7.

37.

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gordân R.

Bioinformatics. 2013 Jul 1;29(13):i117-25. doi: 10.1093/bioinformatics/btt221.

38.

Increased sarcolipin expression and decreased sarco(endo)plasmic reticulum Ca2+ uptake in skeletal muscles of mouse models of Duchenne muscular dystrophy.

Schneider JS, Shanmugam M, Gonzalez JP, Lopez H, Gordan R, Fraidenraich D, Babu GJ.

J Muscle Res Cell Motil. 2013 Dec;34(5-6):349-56. doi: 10.1007/s10974-013-9350-0. Epub 2013 Jun 8.

PMID:
23748997
39.

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.

Cell Rep. 2013 Apr 25;3(4):1093-104. doi: 10.1016/j.celrep.2013.03.014. Epub 2013 Apr 4.

40.

Dystrophin-compromised sarcoglycan-δ-knockout diaphragm requires full wild-type embryonic stem cell reconstitution for correction.

Vitale JM, Schneider JS, Beck AJ, Zhao Q, Chang C, Gordan R, Michaels J, Bhaumik M, Fraidenraich D.

J Cell Sci. 2012 Apr 1;125(Pt 7):1807-13. doi: 10.1242/jcs.100537. Epub 2012 Feb 10.

41.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML.

Genome Biol. 2011 Dec 21;12(12):R125. doi: 10.1186/gb-2011-12-12-r125.

42.

Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.

Gordân R, Pyne S, Bulyk ML.

Pac Symp Biocomput. 2012:299-310.

43.

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.

Miller HB, Robinson TJ, Gordân R, Hartemink AJ, Garcia-Blanco MA.

RNA. 2011 Apr;17(4):665-74. doi: 10.1261/rna.2462011. Epub 2011 Jan 31.

44.

Finding regulatory DNA motifs using alignment-free evolutionary conservation information.

Gordân R, Narlikar L, Hartemink AJ.

Nucleic Acids Res. 2010 Apr;38(6):e90. doi: 10.1093/nar/gkp1166. Epub 2010 Jan 4.

45.

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.

MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM.

Genome Res. 2010 Feb;20(2):201-11. doi: 10.1101/gr.097873.109. Epub 2009 Dec 7.

46.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

47.
48.

A nucleosome-guided map of transcription factor binding sites in yeast.

Narlikar L, Gordân R, Hartemink AJ.

PLoS Comput Biol. 2007 Nov;3(11):e215. Epub 2007 Sep 24.

49.

Informative priors based on transcription factor structural class improve de novo motif discovery.

Narlikar L, Gordân R, Ohler U, Hartemink AJ.

Bioinformatics. 2006 Jul 15;22(14):e384-92.

PMID:
16873497
50.

Patient dumping: the Texas experience.

Gordan RK, Bridenbaugh SK.

Ky Hosp Mag. 1989 Winter;6(1):24-6. No abstract available.

PMID:
10292070

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