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Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks.

Singh S, Szlachta K, Manukyan A, Raimer HM, Dinda M, Bekiranov S, Wang YH.

J Biol Chem. 2020 Feb 6. pii: jbc.RA119.011665. doi: 10.1074/jbc.RA119.011665. [Epub ahead of print]


HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA.

Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML.

Retrovirology. 2019 Dec 16;16(1):40. doi: 10.1186/s12977-019-0505-y.


Systems analysis of barrier molecule and ARNT-related gene expression regulation in melanoma.

Leick KM, Obeid JM, Bekiranov S, Slingluff CL Jr.

Oncoimmunology. 2019 Sep 24;8(12):e1665978. doi: 10.1080/2162402X.2019.1665978. eCollection 2019.


A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure.

Li M, Fine RD, Dinda M, Bekiranov S, Smith JS.

PLoS Genet. 2019 Aug 28;15(8):e1008339. doi: 10.1371/journal.pgen.1008339. eCollection 2019 Aug.


Antitumor effect of insulin-like growth factor-1 receptor inhibition in head and neck squamous cell carcinoma.

Lehman CE, Khalil AA, Axelrod MJ, Dougherty MI, Schoeff SS, Taniguchi LE, Mendez RE, David AP, McGarey PO Jr.,, Hubbard MA, Donaldson L, Frierson HF Jr.,, Stelow EB, Bekiranov S, Wulfkuhle JD, Petricoin EF, Gioeli DG, Jameson MJ.

Laryngoscope. 2019 Aug 21. doi: 10.1002/lary.28236. [Epub ahead of print]


NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer.

Szymura SJ, Zaemes JP, Allison DF, Clift SH, D'Innocenzi JM, Gray LG, McKenna BD, Morris BB, Bekiranov S, LeGallo RD, Jones DR, Mayo MW.

Cell Commun Signal. 2019 Mar 18;17(1):24. doi: 10.1186/s12964-019-0335-5.


Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex.

Chronister WD, Burbulis IE, Wierman MB, Wolpert MJ, Haakenson MF, Smith ACB, Kleinman JE, Hyde TM, Weinberger DR, Bekiranov S, McConnell MJ.

Cell Rep. 2019 Jan 22;26(4):825-835.e7. doi: 10.1016/j.celrep.2018.12.107.


High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets.

Woo LA, Tkachenko S, Ding M, Plowright AT, Engkvist O, Andersson H, Drowley L, Barrett I, Firth M, Akerblad P, Wolf MJ, Bekiranov S, Brautigan DL, Wang QD, Saucerman JJ.

J Mol Cell Cardiol. 2019 Feb;127:204-214. doi: 10.1016/j.yjmcc.2018.12.015. Epub 2018 Dec 28.


Histone H3 lysine 4 methylation signature associated with human undernutrition.

Uchiyama R, Kupkova K, Shetty SJ, Linford AS, Pray-Grant MG, Wagar LE, Davis MM, Haque R, Gaultier A, Mayo MW, Grant PA, Petri WA Jr, Bekiranov S, Auble DT.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11264-E11273. doi: 10.1073/pnas.1722125115. Epub 2018 Nov 12.


Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells.

Kuscu C, Mammadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M.

J Mol Biol. 2019 Jan 4;431(1):111-121. doi: 10.1016/j.jmb.2018.08.001. Epub 2018 Aug 9.


Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human.

Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH.

Genome Biol. 2018 Jul 12;19(1):89. doi: 10.1186/s13059-018-1463-8.


An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking.

Hoffman EA, Zaidi H, Shetty SJ, Bekiranov S, Auble DT.

Bio Protoc. 2018 Feb 20;8(4). pii: e2905. doi: 10.21769/bioprotoc.2905.


Microenvironmental agonists generate de novo phenotypic resistance to combined ibrutinib plus venetoclax in CLL and MCL.

Jayappa KD, Portell CA, Gordon VL, Capaldo BJ, Bekiranov S, Axelrod MJ, Brett LK, Wulfkuhle JD, Gallagher RI, Petricoin EF, Bender TP, Williams ME, Weber MJ.

Blood Adv. 2017 Jun 13;1(14):933-946. Erratum in: Blood Adv. 2017 Aug 17;1(19):1537.


Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics.

Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT.

J Biol Chem. 2017 Nov 24;292(47):19338-19355. doi: 10.1074/jbc.M117.796441. Epub 2017 Sep 26.


Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome.

Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA.

PLoS Genet. 2017 Jun 30;13(6):e1006863. doi: 10.1371/journal.pgen.1006863. eCollection 2017 Jun.


RNA synthesis is associated with multiple TBP-chromatin binding events.

Zaidi HA, Auble DT, Bekiranov S.

Sci Rep. 2017 Jan 4;7:39631. doi: 10.1038/srep39631.


The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.

True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT.

J Biol Chem. 2016 Jul 15;291(29):15307-19. doi: 10.1074/jbc.M116.735134. Epub 2016 May 16.


Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective.

Cherepanova OA, Gomez D, Shankman LS, Swiatlowska P, Williams J, Sarmento OF, Alencar GF, Hess DL, Bevard MH, Greene ES, Murgai M, Turner SD, Geng YJ, Bekiranov S, Connelly JJ, Tomilin A, Owens GK.

Nat Med. 2016 Jun;22(6):657-65. doi: 10.1038/nm.4109. Epub 2016 May 16.


Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas.

Roller DG, Capaldo B, Bekiranov S, Mackey AJ, Conaway MR, Petricoin EF, Gioeli D, Weber MJ.

Oncotarget. 2016 Jan 19;7(3):2734-53. doi: 10.18632/oncotarget.6548.


Genome-wide predictors of NF-κB recruitment and transcriptional activity.

Cieślik M, Bekiranov S.

BioData Min. 2015 Nov 26;8:37. doi: 10.1186/s13040-015-0071-3. eCollection 2015.


Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma.

Capaldo BJ, Roller D, Axelrod MJ, Koeppel AF, Petricoin EF, Slingluff CL Jr, Weber MJ, Mackey AJ, Gioeli D, Bekiranov S.

PLoS One. 2015 Sep 25;10(9):e0138210. doi: 10.1371/journal.pone.0138210. eCollection 2015.


Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations.

Wierman MB, Matecic M, Valsakumar V, Li M, Smith DL Jr, Bekiranov S, Smith JS.

Aging (Albany NY). 2015 Mar;7(3):177-94.


A pan-cancer analysis of prognostic genes.

Anaya J, Reon B, Chen WM, Bekiranov S, Dutta A.

PeerJ. 2016 Feb 16;3:e1499. doi: 10.7717/peerj.1499. eCollection 2015.


Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method.

Viswanathan R, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT.

Methods. 2014 Dec;70(2-3):97-107. doi: 10.1016/j.ymeth.2014.10.029. Epub 2014 Nov 1.


Activin upregulation by NF-κB is required to maintain mesenchymal features of cancer stem-like cells in non-small cell lung cancer.

Wamsley JJ, Kumar M, Allison DF, Clift SH, Holzknecht CM, Szymura SJ, Hoang SA, Xu X, Moskaluk CA, Jones DR, Bekiranov S, Mayo MW.

Cancer Res. 2015 Jan 15;75(2):426-35. doi: 10.1158/0008-5472.CAN-13-2702. Epub 2014 Nov 28.


Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment.

Cohen JN, Tewalt EF, Rouhani SJ, Buonomo EL, Bruce AN, Xu X, Bekiranov S, Fu YX, Engelhard VH.

PLoS One. 2014 Feb 4;9(2):e87740. doi: 10.1371/journal.pone.0087740. eCollection 2014.


Combinatorial epigenetic patterns as quantitative predictors of chromatin biology.

Cieślik M, Bekiranov S.

BMC Genomics. 2014 Jan 28;15:76. doi: 10.1186/1471-2164-15-76.


The network architecture of the Saccharomyces cerevisiae genome.

Hoang SA, Bekiranov S.

PLoS One. 2013 Dec 9;8(12):e81972. doi: 10.1371/journal.pone.0081972. eCollection 2013.


Measuring chromatin interaction dynamics on the second time scale at single-copy genes.

Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT.

Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3.


Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition.

Cieślik M, Hoang SA, Baranova N, Chodaparambil S, Kumar M, Allison DF, Xu X, Wamsley JJ, Gray L, Jones DR, Mayo MW, Bekiranov S.

Epigenetics Chromatin. 2013 Sep 2;6(1):28. doi: 10.1186/1756-8935-6-28.


NF-κB regulates mesenchymal transition for the induction of non-small cell lung cancer initiating cells.

Kumar M, Allison DF, Baranova NN, Wamsley JJ, Katz AJ, Bekiranov S, Jones DR, Mayo MW.

PLoS One. 2013 Jul 30;8(7):e68597. doi: 10.1371/journal.pone.0068597. Print 2013.


Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.

Mesner LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, Bekiranov S.

Genome Res. 2013 Nov;23(11):1774-88. doi: 10.1101/gr.155218.113. Epub 2013 Jul 16.


Genome-wide analysis of functional sirtuin chromatin targets in yeast.

Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS.

Genome Biol. 2013 May 27;14(5):R48. doi: 10.1186/gb-2013-14-5-r48.


Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7 (SCA7) astrocytes.

McCullough SD, Xu X, Dent SY, Bekiranov S, Roeder RG, Grant PA.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21319-24. doi: 10.1073/pnas.1218331110. Epub 2012 Dec 10.


Sexual differentiation in the developing mouse brain: contributions of sex chromosome genes.

Wolstenholme JT, Rissman EF, Bekiranov S.

Genes Brain Behav. 2013 Mar;12(2):166-80. doi: 10.1111/gbb.12010. Epub 2013 Jan 10.


Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications.

Hoang SA, Xu X, Bekiranov S.

BMC Res Notes. 2011 Aug 11;4:288. doi: 10.1186/1756-0500-4-288.


Compensatory pathways induced by MEK inhibition are effective drug targets for combination therapy against castration-resistant prostate cancer.

Gioeli D, Wunderlich W, Sebolt-Leopold J, Bekiranov S, Wulfkuhle JD, Petricoin EF 3rd, Conaway M, Weber MJ.

Mol Cancer Ther. 2011 Sep;10(9):1581-90. doi: 10.1158/1535-7163.MCT-10-1033. Epub 2011 Jun 28.


An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.

Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD.

Genes Dev. 2011 Jun 15;25(12):1306-19. doi: 10.1101/gad.2050311.


Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agents.

Smith SC, Havaleshko DM, Moon K, Baras AS, Lee J, Bekiranov S, Burke DJ, Theodorescu D.

Neoplasia. 2011 Jan;13(1):72-80.


Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription.

Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S.

Genome Res. 2011 Mar;21(3):377-89. doi: 10.1101/gr.111328.110. Epub 2010 Dec 20. Erratum in: Genome Res. 2011 Sep;21(9):1561.


Epigenetic methodologies for behavioral scientists.

Stolzenberg DS, Grant PA, Bekiranov S.

Horm Behav. 2011 Mar;59(3):407-16. doi: 10.1016/j.yhbeh.2010.10.007. Epub 2010 Oct 15.


RNA synthesis precision is regulated by preinitiation complex turnover.

Poorey K, Sprouse RO, Wells MN, Viswanathan R, Bekiranov S, Auble DT.

Genome Res. 2010 Dec;20(12):1679-88. doi: 10.1101/gr.109504.110. Epub 2010 Sep 20.


Amyloid beta precursor protein regulates male sexual behavior.

Park JH, Bonthius PJ, Tsai HW, Bekiranov S, Rissman EF.

J Neurosci. 2010 Jul 28;30(30):9967-72. doi: 10.1523/JNEUROSCI.1988-10.2010.


Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression.

Xu X, Hoang S, Mayo MW, Bekiranov S.

BMC Bioinformatics. 2010 Jul 23;11:396. doi: 10.1186/1471-2105-11-396.


Thiamine biosynthesis in Saccharomyces cerevisiae is regulated by the NAD+-dependent histone deacetylase Hst1.

Li M, Petteys BJ, McClure JM, Valsakumar V, Bekiranov S, Frank EL, Smith JS.

Mol Cell Biol. 2010 Jul;30(13):3329-41. doi: 10.1128/MCB.01590-09. Epub 2010 May 3.


A microarray-based genetic screen for yeast chronological aging factors.

Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS.

PLoS Genet. 2010 Apr 22;6(4):e1000921. doi: 10.1371/journal.pgen.1000921.


Human adipose-derived stromal cells accelerate diabetic wound healing: impact of cell formulation and delivery.

Amos PJ, Kapur SK, Stapor PC, Shang H, Bekiranov S, Khurgel M, Rodeheaver GT, Peirce SM, Katz AJ.

Tissue Eng Part A. 2010 May;16(5):1595-606. doi: 10.1089/ten.TEA.2009.0616.


Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.

Shibata Y, Malhotra A, Bekiranov S, Dutta A.

Nucleic Acids Res. 2009 Oct;37(19):6454-65. doi: 10.1093/nar/gkp650. Epub 2009 Aug 26.


The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression.

Wade SL, Poorey K, Bekiranov S, Auble DT.

EMBO J. 2009 Oct 7;28(19):2919-31. doi: 10.1038/emboj.2009.229. Epub 2009 Aug 13.


Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication.

Kim Y, Bekiranov S, Lee JK, Park T.

Bioinformatics. 2009 Oct 1;25(19):2486-91. doi: 10.1093/bioinformatics/btp471. Epub 2009 Aug 10.

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