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Items: 1 to 50 of 54

1.

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.

2.

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.

PMID:
28972159
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.
40.

Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells.

Aiyar SE, Blair AL, Hopkinson DA, Bekiranov S, Li R.

Oncogene. 2007 Apr 19;26(18):2543-53. Epub 2006 Oct 16.

PMID:
17043641
41.

Genome-wide analysis of estrogen receptor binding sites.

Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M.

Nat Genet. 2006 Nov;38(11):1289-97. Epub 2006 Oct 1.

PMID:
17013392
42.

Temporal profile of replication of human chromosomes.

Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A.

Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24. Epub 2005 Apr 21.

43.

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR.

Science. 2005 May 20;308(5725):1149-54. Epub 2005 Mar 24.

44.

Genomic maps and comparative analysis of histone modifications in human and mouse.

Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ 3rd, Gingeras TR, Schreiber SL, Lander ES.

Cell. 2005 Jan 28;120(2):169-81.

45.

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.

Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR.

Genome Res. 2004 Mar;14(3):331-42.

46.

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR.

Cell. 2004 Feb 20;116(4):499-509.

47.

Probe selection for high-density oligonucleotide arrays.

Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, Kaplan P, Kulp D, Webster TA.

Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11237-42. Epub 2003 Sep 19.

48.

Large-scale transcriptional activity in chromosomes 21 and 22.

Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR.

Science. 2002 May 3;296(5569):916-9.

49.

Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase.

Ehrt S, Schnappinger D, Bekiranov S, Drenkow J, Shi S, Gingeras TR, Gaasterland T, Schoolnik G, Nathan C.

J Exp Med. 2001 Oct 15;194(8):1123-40.

50.

Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds.

Zuckerman DM, Fisher ME, Bekiranov S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jul;64(1 Pt 1):011206. Epub 2001 Jun 21.

PMID:
11461239

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