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DNA Sequencing and Computational Biology Core

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A Role for Phosphodiesterase 3B in Acquisition of Brown Fat Characteristics by White Adipose Tissue in Male Mice.
Guirguis E, Hockman S, Chung YW, Ahmad F, Gavrilova O, Raghavachari N, Yang Y, Niu G, Chen X, Yu ZX, Liu S, Degerman E, Manganiello V.
Endocrinology. 2013 Sep ;154(9):3152-67.
[Text Abstract on PubMed]

BAF complexes facilitate decatenation of DNA by topoisomerase IIα.
Dykhuizen EC, Hargreaves DC, Miller EL, Cui K, Korshunov A, Kool M, Pfister S, Cho YJ, Zhao K, Crabtree GR.
Nature. 2013 May 30;497(7451):624-7.
[Text Abstract on PubMed]

Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation.
Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE.
Blood. 2013 May 30;121(22):4575-85.
[Text Abstract on PubMed]

Circulating Blood Endothelial Nitric Oxide Synthase Contributes to the Regulation of Systemic Blood Pressure and Nitrite Homeostasis.
Wood KC, Cortese-Krott MM, Kovacic JC, Noguchi A, Liu VB, Wang X, Raghavachari N, Boehm M, Kato GJ, Kelm M, Gladwin MT.
Arterioscler Thromb Vasc Biol. 2013 May 23.
[Text Abstract on PubMed]

Defective telomere elongation and hematopoiesis from telomerase-mutant aplastic anemia iPSCs.
Winkler T, Hong SG, Decker JE, Morgan MJ, Wu C, Hughes WM 5th, Yang Y, Wangsa D, Padilla-Nash HM, Ried T, Young NS, Dunbar CE, Calado RT.
J Clin Invest. 2013 May 1;123(5):1952-63.
[Text Abstract on PubMed]

Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia.
Wang E, Kawaoka S, Yu M, Shi J, Ni T, Yang W, Zhu J, Roeder RG, Vakoc CR.
Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3901-6.
[Text Abstract on PubMed]

BACH2 represses effector programs to stabilize T(reg)-mediated immune homeostasis.
Roychoudhuri R, Hirahara K, Mousavi K, Clever D, Klebanoff CA, Bonelli M, Sciumè G, Zare H, Vahedi G, Dema B, Yu Z, Liu H, Takahashi H, Rao M, Muranski P, Crompton JG, Punkosdy G, Bedognetti D, Wang E, Hoffmann V, Rivera J, Marincola FM, Nakamura A, Sartorelli V, Kanno Y, Gattinoni L, Muto A, Igarashi K, O'Shea JJ, Restifo NP.
Nature. 2013 Jun 27;498(7455):506-10.
[Text Abstract on PubMed]

Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing.
Xu B, Zhi N, Hu G, Wan Z, Zheng X, Liu X, Wong S, Kajigaya S, Zhao K, Mao Q, Young NS.
Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10264-9.
[Text Abstract on PubMed]

miR-222 contributes to sex-dimorphic cardiac eNOS expression via ets-1.
Evangelista AM, Deschamps AM, Liu D, Raghavachari N, Murphy E.
Physiol Genomics. 2013 Jun 17;45(12):493-8.
[Text Abstract on PubMed]

Gene expression signatures of coronary heart disease.
Joehanes R, Ying S, Huan T, Johnson AD, Raghavachari N, Wang R, Liu P, Woodhouse KA, Sen SK, Tanriverdi K, Courchesne P, Freedman JE, O'Donnell CJ, Levy D, Munson PJ.
Arterioscler Thromb Vasc Biol. 2013 Jun ;33(6):1418-26.
[Text Abstract on PubMed]

A systems biology framework identifies molecular underpinnings of coronary heart disease.
Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, Ying S, Munson PJ, Raghavachari N, Wang R, Liu P, Courchesne P, Hwang SJ, Assimes TL, McPherson R, Samani NJ, Schunkert H, null null, Meng Q, Suver C, O'Donnell CJ, Derry J, Yang X, Levy D.
Arterioscler Thromb Vasc Biol. 2013 Jun ;33(6):1427-34.
[Text Abstract on PubMed]

PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum.
Jiang L, Mu J, Zhang Q, Ni T, Srinivasan P, Rayavara K, Yang W, Turner L, Lavstsen T, Theander TG, Peng W, Wei G, Jing Q, Wakabayashi Y, Bansal A, Luo Y, Ribeiro JM, Scherf A, Aravind L, Zhu J, Zhao K, Miller LH.
Nature. 2013 Jul 11;499(7457):223-7.
[Text Abstract on PubMed]

Identification of an ABCB1 (P-glycoprotein)-positive carfilzomib-resistant myeloma subpopulation by the pluripotent stem cell fluorescent dye CDy1.
Hawley TS, Riz I, Yang W, Wakabayashi Y, Depalma L, Chang YT, Peng W, Zhu J, Hawley RG.
Am J Hematol. 2013 Jan 22.
[Text Abstract on PubMed]

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation.
Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K.
Cell Stem Cell. 2013 Feb 7;12(2):180-92.
[Text Abstract on PubMed]

The Cytokines IL-21 and GM-CSF Have Opposing Regulatory Roles in the Apoptosis of Conventional Dendritic Cells.
Wan CK, Oh J, Li P, West EE, Wong EA, Andraski AB, Spolski R, Yu ZX, He J, Kelsall BL, Leonard WJ.
Immunity. 2013 Feb 26.
[Text Abstract on PubMed]

Human papillomavirus type 58 genome variations and RNA expression in cervical lesions.
Li Y, Wang X, Ni T, Wang F, Lu W, Zhu J, Xie X, Zheng ZM.
J Virol. 2013 Aug ;87(16):9313-22.
[Text Abstract on PubMed]

Expression of regulatory platelet microRNAs in patients with sickle cell disease.
Jain S, Kapetanaki MG, Raghavachari N, Woodhouse K, Yu G, Barge S, Coronnello C, Benos PV, Kato GJ, Kaminski N, Gladwin MT.
PLoS One. 2013 01 ;8(4):e60932.
[Text Abstract on PubMed]

Dynamic regulation of epigenomic landscapes during hematopoiesis.
Abraham BJ, Cui K, Tang Q, Zhao K.
BMC Genomics. 2013 01 ;14:193.
[Text Abstract on PubMed]

c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells.
Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green DR, Tessarollo L, Casellas R, Zhao K, Levens D.
Cell. 2012 Sep 28;151(1):68-79.
[Text Abstract on PubMed]

BATF-JUN is critical for IRF4-mediated transcription in T cells.
Li P, Spolski R, Liao W, Wang L, Murphy TL, Murphy KM, Leonard WJ.
Nature. 2012 Oct 25;490(7421):543-6.
[Text Abstract on PubMed]

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.
Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.
Proc. Natl. Acad. Sci. U.S.A. 2012 Nov 26.
[Text Abstract on PubMed]

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.
Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K.
Cell Res. 2012 Mar;22(3):490-503.
[Text Abstract on PubMed]

Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.
Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM.
Development. 2012 Mar;139(6):1164-74.
[Text Abstract on PubMed]

Nuclear miRNA regulates the mitochondrial genome in the heart.
Das S, Ferlito M, Kent OA, Fox-Talbot K, Wang R, Liu D, Raghavachari N, Yang Y, Wheelan SJ, Murphy E, Steenbergen C.
Circ. Res. 2012 Jun 8;110(12):1596-603.
[Text Abstract on PubMed]

MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia.
Vickers KC, Shoucri BM, Levin MG, Wu H, Pearson DS, Osei-Hwedieh D, Collins FS, Remaley AT, Sethupathy P.
Hepatology. 2012 Jul 6.
[Text Abstract on PubMed]

Two forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway.
Ahmad SM, Tansey TR, Busser BW, Nolte MT, Jeffries N, Gisselbrecht SS, Rusan NM, Michelson AM.
Dev. Cell. 2012 Jul 17;23(1):97-111.
[Text Abstract on PubMed]

Gene expression analysis of whole blood, peripheral blood mononuclear cells, and lymphoblastoid cell lines from the Framingham Heart Study.
Joehanes R, Johnson AD, Barb JJ, Raghavachari N, Liu P, Woodhouse KA, O'Donnell CJ, Munson PJ, Levy D.
Physiol. Genomics. 2012 Jan 18;44(1):59-75.
[Text Abstract on PubMed]

A novel molecular signature for elevated tricuspid regurgitation velocity in sickle cell disease.
Desai AA, Zhou T, Ahmad H, Zhang W, Mu W, Trevino S, Wade MS, Raghavachari N, Kato GJ, Peters-Lawrence MH, Thiruvoipati T, Turner K, Artz N, Huang Y, Patel AR, Yuan JX, Gordeuk VR, Lang RM, Garcia JG, Machado RF.
Am. J. Respir. Crit. Care Med. 2012 Aug 15;186(4):359-68.
[Text Abstract on PubMed]

Critical Role of STAT5 transcription factor tetramerization for cytokine responses and normal immune function.
Lin JX, Li P, Liu D, Jin HT, He J, Ata Ur Rasheed M, Rochman Y, Wang L, Cui K, Liu C, Kelsall BL, Ahmed R, Leonard WJ.
Immunity. 2012 Apr 20;36(4):586-99.
[Text Abstract on PubMed]

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
Raghavachari N, Barb J, Yang Y, Liu P, Woodhouse K, Levy D, O'Donnell CJ, Munson PJ, Kato GJ.
BMC Med Genomics. 2012;5:28.
[Text Abstract on PubMed]

Expression of miRNAs and their cooperative regulation of the pathophysiology in traumatic brain injury.
Hu Z, Yu D, Almeida-Suhett C, Tu K, Marini AM, Eiden L, Braga MF, Zhu J, Li Z.
PLoS ONE. 2012;7(6):e39357.
[Text Abstract on PubMed]

Genome-wide mapping of nucleosomes in yeast using paired-end sequencing.
Cole HA, Howard BH, Clark DJ.
Meth. Enzymol. 2012;513:145-68.
[Text Abstract on PubMed]

Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.
Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U.
PLoS Genet. 2011;7(1):e1001274.
[Text Abstract on PubMed]

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum.
López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K, Su XZ.
BMC Genomics. 2011;12:587.
[Text Abstract on PubMed]

The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe.
Ni T, Tu K, Wang Z, Song S, Wu H, Xie B, Scott KC, Grewal SI, Gao Y, Zhu J.
PLoS ONE. 2010;5(12):e15271.
[Text Abstract on PubMed]

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