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Creative Data Solutions (CDS) is a Vanderbilt Shared Resource and has extensive experience in providing effective and robust solutions to challenges pertaining to research data using modern informatics and bioinformatics approaches.
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Publications
- NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein.
Tooley CE, Petkowski JJ, Muratore-Schroeder TL, Balsbaugh JL, Shabanowitz J, Sabat M, Minor W, Hunt DF, Macara IG
(2010) Nature 466: 1125-8 - The landscape of recombination in African Americans.
Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Cupples LA, Deming SL, Diver WR, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, Hu JJ, Ingles SA, Isaacs W, John EM, Kao WH, Keating B, Kittles RA, Kolonel LN, Larkin E, Le Marchand L, McNeill LH, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, Nyante S, Papanicolaou GJ, Press MF, Psaty BM, Reiner AP, Rich SS, Rodriguez-Gil JL, Rotter JI, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Thun MJ, Tucker MA, Wang Z, Wiencke JK, Witte JS, Wrensch M, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Zhu X, Redline S, Hirschhorn JN, Henderson BE, Taylor HA, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich D, Myers SR
(2011) Nature 476: 170-5 - Cellular protein synthesis and inhibition of cell division are independent of butyrate-induced histone hyperacetylation.
Rubenstein P, Sealy L, Marshall S, Chalkley R
(1979) Nature 280: 692-3 - Nucleosome organization in the Drosophila genome.
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF
(2008) Nature 453: 358-62 - Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis.
McDonald OG, Li X, Saunders T, Tryggvadottir R, Mentch SJ, Warmoes MO, Word AE, Carrer A, Salz TH, Natsume S, Stauffer KM, Makohon-Moore A, Zhong Y, Wu H, Wellen KE, Locasale JW, Iacobuzio-Donahue CA, Feinberg AP
(2017) Nat Genet 49: 367-376 - Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.
Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T, Menon R, Koker M, Dahmen I, Müller C, Di Cerbo V, Schildhaus HU, Altmüller J, Baessmann I, Becker C, de Wilde B, Vandesompele J, Böhm D, Ansén S, Gabler F, Wilkening I, Heynck S, Heuckmann JM, Lu X, Carter SL, Cibulskis K, Banerji S, Getz G, Park KS, Rauh D, Grütter C, Fischer M, Pasqualucci L, Wright G, Wainer Z, Russell P, Petersen I, Chen Y, Stoelben E, Ludwig C, Schnabel P, Hoffmann H, Muley T, Brockmann M, Engel-Riedel W, Muscarella LA, Fazio VM, Groen H, Timens W, Sietsma H, Thunnissen E, Smit E, Heideman DA, Snijders PJ, Cappuzzo F, Ligorio C, Damiani S, Field J, Solberg S, Brustugun OT, Lund-Iversen M, Sänger J, Clement JH, Soltermann A, Moch H, Weder W, Solomon B, Soria JC, Validire P, Besse B, Brambilla E, Brambilla C, Lantuejoul S, Lorimier P, Schneider PM, Hallek M, Pao W, Meyerson M, Sage J, Shendure J, Schneider R, Büttner R, Wolf J, Nürnberg P, Perner S, Heukamp LC, Brindle PK, Haas S, Thomas RK
(2012) Nat Genet 44: 1104-10 - Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms.
Rusu V, Hoch E, Mercader JM, Tenen DE, Gymrek M, Hartigan CR, DeRan M, von Grotthuss M, Fontanillas P, Spooner A, Guzman G, Deik AA, Pierce KA, Dennis C, Clish CB, Carr SA, Wagner BK, Schenone M, Ng MCY, Chen BH, MEDIA Consortium, SIGMA T2D Consortium, Centeno-Cruz F, Zerrweck C, Orozco L, Altshuler DM, Schreiber SL, Florez JC, Jacobs SBR, Lander ES
(2017) Cell 170: 199-212.e20 - The effect of sodium butyrate on histone modification.
Sealy L, Chalkley R
(1978) Cell 14: 115-21 - The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators.
Lee D, Ezhkova E, Li B, Pattenden SG, Tansey WP, Workman JL
(2005) Cell 123: 423-36 - Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA.
Saitoh S, Chabes A, McDonald WH, Thelander L, Yates JR, Russell P
(2002) Cell 109: 563-73 - From silencing to gene expression: real-time analysis in single cells.
Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH, Spector DL
(2004) Cell 116: 683-98 - The chromosomal passenger complex is required for chromatin-induced microtubule stabilization and spindle assembly.
Sampath SC, Ohi R, Leismann O, Salic A, Pozniakovski A, Funabiki H
(2004) Cell 118: 187-202 - Shape analysis of the histone octamer in solution.
Uberbacher EC, Harp JM, Wilkinson-Singley E, Bunick GJ
(1986) Science 232: 1247-9 - Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH
(2010) Science 330: 1775-87 - Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus.
Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL
(2016) Science 351: aac6633 - Dynamic changes in histone-methylation 'marks' across the locus encoding interferon-gamma during the differentiation of T helper type 2 cells.
Chang S, Aune TM
(2007) Nat Immunol 8: 723-31 - Hdac3 is essential for the maintenance of chromatin structure and genome stability.
Bhaskara S, Knutson SK, Jiang G, Chandrasekharan MB, Wilson AJ, Zheng S, Yenamandra A, Locke K, Yuan JL, Bonine-Summers AR, Wells CE, Kaiser JF, Washington MK, Zhao Z, Wagner FF, Sun ZW, Xia F, Holson EB, Khabele D, Hiebert SW
(2010) Cancer Cell 18: 436-47 - Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming.
Tiwari N, Tiwari VK, Waldmeier L, Balwierz PJ, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G
(2013) Cancer Cell 23: 768-83 - LZAP, a putative tumor suppressor, selectively inhibits NF-kappaB.
Wang J, An H, Mayo MW, Baldwin AS, Yarbrough WG
(2007) Cancer Cell 12: 239-51 - Mutant p53 prolongs NF-κB activation and promotes chronic inflammation and inflammation-associated colorectal cancer.
Cooks T, Pateras IS, Tarcic O, Solomon H, Schetter AJ, Wilder S, Lozano G, Pikarsky E, Forshew T, Rosenfeld N, Rozenfeld N, Harpaz N, Itzkowitz S, Harris CC, Rotter V, Gorgoulis VG, Oren M
(2013) Cancer Cell 23: 634-46 - Relating form and function of EF-hand calcium binding proteins.
Chazin WJ
(2011) Acc Chem Res 44: 171-9 - Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3.
Ezhkova E, Tansey WP
(2004) Mol Cell 13: 435-42 - Crystallographic identification and functional characterization of phospholipids as ligands for the orphan nuclear receptor steroidogenic factor-1.
Li Y, Choi M, Cavey G, Daugherty J, Suino K, Kovach A, Bingham NC, Kliewer SA, Xu HE
(2005) Mol Cell 17: 491-502 - Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.
Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M
(2013) Mol Cell 52: 314-24 - NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis.
Brown JD, Lin CY, Duan Q, Griffin G, Federation A, Paranal RM, Bair S, Newton G, Lichtman A, Kung A, Yang T, Wang H, Luscinskas FW, Croce K, Bradner JE, Plutzky J
(2014) Mol Cell 56: 219-231 - N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso.
Yoon HG, Chan DW, Reynolds AB, Qin J, Wong J
(2003) Mol Cell 12: 723-34 - Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.
Bhaskara S, Chyla BJ, Amann JM, Knutson SK, Cortez D, Sun ZW, Hiebert SW
(2008) Mol Cell 30: 61-72 - Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.
Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, Bottino R, Powers AC, Chang HY, Kim SK
(2016) Cell Metab 23: 909-20 - Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, Lahn BT
(2014) Genome Res 24: 267-80 - Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.
Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ
(2014) Genome Res 24: 241-50 - Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography.
Harp JM, Timm DE, Bunick GJ
(1998) Acta Crystallogr D Biol Crystallogr 54: 622-8 - Asymmetries in the nucleosome core particle at 2.5 A resolution.
Harp JM, Hanson BL, Timm DE, Bunick GJ
(2000) Acta Crystallogr D Biol Crystallogr 56: 1513-34 - In and out: histone variant exchange in chromatin.
Jin J, Cai Y, Li B, Conaway RC, Workman JL, Conaway JW, Kusch T
(2005) Trends Biochem Sci 30: 680-7 - An inner centromere protein that stimulates the microtubule depolymerizing activity of a KinI kinesin.
Ohi R, Coughlin ML, Lane WS, Mitchison TJ
(2003) Dev Cell 5: 309-21
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