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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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- Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R
(2014) Nature 512: 445-8 - Generalized lacZ expression with the ROSA26 Cre reporter strain.
Soriano P
(1999) Nat Genet 21: 70-1 - Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.
Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y
(2008) Cell 133: 116-27 - Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
GTEx Consortium
(2015) Science 348: 648-60 - 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 - Identification of functional elements and regulatory circuits by Drosophila modENCODE.
modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M
(2010) Science 330: 1787-97 - Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment.
Bumgarner SL, Neuert G, Voight BF, Symbor-Nagrabska A, Grisafi P, van Oudenaarden A, Fink GR
(2012) Mol Cell 45: 470-82 - De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.
Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E
(2013) Genome Res 23: 1601-14 - Mining diverse small RNA species in the deep transcriptome.
Vickers KC, Roteta LA, Hucheson-Dilks H, Han L, Guo Y
(2015) Trends Biochem Sci 40: 4-7 - Genetic labeling does not detect epithelial-to-mesenchymal transition of cholangiocytes in liver fibrosis in mice.
Scholten D, Osterreicher CH, Scholten A, Iwaisako K, Gu G, Brenner DA, Kisseleva T
(2010) Gastroenterology 139: 987-98 - Ectopic pancreas formation in Hes1 -knockout mice reveals plasticity of endodermal progenitors of the gut, bile duct, and pancreas.
Fukuda A, Kawaguchi Y, Furuyama K, Kodama S, Horiguchi M, Kuhara T, Koizumi M, Boyer DF, Fujimoto K, Doi R, Kageyama R, Wright CV, Chiba T
(2006) J Clin Invest 116: 1484-93 - Association of in vitro fertilization with Beckwith-Wiedemann syndrome and epigenetic alterations of LIT1 and H19.
DeBaun MR, Niemitz EL, Feinberg AP
(2003) Am J Hum Genet 72: 156-60 - Epigenetic alterations of H19 and LIT1 distinguish patients with Beckwith-Wiedemann syndrome with cancer and birth defects.
DeBaun MR, Niemitz EL, McNeil DE, Brandenburg SA, Lee MP, Feinberg AP
(2002) Am J Hum Genet 70: 604-11 - Mouse/human sequence divergence in a region with a paternal-specific methylation imprint at the human H19 locus.
Jinno Y, Sengoku K, Nakao M, Tamate K, Miyamoto T, Matsuzaka T, Sutcliffe JS, Anan T, Takuma N, Nishiwaki K, Ikeda Y, Ishimaru T, Ishikawa M, Niikawa N
(1996) Hum Mol Genet 5: 1155-61 - Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation.
Osipovich AB, Gangula R, Vianna PG, Magnuson MA
(2016) Development 143: 4595-4607 - Melanocyte-lineage expression of Cre recombinase using Mitf regulatory elements.
Alizadeh A, Fitch KR, Niswender CM, McKnight GS, Barsh GS
(2008) Pigment Cell Melanoma Res 21: 63-9 - Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells.
Collier SP, Collins PL, Williams CL, Boothby MR, Aune TM
(2012) J Immunol 189: 2084-8 - Diverse functions of distal regulatory elements at the IFNG locus.
Collins PL, Henderson MA, Aune TM
(2012) J Immunol 188: 1726-33 - Functional characterization of a testis-specific DNA binding activity at the H19/Igf2 imprinting control region.
Bowman AB, Levorse JM, Ingram RS, Tilghman SM
(2003) Mol Cell Biol 23: 8345-51 - EWS/FLI-1 induces rapid onset of myeloid/erythroid leukemia in mice.
Torchia EC, Boyd K, Rehg JE, Qu C, Baker SJ
(2007) Mol Cell Biol 27: 7918-34 - Defining the optimal parameters for hairpin-based knockdown constructs.
Li L, Lin X, Khvorova A, Fesik SW, Shen Y
(2007) RNA 13: 1765-74 - Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice.
Serup P, Gustavsen C, Klein T, Potter LA, Lin R, Mullapudi N, Wandzioch E, Hines A, Davis A, Bruun C, Engberg N, Petersen DR, Peterslund JM, Macdonald RJ, Grapin-Botton A, Magnuson MA, Zaret KS
(2012) Dis Model Mech 5: 956-66 - Quantification of factors influencing fluorescent protein expression using RMCE to generate an allelic series in the ROSA26 locus in mice.
Chen SX, Osipovich AB, Ustione A, Potter LA, Hipkens S, Gangula R, Yuan W, Piston DW, Magnuson MA
(2011) Dis Model Mech 4: 537-47 - Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice.
Anastassiadis K, Fu J, Patsch C, Hu S, Weidlich S, Duerschke K, Buchholz F, Edenhofer F, Stewart AF
(2009) Dis Model Mech 2: 508-15 - Small RNAs have a big impact on regeneration.
Thatcher EJ, Patton JG
(2010) RNA Biol 7: 333-8 - Mechanism of down-regulation of RNA polymerase III-transcribed non-coding RNA genes in macrophages by Leishmania.
Rana T, Misra S, Mittal MK, Farrow AL, Wilson KT, Linton MF, Fazio S, Willis IM, Chaudhuri G
(2011) J Biol Chem 286: 6614-26 - Modulation of NFkappaB activity and E-cadherin by the type III transforming growth factor beta receptor regulates cell growth and motility.
Criswell TL, Arteaga CL
(2007) J Biol Chem 282: 32491-500 - Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing.
Guo Y, Vickers K, Xiong Y, Zhao S, Sheng Q, Zhang P, Zhou W, Flynn CR
(2017) BMC Genomics 18: 50 - Addition of H19 'loss of methylation testing' for Beckwith-Wiedemann syndrome (BWS) increases the diagnostic yield.
Lennerz JK, Timmerman RJ, Grange DK, DeBaun MR, Feinberg AP, Zehnbauer BA
(2010) J Mol Diagn 12: 576-88 - Advanced Intestinal Cancers often Maintain a Multi-Ancestral Architecture.
Zahm CD, Szulczewski JM, Leystra AA, Paul Olson TJ, Clipson L, Albrecht DM, Middlebrooks M, Thliveris AT, Matkowskyj KA, Washington MK, Newton MA, Eliceiri KW, Halberg RB
(2016) PLoS One 11: e0150170 - Genetic variation in the HLA region is associated with susceptibility to herpes zoster.
Crosslin DR, Carrell DS, Burt A, Kim DS, Underwood JG, Hanna DS, Comstock BA, Baldwin E, de Andrade M, Kullo IJ, Tromp G, Kuivaniemi H, Borthwick KM, McCarty CA, Peissig PL, Doheny KF, Pugh E, Kho A, Pacheco J, Hayes MG, Ritchie MD, Verma SS, Armstrong G, Stallings S, Denny JC, Carroll RJ, Crawford DC, Crane PK, Mukherjee S, Bottinger E, Li R, Keating B, Mirel DB, Carlson CS, Harley JB, Larson EB, Jarvik GP
(2015) Genes Immun 16: 1-7 - Lineage-specific adjacent IFNG and IL26 genes share a common distal enhancer element.
Collins PL, Henderson MA, Aune TM
(2012) Genes Immun 13: 481-8 - Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus.
Srinivas S, Watanabe T, Lin CS, William CM, Tanabe Y, Jessell TM, Costantini F
(2001) BMC Dev Biol 1: 4 - CM156, a sigma receptor ligand, reverses cocaine-induced place conditioning and transcriptional responses in the brain.
Xu YT, Robson MJ, Szeszel-Fedorowicz W, Patel D, Rooney R, McCurdy CR, Matsumoto RR
(2012) Pharmacol Biochem Behav 101: 174-80 - Highly-efficient, fluorescent, locus directed cre and FlpO deleter mice on a pure C57BL/6N genetic background.
Birling MC, Dierich A, Jacquot S, Hérault Y, Pavlovic G
(2012) Genesis 50: 482-9 - Leishmania-induced repression of selected non-coding RNA genes containing B-box element at their promoters in alternatively polarized M2 macrophages.
Farrow AL, Rana T, Mittal MK, Misra S, Chaudhuri G
(2011) Mol Cell Biochem 350: 47-57 - LIT1 and H19 methylation defects in isolated hemihyperplasia.
Martin RA, Grange DK, Zehnbauer B, Debaun MR
(2005) Am J Med Genet A 134A: 129-31 - Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes.
Chu VT, Weber T, Graf R, Sommermann T, Petsch K, Sack U, Volchkov P, Rajewsky K, Kühn R
(2016) BMC Biotechnol 16: 4
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