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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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- Inferring ancient divergences requires genes with strong phylogenetic signals.
Salichos L, Rokas A
(2013) Nature 497: 327-31 - Patterns and rates of exonic de novo mutations in autism spectrum disorders.
Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ
(2012) Nature 485: 242-5 - The impact of rare variation on gene expression across tissues.
Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB
(2017) Nature 550: 239-243 - A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes.
Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, Mann JR, Dahl HH, Chinnery PF
(2008) Nat Genet 40: 249-54 - The K-Cl cotransporter KCC3 is mutant in a severe peripheral neuropathy associated with agenesis of the corpus callosum.
Howard HC, Mount DB, Rochefort D, Byun N, Dupré N, Lu J, Fan X, Song L, Rivière JB, Prévost C, Horst J, Simonati A, Lemcke B, Welch R, England R, Zhan FQ, Mercado A, Siesser WB, George AL, McDonald MP, Bouchard JP, Mathieu J, Delpire E, Rouleau GA
(2002) Nat Genet 32: 384-92 - Reassessing evidence for a postnatal mitochondrial genetic bottleneck.
Samuels DC, Wonnapinij P, Cree LM, Chinnery PF
(2010) Nat Genet 42: 471-2; author reply 472-3 - Duplication of Atxn1l suppresses SCA1 neuropathology by decreasing incorporation of polyglutamine-expanded ataxin-1 into native complexes.
Bowman AB, Lam YC, Jafar-Nejad P, Chen HK, Richman R, Samaco RC, Fryer JD, Kahle JJ, Orr HT, Zoghbi HY
(2007) Nat Genet 39: 373-9 - Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair.
Day FR, Ruth KS, Thompson DJ, Lunetta KL, Pervjakova N, Chasman DI, Stolk L, Finucane HK, Sulem P, Bulik-Sullivan B, Esko T, Johnson AD, Elks CE, Franceschini N, He C, Altmaier E, Brody JA, Franke LL, Huffman JE, Keller MF, McArdle PF, Nutile T, Porcu E, Robino A, Rose LM, Schick UM, Smith JA, Teumer A, Traglia M, Vuckovic D, Yao J, Zhao W, Albrecht E, Amin N, Corre T, Hottenga JJ, Mangino M, Smith AV, Tanaka T, Abecasis G, Andrulis IL, Anton-Culver H, Antoniou AC, Arndt V, Arnold AM, Barbieri C, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bernstein L, Bielinski SJ, Blomqvist C, Boerwinkle E, Bogdanova NV, Bojesen SE, Bolla MK, Borresen-Dale AL, Boutin TS, Brauch H, Brenner H, Brüning T, Burwinkel B, Campbell A, Campbell H, Chanock SJ, Chapman JR, Chen YI, Chenevix-Trench G, Couch FJ, Coviello AD, Cox A, Czene K, Darabi H, De Vivo I, Demerath EW, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Dunning AM, Eicher JD, Fasching PA, Faul JD, Figueroa J, Flesch-Janys D, Gandin I, Garcia ME, García-Closas M, Giles GG, Girotto GG, Goldberg MS, González-Neira A, Goodarzi MO, Grove ML, Gudbjartsson DF, Guénel P, Guo X, Haiman CA, Hall P, Hamann U, Henderson BE, Hocking LJ, Hofman A, Homuth G, Hooning MJ, Hopper JL, Hu FB, Huang J, Humphreys K, Hunter DJ, Jakubowska A, Jones SE, Kabisch M, Karasik D, Knight JA, Kolcic I, Kooperberg C, Kosma VM, Kriebel J, Kristensen V, Lambrechts D, Langenberg C, Li J, Li X, Lindström S, Liu Y, Luan J, Lubinski J, Mägi R, Mannermaa A, Manz J, Margolin S, Marten J, Martin NG, Masciullo C, Meindl A, Michailidou K, Mihailov E, Milani L, Milne RL, Müller-Nurasyid M, Nalls M, Neale BM, Nevanlinna H, Neven P, Newman AB, Nordestgaard BG, Olson JE, Padmanabhan S, Peterlongo P, Peters U, Petersmann A, Peto J, Pharoah PDP, Pirastu NN, Pirie A, Pistis G, Polasek O, Porteous D, Psaty BM, Pylkäs K, Radice P, Raffel LJ, Rivadeneira F, Rudan I, Rudolph A, Ruggiero D, Sala CF, Sanna S, Sawyer EJ, Schlessinger D, Schmidt MK, Schmidt F, Schmutzler RK, Schoemaker MJ, Scott RA, Seynaeve CM, Simard J, Sorice R, Southey MC, Stöckl D, Strauch K, Swerdlow A, Taylor KD, Thorsteinsdottir U, Toland AE, Tomlinson I, Truong T, Tryggvadottir L, Turner ST, Vozzi D, Wang Q, Wellons M, Willemsen G, Wilson JF, Winqvist R, Wolffenbuttel BBHR, Wright AF, Yannoukakos D, Zemunik T, Zheng W, Zygmunt M, Bergmann S, Boomsma DI, Buring JE, Ferrucci L, Montgomery GW, Gudnason V, Spector TD, van Duijn CM, Alizadeh BZ, Ciullo M, Crisponi L, Easton DF, Gasparini PP, Gieger C, Harris TB, Hayward C, Kardia SLR, Kraft P, McKnight B, Metspalu A, Morrison AC, Reiner AP, Ridker PM, Rotter JI, Toniolo D, Uitterlinden AG, Ulivi S, Völzke H, Wareham NJ, Weir DR, Yerges-Armstrong LM, PRACTICAL consortium, kConFab Investigators, AOCS Investigators, Generation Scotland, EPIC-InterAct Consortium, LifeLines Cohort Study, Price AL, Stefansson K, Visser JA, Ong KK, Chang-Claude J, Murabito JM, Perry JRB, Murray A
(2015) Nat Genet 47: 1294-1303 - PIQ-ing into chromatin architecture.
Rieck S, Wright C
(2014) Nat Biotechnol 32: 138-40 - Mus81-Eme1 are essential components of a Holliday junction resolvase.
Boddy MN, Gaillard PHL, McDonald WH, Shanahan P, Yates JR, Russell P
(2001) Cell 107: 537-48 - Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5.
de Bruin RA, McDonald WH, Kalashnikova TI, Yates J, Wittenberg C
(2004) Cell 117: 887-98 - A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.
Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A
(2013) Cell 155: 70-80 - A genetic atlas of human admixture history.
Hellenthal G, Busby GBJ, Band G, Wilson JF, Capelli C, Falush D, Myers S
(2014) Science 343: 747-751 - Systematic identification of signal-activated stochastic gene regulation.
Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A
(2013) Science 339: 584-7 - 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 - Using gene expression noise to understand gene regulation.
Munsky B, Neuert G, van Oudenaarden A
(2012) Science 336: 183-7 - Aberrant cannabinoid signaling impairs oviductal transport of embryos.
Wang H, Guo Y, Wang D, Kingsley PJ, Marnett LJ, Das SK, DuBois RN, Dey SK
(2004) Nat Med 10: 1074-80 - EML4-ALK: honing in on a new target in non-small-cell lung cancer.
Horn L, Pao W
(2009) J Clin Oncol 27: 4232-5 - XIAP monoubiquitylates Groucho/TLE to promote canonical Wnt signaling.
Hanson AJ, Wallace HA, Freeman TJ, Beauchamp RD, Lee LA, Lee E
(2012) Mol Cell 45: 619-28 - Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback.
de Bruin RA, Kalashnikova TI, Chahwan C, McDonald WH, Wohlschlegel J, Yates J, Russell P, Wittenberg C
(2006) Mol Cell 23: 483-96 - HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal.
Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM, Bezsonova I, Eichman BF, Cimprich KA
(2015) Mol Cell 58: 1090-100 - 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 - Initial sequence and comparative analysis of the cat genome.
Pontius JU, Mullikin JC, Smith DR, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program, O'Brien SJ
(2007) Genome Res 17: 1675-89 - A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF
(2008) Genome Res 18: 1073-83 - Murine double minute 2: p53-independent roads lead to genome instability or death.
Bouska A, Eischen CM
(2009) Trends Biochem Sci 34: 279-86 - Mitochondrial DNA mutations in human colonic crypt stem cells.
Taylor RW, Barron MJ, Borthwick GM, Gospel A, Chinnery PF, Samuels DC, Taylor GA, Plusa SM, Needham SJ, Greaves LC, Kirkwood TB, Turnbull DM
(2003) J Clin Invest 112: 1351-60 - Multiple determinants controlling activation of yeast replication origins late in S phase.
Friedman KL, Diller JD, Ferguson BM, Nyland SV, Brewer BJ, Fangman WL
(1996) Genes Dev 10: 1595-607 - Neurogenin 3 is essential for the proper specification of gastric enteroendocrine cells and the maintenance of gastric epithelial cell identity.
Lee CS, Perreault N, Brestelli JE, Kaestner KH
(2002) Genes Dev 16: 1488-97 - Chk1 is an essential kinase that is regulated by Atr and required for the G(2)/M DNA damage checkpoint.
Liu Q, Guntuku S, Cui XS, Matsuoka S, Cortez D, Tamai K, Luo G, Carattini-Rivera S, DeMayo F, Bradley A, Donehower LA, Elledge SJ
(2000) Genes Dev 14: 1448-59 - HIF-2alpha regulates Oct-4: effects of hypoxia on stem cell function, embryonic development, and tumor growth.
Covello KL, Kehler J, Yu H, Gordan JD, Arsham AM, Hu CJ, Labosky PA, Simon MC, Keith B
(2006) Genes Dev 20: 557-70 - Pathogenic mitochondrial DNA mutations are common in the general population.
Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF
(2008) Am J Hum Genet 83: 254-60 - Shwachman-Diamond syndrome with exocrine pancreatic dysfunction and bone marrow failure maps to the centromeric region of chromosome 7.
Goobie S, Popovic M, Morrison J, Ellis L, Ginzberg H, Boocock GR, Ehtesham N, Bétard C, Brewer CG, Roslin NM, Hudson TJ, Morgan K, Fujiwara TM, Durie PR, Rommens JM
(2001) Am J Hum Genet 68: 1048-54 - Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age.
Elson JL, Samuels DC, Turnbull DM, Chinnery PF
(2001) Am J Hum Genet 68: 802-6 - Rational inferences about departures from Hardy-Weinberg equilibrium.
Wittke-Thompson JK, Pluzhnikov A, Cox NJ
(2005) Am J Hum Genet 76: 967-86 - Genetic architecture of microRNA expression: implications for the transcriptome and complex traits.
Gamazon ER, Ziliak D, Im HK, LaCroix B, Park DS, Cox NJ, Huang RS
(2012) Am J Hum Genet 90: 1046-63 - An exponential combination procedure for set-based association tests in sequencing studies.
Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DL
(2012) Am J Hum Genet 91: 977-86 - Structural architecture of SNP effects on complex traits.
Gamazon ER, Cox NJ, Davis LK
(2014) Am J Hum Genet 95: 477-89 - Relaxed replication of mtDNA: A model with implications for the expression of disease.
Chinnery PF, Samuels DC
(1999) Am J Hum Genet 64: 1158-65 - Allelic heterogeneity at the serotonin transporter locus (SLC6A4) confers susceptibility to autism and rigid-compulsive behaviors.
Sutcliffe JS, Delahanty RJ, Prasad HC, McCauley JL, Han Q, Jiang L, Li C, Folstein SE, Blakely RD
(2005) Am J Hum Genet 77: 265-79 - Scan-statistic approach identifies clusters of rare disease variants in LRP2, a gene linked and associated with autism spectrum disorders, in three datasets.
Ionita-Laza I, Makarov V, ARRA Autism Sequencing Consortium, Buxbaum JD
(2012) Am J Hum Genet 90: 1002-13
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