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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
- Functional impact of global rare copy number variation in autism spectrum disorders.
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C
(2010) Nature 466: 368-72 - Somatic mutations affect key pathways in lung adenocarcinoma.
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK
(2008) Nature 455: 1069-75 - Comprehensive molecular profiling of lung adenocarcinoma.
Cancer Genome Atlas Research Network
(2014) Nature 511: 543-50 - Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.
Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, Game RM, Rudd DS, Zurawiecki D, McDougle CJ, Davis LK, Miller J, Posey DJ, Michaels S, Kolevzon A, Silverman JM, Bernier R, Levy SE, Schultz RT, Dawson G, Owley T, McMahon WM, Wassink TH, Sweeney JA, Nurnberger JI, Coon H, Sutcliffe JS, Minshew NJ, Grant SF, Bucan M, Cook EH, Buxbaum JD, Devlin B, Schellenberg GD, Hakonarson H
(2009) Nature 459: 569-73 - Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.
Veeriah S, Taylor BS, Meng S, Fang F, Yilmaz E, Vivanco I, Janakiraman M, Schultz N, Hanrahan AJ, Pao W, Ladanyi M, Sander C, Heguy A, Holland EC, Paty PB, Mischel PS, Liau L, Cloughesy TF, Mellinghoff IK, Solit DB, Chan TA
(2010) Nat Genet 42: 77-82 - A copy number variation morbidity map of developmental delay.
Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif BC, Shaffer LG, Eichler EE
(2011) Nat Genet 43: 838-46 - 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 - Strong association of de novo copy number mutations with autism.
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M
(2007) Science 316: 445-9 - Genetics. Insights into the pathogenesis of autism.
Sutcliffe JS
(2008) Science 321: 208-9 - Increased epidermal growth factor receptor gene copy number is associated with poor prognosis in head and neck squamous cell carcinomas.
Chung CH, Ely K, McGavran L, Varella-Garcia M, Parker J, Parker N, Jarrett C, Carter J, Murphy BA, Netterville J, Burkey BB, Sinard R, Cmelak A, Levy S, Yarbrough WG, Slebos RJ, Hirsch FR
(2006) J Clin Oncol 24: 4170-6 - Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans.
Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR
(2016) Cell Metab 24: 91-103 - Developmental control of gene copy number by repression of replication initiation and fork progression.
Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL
(2012) Genome Res 22: 64-75 - The E6-Ap ubiquitin-protein ligase (UBE3A) gene is localized within a narrowed Angelman syndrome critical region.
Sutcliffe JS, Jiang YH, Galijaard RJ, Matsuura T, Fang P, Kubota T, Christian SL, Bressler J, Cattanach B, Ledbetter DH, Beaudet AL
(1997) Genome Res 7: 368-77 - Genetic differences between adenocarcinomas arising in Barrett's esophagus and gastric mucosa.
El-Rifai W, Frierson HF, Moskaluk CA, Harper JC, Petroni GR, Bissonette EA, Jones DR, Knuutila S, Powell SM
(2001) Gastroenterology 121: 592-8 - ErbB3 downregulation enhances luminal breast tumor response to antiestrogens.
Morrison MM, Hutchinson K, Williams MM, Stanford JC, Balko JM, Young C, Kuba MG, Sánchez V, Williams AJ, Hicks DJ, Arteaga CL, Prat A, Perou CM, Earp HS, Massarweh S, Cook RS
(2013) J Clin Invest 123: 4329-43 - 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 - Smoking-related genomic signatures in non-small cell lung cancer.
Massion PP, Zou Y, Chen H, Jiang A, Coulson P, Amos CI, Wu X, Wistuba I, Wei Q, Shyr Y, Spitz MR
(2008) Am J Respir Crit Care Med 178: 1164-72 - Copy number polymorphisms and anticancer pharmacogenomics.
Gamazon ER, Huang RS, Dolan ME, Cox NJ
(2011) Genome Biol 12: R46 - Chromosomal breakpoints and changes in DNA copy number in refractory acute myeloid leukemia.
El-Rifai W, Elonen E, Larramendy M, Ruutu T, Knuutila S
(1997) Leukemia 11: 958-63 - Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.
Fernandez-Cuesta L, Peifer M, Lu X, Sun R, Ozretić L, Seidal D, Zander T, Leenders F, George J, Müller C, Dahmen I, Pinther B, Bosco G, Konrad K, Altmüller J, Nürnberg P, Achter V, Lang U, Schneider PM, Bogus M, Soltermann A, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Ansén S, Stoelben E, Wright GM, Russell P, Wainer Z, Solomon B, Field JK, Hyde R, Davies MP, Heukamp LC, Petersen I, Perner S, Lovly C, Cappuzzo F, Travis WD, Wolf J, Vingron M, Brambilla E, Haas SA, Buettner R, Thomas RK
(2014) Nat Commun 5: 3518 - Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.
McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H
(2016) Proc Natl Acad Sci U S A 113: E6409-E6417 - Targets of gene amplification and overexpression at 17q in gastric cancer.
Varis A, Wolf M, Monni O, Vakkari ML, Kokkola A, Moskaluk C, Frierson H, Powell SM, Knuutila S, Kallioniemi A, El-Rifai W
(2002) Cancer Res 62: 2625-9 - Oncogenic protein MTBP interacts with MYC to promote tumorigenesis.
Grieb BC, Gramling MW, Arrate MP, Chen X, Beauparlant SL, Haines DS, Xiao H, Eischen CM
(2014) Cancer Res 74: 3591-602 - Significance of p63 amplification and overexpression in lung cancer development and prognosis.
Massion PP, Taflan PM, Jamshedur Rahman SM, Yildiz P, Shyr Y, Edgerton ME, Westfall MD, Roberts JR, Pietenpol JA, Carbone DP, Gonzalez AL
(2003) Cancer Res 63: 7113-21 - Darpp-32: a novel antiapoptotic gene in upper gastrointestinal carcinomas.
Belkhiri A, Zaika A, Pidkovka N, Knuutila S, Moskaluk C, El-Rifai W
(2005) Cancer Res 65: 6583-92 - Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway.
Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polikoff D, Jain AN, Pinkel D, Albertson DG, Jablons DM, Gray JW
(2002) Cancer Res 62: 3636-40 - DNA sequence copy number changes in gastrointestinal stromal tumors: tumor progression and prognostic significance.
El-Rifai W, Sarlomo-Rikala M, Andersson LC, Knuutila S, Miettinen M
(2000) Cancer Res 60: 3899-903 - Mitochondrial DNA copy number threshold in mtDNA depletion myopathy.
Durham SE, Bonilla E, Samuels DC, DiMauro S, Chinnery PF
(2005) Neurology 65: 453-5 - Reduction of Ptf1a gene dosage causes pancreatic hypoplasia and diabetes in mice.
Fukuda A, Kawaguchi Y, Furuyama K, Kodama S, Horiguchi M, Kuhara T, Kawaguchi M, Terao M, Doi R, Wright CV, Hoshino M, Chiba T, Uemoto S
(2008) Diabetes 57: 2421-31 - Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors.
Balak MN, Gong Y, Riely GJ, Somwar R, Li AR, Zakowski MF, Chiang A, Yang G, Ouerfelli O, Kris MG, Ladanyi M, Miller VA, Pao W
(2006) Clin Cancer Res 12: 6494-501 - Development of an integrated genomic classifier for a novel agent in colorectal cancer: approach to individualized therapy in early development.
Pitts TM, Tan AC, Kulikowski GN, Tentler JJ, Brown AM, Flanigan SA, Leong S, Coldren CD, Hirsch FR, Varella-Garcia M, Korch C, Eckhardt SG
(2010) Clin Cancer Res 16: 3193-204 - Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431).
Moore SR, Persons DL, Sosman JA, Bobadilla D, Bedell V, Smith DD, Wolman SR, Tuthill RJ, Moon J, Sondak VK, Slovak ML
(2008) Clin Cancer Res 14: 2927-35 - Population-specific GSTM1 copy number variation.
Huang RS, Chen P, Wisel S, Duan S, Zhang W, Cook EH, Das S, Cox NJ, Dolan ME
(2009) Hum Mol Genet 18: 366-72 - DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway.
Ocak S, Yamashita H, Udyavar AR, Miller AN, Gonzalez AL, Zou Y, Jiang A, Yi Y, Shyr Y, Estrada L, Quaranta V, Massion PP
(2010) Oncogene 29: 6331-42 - An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors.
Chitale D, Gong Y, Taylor BS, Broderick S, Brennan C, Somwar R, Golas B, Wang L, Motoi N, Szoke J, Reinersman JM, Major J, Sander C, Seshan VE, Zakowski MF, Rusch V, Pao W, Gerald W, Ladanyi M
(2009) Oncogene 28: 2773-83 - Neuropathology of degenerative cell death in Caenorhabditis elegans.
Hall DH, Gu G, García-Añoveros J, Gong L, Chalfie M, Driscoll M
(1997) J Neurosci 17: 1033-45 - A transcription factor network controls cell migration and fate decisions in the developing zebrafish pineal complex.
Khuansuwan S, Clanton JA, Dean BJ, Patton JG, Gamse JT
(2016) Development 143: 2641-50 - Mutation of an upstream cleavage site in the BMP4 prodomain leads to tissue-specific loss of activity.
Goldman DC, Hackenmiller R, Nakayama T, Sopory S, Wong C, Kulessa H, Christian JL
(2006) Development 133: 1933-42 - ROCK-nmMyoII, Notch and gene-dosage link epithelial morphogenesis with cell fate in the pancreatic endocrine-progenitor niche.
Bankaitis ED, Bechard ME, Gu G, Magnuson MA, Wright CVE
(2018) Development 145: - Coamplified and overexpressed genes at ERBB2 locus in gastric cancer.
Varis A, Zaika A, Puolakkainen P, Nagy B, Madrigal I, Kokkola A, Väyrynen A, Kärkkäinen P, Moskaluk C, El-Rifai W, Knuutila S
(2004) Int J Cancer 109: 548-53
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