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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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- Comprehensive molecular portraits of human breast tumours.
Cancer Genome Atlas Network
(2012) Nature 490: 61-70 - Active medulloblastoma enhancers reveal subgroup-specific cellular origins.
Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DT, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA
(2016) Nature 530: 57-62 - Oncogenic Signaling Pathways in The Cancer Genome Atlas.
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N
(2018) Cell 173: 321-337.e10 - Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G, Cancer Genome Atlas Research Network
(2018) Cell 173: 305-320.e10 - Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.
Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M
(2012) Cell 150: 1107-20 - The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma.
Rosenwald A, Wright G, Wiestner A, Chan WC, Connors JM, Campo E, Gascoyne RD, Grogan TM, Muller-Hermelink HK, Smeland EB, Chiorazzi M, Giltnane JM, Hurt EM, Zhao H, Averett L, Henrickson S, Yang L, Powell J, Wilson WH, Jaffe ES, Simon R, Klausner RD, Montserrat E, Bosch F, Greiner TC, Weisenburger DD, Sanger WG, Dave BJ, Lynch JC, Vose J, Armitage JO, Fisher RI, Miller TP, LeBlanc M, Ott G, Kvaloy S, Holte H, Delabie J, Staudt LM
(2003) Cancer Cell 3: 185-97 - Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance.
Balko JM, Cook RS, Vaught DB, Kuba MG, Miller TW, Bhola NE, Sanders ME, Granja-Ingram NM, Smith JJ, Meszoely IM, Salter J, Dowsett M, Stemke-Hale K, González-Angulo AM, Mills GB, Pinto JA, Gómez HL, Arteaga CL
(2012) Nat Med 18: 1052-9 - Translating genomic information into clinical medicine: lung cancer as a paradigm.
Levy MA, Lovly CM, Pao W
(2012) Genome Res 22: 2101-8 - Characterization of HPV and host genome interactions in primary head and neck cancers.
Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R, Cancer Genome Atlas Network
(2014) Proc Natl Acad Sci U S A 111: 15544-9 - Comparative analysis of the GNAQ, GNA11, SF3B1, and EIF1AX driver mutations in melanoma and across the cancer spectrum.
Johnson DB, Roszik J, Shoushtari AN, Eroglu Z, Balko JM, Higham C, Puzanov I, Patel SP, Sosman JA, Woodman SE
(2016) Pigment Cell Melanoma Res 29: 470-3 - Survivin depletion preferentially reduces the survival of activated K-Ras-transformed cells.
Sarthy AV, Morgan-Lappe SE, Zakula D, Vernetti L, Schurdak M, Packer JC, Anderson MG, Shirasawa S, Sasazuki T, Fesik SW
(2007) Mol Cancer Ther 6: 269-76 - Aberrant promoter methylation of multiple genes in malignant ovarian tumors and in ovarian tumors with low malignant potential.
Wiley A, Katsaros D, Chen H, Rigault de la Longrais IA, Beeghly A, Puopolo M, Singal R, Zhang Y, Amoako A, Zelterman D, Yu H
(2006) Cancer 107: 299-308 - Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer.
Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z
(2014) RNA 20: 1356-68 - RAMP1 is a direct NKX3.1 target gene up-regulated in prostate cancer that promotes tumorigenesis.
Logan M, Anderson PD, Saab ST, Hameed O, Abdulkadir SA
(2013) Am J Pathol 183: 951-63 - Location-specific epigenetic regulation of the metallothionein 3 gene in esophageal adenocarcinomas.
Peng D, Hu TL, Jiang A, Washington MK, Moskaluk CA, Schneider-Stock R, El-Rifai W
(2011) PLoS One 6: e22009 - Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.
Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y
(2013) PLoS One 8: e71462 - Personalized pathway enrichment map of putative cancer genes from next generation sequencing data.
Jia P, Zhao Z
(2012) PLoS One 7: e37595 - Modulators of prostate cancer cell proliferation and viability identified by short-hairpin RNA library screening.
Dahlman KB, Parker JS, Shamu T, Hieronymus H, Chapinski C, Carver B, Chang K, Hannon GJ, Sawyers CL
(2012) PLoS One 7: e34414 - Spectrum of oncogenic driver mutations in lung adenocarcinomas from East Asian never smokers.
Li C, Fang R, Sun Y, Han X, Li F, Gao B, Iafrate AJ, Liu XY, Pao W, Chen H, Ji H
(2011) PLoS One 6: e28204 - CpG island methylation of genes accumulates during the adenoma progression step of the multistep pathogenesis of colorectal cancer.
Kim YH, Petko Z, Dzieciatkowski S, Lin L, Ghiassi M, Stain S, Chapman WC, Washington MK, Willis J, Markowitz SD, Grady WM
(2006) Genes Chromosomes Cancer 45: 781-9
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