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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, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J
(2015) N Engl J Med 372: 2481-98 - 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 - Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW
(2018) Cell 173: 291-304.e6 - Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas.
Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca, Cancer Genome Atlas Research Network
(2017) Cell 171: 950-965.e28 - Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.
Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP
(2017) Cell 171: 540-556.e25 - Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.
Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH, TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG
(2016) Cell 164: 550-63 - Altered expression of genes involved in inflammation and apoptosis in frontal cortex in major depression.
Shelton RC, Claiborne J, Sidoryk-Wegrzynowicz M, Reddy R, Aschner M, Lewis DA, Mirnics K
(2011) Mol Psychiatry 16: 751-62 - Improving blood pressure control through provider education, provider alerts, and patient education: a cluster randomized trial.
Roumie CL, Elasy TA, Greevy R, Griffin MR, Liu X, Stone WJ, Wallston KA, Dittus RS, Alvarez V, Cobb J, Speroff T
(2006) Ann Intern Med 145: 165-75 - Differences in DNA methylation signatures reveal multiple pathways of progression from adenoma to colorectal cancer.
Luo Y, Wong CJ, Kaz AM, Dzieciatkowski S, Carter KT, Morris SM, Wang J, Willis JE, Makar KW, Ulrich CM, Lutterbaugh JD, Shrubsole MJ, Zheng W, Markowitz SD, Grady WM
(2014) Gastroenterology 147: 418-29.e8 - Chronic rhinosinusitis in elderly patients is associated with an exaggerated neutrophilic proinflammatory response to pathogenic bacteria.
Morse JC, Li P, Ely KA, Shilts MH, Wannemuehler TJ, Huang LC, Sheng Q, Chowdhury NI, Chandra RK, Das SR, Turner JH
(2019) J Allergy Clin Immunol 143: 990-1002.e6 - Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures.
Sivley RM, Dou X, Meiler J, Bush WS, Capra JA
(2018) Am J Hum Genet 102: 415-426 - Prognostic gene expression signature associated with two molecularly distinct subtypes of colorectal cancer.
Oh SC, Park YY, Park ES, Lim JY, Kim SM, Kim SB, Kim J, Kim SC, Chu IS, Smith JJ, Beauchamp RD, Yeatman TJ, Kopetz S, Lee JS
(2012) Gut 61: 1291-8 - Meta-analysis of clear cell renal cell carcinoma gene expression defines a variant subgroup and identifies gender influences on tumor biology.
Brannon AR, Haake SM, Hacker KE, Pruthi RS, Wallen EM, Nielsen ME, Rathmell WK
(2012) Eur Urol 61: 258-68 - Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets.
Balko JM, Giltnane JM, Wang K, Schwarz LJ, Young CD, Cook RS, Owens P, Sanders ME, Kuba MG, Sánchez V, Kurupi R, Moore PD, Pinto JA, Doimi FD, Gómez H, Horiuchi D, Goga A, Lehmann BD, Bauer JA, Pietenpol JA, Ross JS, Palmer GA, Yelensky R, Cronin M, Miller VA, Stephens PJ, Arteaga CL
(2014) Cancer Discov 4: 232-45 - Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans.
Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM, Horvitz HR, Sternberg PW, Ringstad N
(2011) Proc Natl Acad Sci U S A 108: 254-9 - Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae.
Rinker DC, Pitts RJ, Zhou X, Suh E, Rokas A, Zwiebel LJ
(2013) Proc Natl Acad Sci U S A 110: 8260-5 - Genomic landscape of human allele-specific DNA methylation.
Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, Smith AD
(2012) Proc Natl Acad Sci U S A 109: 7332-7 - Antipsychotic drugs elevate mRNA levels of presynaptic proteins in the frontal cortex of the rat.
MacDonald ML, Eaton ME, Dudman JT, Konradi C
(2005) Biol Psychiatry 57: 1041-51 - Molecular evidence for increased expression of genes related to immune and chaperone function in the prefrontal cortex in schizophrenia.
Arion D, Unger T, Lewis DA, Levitt P, Mirnics K
(2007) Biol Psychiatry 62: 711-21 - PTEN loss contributes to erlotinib resistance in EGFR-mutant lung cancer by activation of Akt and EGFR.
Sos ML, Koker M, Weir BA, Heynck S, Rabinovsky R, Zander T, Seeger JM, Weiss J, Fischer F, Frommolt P, Michel K, Peifer M, Mermel C, Girard L, Peyton M, Gazdar AF, Minna JD, Garraway LA, Kashkar H, Pao W, Meyerson M, Thomas RK
(2009) Cancer Res 69: 3256-61 - Epithelial cell organization suppresses Myc function by attenuating Myc expression.
Simpson DR, Yu M, Zheng S, Zhao Z, Muthuswamy SK, Tansey WP
(2011) Cancer Res 71: 3822-30 - Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma.
Slebos RJ, Yi Y, Ely K, Carter J, Evjen A, Zhang X, Shyr Y, Murphy BM, Cmelak AJ, Burkey BB, Netterville JL, Levy S, Yarbrough WG, Chung CH
(2006) Clin Cancer Res 12: 701-9 - Molecular study of malignant gliomas treated with epidermal growth factor receptor inhibitors: tissue analysis from North American Brain Tumor Consortium Trials 01-03 and 00-01.
Lassman AB, Rossi MR, Raizer JJ, Razier JR, Abrey LE, Lieberman FS, Grefe CN, Lamborn K, Pao W, Shih AH, Kuhn JG, Wilson R, Nowak NJ, Cowell JK, DeAngelis LM, Wen P, Gilbert MR, Chang S, Yung WA, Prados M, Holland EC
(2005) Clin Cancer Res 11: 7841-50 - Molecular alterations in primary prostate cancer after androgen ablation therapy.
Best CJ, Gillespie JW, Yi Y, Chandramouli GV, Perlmutter MA, Gathright Y, Erickson HS, Georgevich L, Tangrea MA, Duray PH, González S, Velasco A, Linehan WM, Matusik RJ, Price DK, Figg WD, Emmert-Buck MR, Chuaqui RF
(2005) Clin Cancer Res 11: 6823-34 - Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes.
Masuda H, Baggerly KA, Wang Y, Zhang Y, Gonzalez-Angulo AM, Meric-Bernstam F, Valero V, Lehmann BD, Pietenpol JA, Hortobagyi GN, Symmans WF, Ueno NT
(2013) Clin Cancer Res 19: 5533-40 - Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.
Girard N, Shen R, Guo T, Zakowski MF, Heguy A, Riely GJ, Huang J, Lau C, Lash AE, Ladanyi M, Viale A, Antonescu CR, Travis WD, Rusch VW, Kris MG, Pao W
(2009) Clin Cancer Res 15: 6790-9 - Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression.
Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM
(2004) Clin Cancer Res 10: 981-7 - Identification of gene expression signatures in autoimmune disease without the influence of familial resemblance.
Liu Z, Maas K, Aune TM
(2006) Hum Mol Genet 15: 501-9 - 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 - Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling.
Friedman DB, Wang SE, Whitwell CW, Caprioli RM, Arteaga CL
(2007) Mol Cell Proteomics 6: 150-69 - Dietary patterns are associated with lower incidence of type 2 diabetes in middle-aged women: the Shanghai Women's Health Study.
Villegas R, Yang G, Gao YT, Cai H, Li H, Zheng W, Shu XO
(2010) Int J Epidemiol 39: 889-99 - Development of 2dTCA for the detection of irregular, transient BOLD activity.
Morgan VL, Li Y, Abou-Khalil B, Gore JC
(2008) Hum Brain Mapp 29: 57-69 - Functional connectivity-based parcellation of amygdala using self-organized mapping: a data driven approach.
Mishra A, Rogers BP, Chen LM, Gore JC
(2014) Hum Brain Mapp 35: 1247-60 - Detection of irregular, transient fMRI activity in normal controls using 2dTCA: comparison to event-related analysis using known timing.
Morgan VL, Gore JC
(2009) Hum Brain Mapp 30: 3393-405 - Validation of a prognostic multi-gene signature in high-risk neuroblastoma using the high throughput digital NanoString nCounter™ system.
Stricker TP, Morales La Madrid A, Chlenski A, Guerrero L, Salwen HR, Gosiengfiao Y, Perlman EJ, Furman W, Bahrami A, Shohet JM, Zage PE, Hicks MJ, Shimada H, Suganuma R, Park JR, So S, London WB, Pytel P, Maclean KH, Cohn SL
(2014) Mol Oncol 8: 669-78 - Association between adherence to the Mediterranean diet and oxidative stress.
Dai J, Jones DP, Goldberg J, Ziegler TR, Bostick RM, Wilson PW, Manatunga AK, Shallenberger L, Jones L, Vaccarino V
(2008) Am J Clin Nutr 88: 1364-70 - Multiphasic modification of intrinsic functional connectivity of the rat brain during increasing levels of propofol.
Liu X, Pillay S, Li R, Vizuete JA, Pechman KR, Schmainda KM, Hudetz AG
(2013) Neuroimage 83: 581-92 - Resting functional MRI with temporal clustering analysis for localization of epileptic activity without EEG.
Morgan VL, Price RR, Arain A, Modur P, Abou-Khalil B
(2004) Neuroimage 21: 473-81 - Co-activation based parcellation of the human frontal pole.
Ray KL, Zald DH, Bludau S, Riedel MC, Bzdok D, Yanes J, Falcone KE, Amunts K, Fox PT, Eickhoff SB, Laird AR
(2015) Neuroimage 123: 200-11 - Patient-initiated device removal in intensive care units: a national prevalence study.
Mion LC, Minnick AF, Leipzig R, Catrambone CD, Johnson ME
(2007) Crit Care Med 35: 2714-20; quiz 2725
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