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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
- Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R
(2016) N Engl J Med 374: 135-45 - Proteogenomic characterization of human colon and rectal cancer.
Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC
(2014) Nature 513: 382-7 - Increased methylation variation in epigenetic domains across cancer types.
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP
(2011) Nat Genet 43: 768-75 - 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 - lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer.
Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Cancer Genome Atlas Research Network, Xie W, Yang D
(2018) Cancer Cell 33: 706-720.e9 - N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso.
Yoon HG, Chan DW, Reynolds AB, Qin J, Wong J
(2003) Mol Cell 12: 723-34 - Sequencing and functional analysis of the SNRPN promoter: in vitro methylation abolishes promoter activity.
Huq AH, Sutcliffe JS, Nakao M, Shen Y, Gibbs RA, Beaudet AL
(1997) Genome Res 7: 642-8 - High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.
Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB
(2009) Genome Res 19: 1593-605 - 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 - 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 - Low frequency of p57KIP2 mutation in Beckwith-Wiedemann syndrome.
Lee MP, DeBaun M, Randhawa G, Reichard BA, Elledge SJ, Feinberg AP
(1997) Am J Hum Genet 61: 304-9 - 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 - DNA hypermethylation regulates the expression of members of the Mu-class glutathione S-transferases and glutathione peroxidases in Barrett's adenocarcinoma.
Peng DF, Razvi M, Chen H, Washington K, Roessner A, Schneider-Stock R, El-Rifai W
(2009) Gut 58: 5-15 - NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5'-d(GpC) motif.
Dooley PA, Zhang M, Korbel GA, Nechev LV, Harris CM, Stone MP, Harris TM
(2003) J Am Chem Soc 125: 62-72 - Detection of an interchain carbinolamine cross-link formed in a CpG sequence by the acrolein DNA adduct gamma-OH-1,N( 2)-propano-2'-deoxyguanosine.
Kim HY, Voehler M, Harris TM, Stone MP
(2002) J Am Chem Soc 124: 9324-5 - DNA interchain cross-links formed by acrolein and crotonaldehyde.
Kozekov ID, Nechev LV, Moseley MS, Harris CM, Rizzo CJ, Stone MP, Harris TM
(2003) J Am Chem Soc 125: 50-61 - Stereospecific formation of the (R)-gamma-hydroxytrimethylene interstrand N2-dG:N2-dG cross-link arising from the gamma-OH-1,N2-propano-2'-deoxyguanosine adduct in the 5'-CpG-3' DNA sequence.
Huang H, Kim HY, Kozekov ID, Cho YJ, Wang H, Kozekova A, Harris TM, Rizzo CJ, Stone MP
(2009) J Am Chem Soc 131: 8416-24 - Spectroscopic characterization of interstrand carbinolamine cross-links formed in the 5'-CpG-3' sequence by the acrolein-derived gamma-OH-1,N2-propano-2'-deoxyguanosine DNA adduct.
Cho YJ, Kim HY, Huang H, Slutsky A, Minko IG, Wang H, Nechev LV, Kozekov ID, Kozekova A, Tamura P, Jacob J, Voehler M, Harris TM, Lloyd RS, Rizzo CJ, Stone MP
(2005) J Am Chem Soc 127: 17686-96 - Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes.
Jiang C, Han L, Su B, Li WH, Zhao Z
(2007) Mol Biol Evol 24: 1991-2000 - CpG island density and its correlations with genomic features in mammalian genomes.
Han L, Su B, Li WH, Zhao Z
(2008) Genome Biol 9: R79 - 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 - Cationic lipid:bacterial DNA complexes elicit adaptive cellular immunity in murine intraperitoneal tumor models.
Lanuti M, Rudginsky S, Force SD, Lambright ES, Siders WM, Chang MY, Amin KM, Kaiser LR, Scheule RK, Albelda SM
(2000) Cancer Res 60: 2955-63 - The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides.
Daniel JM, Spring CM, Crawford HC, Reynolds AB, Baig A
(2002) Nucleic Acids Res 30: 2911-9 - CpG island methylator phenotype associates with low-degree chromosomal abnormalities in colorectal cancer.
Cheng YW, Pincas H, Bacolod MD, Schemmann G, Giardina SF, Huang J, Barral S, Idrees K, Khan SA, Zeng Z, Rosenberg S, Notterman DA, Ott J, Paty P, Barany F
(2008) Clin Cancer Res 14: 6005-13 - Aberrantly methylated CDKN2A, MGMT, and MLH1 in colon polyps and in fecal DNA from patients with colorectal polyps.
Petko Z, Ghiassi M, Shuber A, Gorham J, Smalley W, Washington MK, Schultenover S, Gautam S, Markowitz SD, Grady WM
(2005) Clin Cancer Res 11: 1203-9 - 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 - Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach.
Jiang W, Jia P, Hutchinson KE, Johnson DB, Sosman JA, Zhao Z
(2015) Oncotarget 6: 2496-508 - Hypermethylation of metallothionein-3 CpG island in gastric carcinoma.
Deng D, El-Rifai W, Ji J, Zhu B, Trampont P, Li J, Smith MF, Powel SM
(2003) Carcinogenesis 24: 25-9 - CpG DNA induces a class II transactivator-independent increase in class II MHC by stabilizing class II MHC mRNA in B lymphocytes.
Kuchtey J, Pennini M, Pai RK, Harding CV
(2003) J Immunol 171: 2320-5 - STAT4 and T-bet are required for the plasticity of IFN-γ expression across Th2 ontogeny and influence changes in Ifng promoter DNA methylation.
Williams CL, Schilling MM, Cho SH, Lee K, Wei M, Aditi , Boothby M
(2013) J Immunol 191: 678-87 - Enhancement of dendritic cell antigen cross-presentation by CpG DNA involves type I IFN and stabilization of class I MHC mRNA.
Kuchtey J, Chefalo PJ, Gray RC, Ramachandra L, Harding CV
(2005) J Immunol 175: 2244-51 - Modeling DNA methylation dynamics with approaches from phylogenetics.
Capra JA, Kostka D
(2014) Bioinformatics 30: i408-14 - CpG island methylation in Schistosoma- and non-Schistosoma-associated bladder cancer.
Gutiérrez MI, Siraj AK, Khaled H, Koon N, El-Rifai W, Bhatia K
(2004) Mod Pathol 17: 1268-74 - DNA methylation profiling in Barrett's esophagus and esophageal adenocarcinoma reveals unique methylation signatures and molecular subclasses.
Kaz AM, Wong CJ, Luo Y, Virgin JB, Washington MK, Willis JE, Leidner RS, Chak A, Grady WM
(2011) Epigenetics 6: 1403-12 - Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes.
Su Z, Han L, Zhao Z
(2011) Epigenetics 6: 134-40 - Genome-wide DNA methylation in neonates exposed to maternal depression, anxiety, or SSRI medication during pregnancy.
Non AL, Binder AM, Kubzansky LD, Michels KB
(2014) Epigenetics 9: 964-72 - Helicobacter pylori and its secreted immunomodulator VacA protect against anaphylaxis in experimental models of food allergy.
Kyburz A, Urban S, Altobelli A, Floess S, Huehn J, Cover TL, Müller A
(2017) Clin Exp Allergy 47: 1331-1341 - CpG methylation at the USF-binding site mediates cell-specific transcription of human ascorbate transporter SVCT2 exon 1a.
Qiao H, May JM
(2011) Biochem J 440: 73-84 - DNA methyltransferase 3a and mitogen-activated protein kinase signaling regulate the expression of fibroblast growth factor-inducible 14 (Fn14) during denervation-induced skeletal muscle atrophy.
Tajrishi MM, Shin J, Hetman M, Kumar A
(2014) J Biol Chem 289: 19985-99 - CpG-B ODNs potently induce low levels of IFN-alphabeta and induce IFN-alphabeta-dependent MHC-I cross-presentation in DCs as effectively as CpG-A and CpG-C ODNs.
Gray RC, Kuchtey J, Harding CV
(2007) J Leukoc Biol 81: 1075-85
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