Publications

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2020
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWing Yiu, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Van Lehmann K-, Li Y, Liu EMinwei, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang C-Z, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, Lopez-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JSkou, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 ;578(7793):102-111.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 ;11(1):736.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JSkou, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, S Sahinalp C, Valencia A, Reimand J, Stuart JM, Raphael BJ. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 ;11(1):729.
2019
Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EAlice, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 ;20(1):209.
Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers. Nat Commun. 2019 ;10(1):5679.
2017
Zhang Y, Ng PKwok-Shing, Kucherlapati M, Chen F, Liu Y, Tsang YHuen, De Velasco G, Jeong KJin, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CSimon, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 ;31(6):820-832.e3.
Allen CE, Laetsch TW, Mody R, Irwin MS, Lim MS, Adamson PC, Seibel NL, D Parsons W, Y Cho J, Janeway K. Target and Agent Prioritization for the Children's Oncology Group-National Cancer Institute Pediatric MATCH Trial. J Natl Cancer Inst. 2017 ;109(5).
2016
McCullough LB, Slashinski MJ, McGuire AL, Street RL, Eng CM, Gibbs RA, D Parsons W, Plon SE. Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors. Pediatr Blood Cancer. 2016 ;63(3):511-5.
2015
Mayle R, Campbell IM, Beck CR, Yu Y, Wilson M, Shaw CA, Bjergbaek L, Lupski JR, Ira G. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015 ;349(6249):742-7.
Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs RA, Wheeler DA, Plon SE. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med. 2015 ;17(10):831-5.
2014
Yang JY, Dunker A, Liu JS, Qin X, Arabnia HR, Yang W, Niemierko A, Chen Z, Luo Z, Wang L, Liu Y, Xu D, Deng Y, Tong W, Yang M. Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics. 2014 ;15 Suppl 17:I1.
Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014 ;5:5274.
Parikh N, Hilsenbeck S, Creighton CJ, Dayaram T, Shuck R, Shinbrot E, Xi L, Gibbs RA, Wheeler DA, Donehower LA. Effects of TP53 mutational status on gene expression patterns across 10 human cancer types. J Pathol. 2014 ;232(5):522-33.
Shinbrot E, Henninger EE, Weinhold N, Covington KR, A Göksenin Y, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 2014 ;24(11):1740-50.
Wang L, Wheeler DA. Genomic sequencing for cancer diagnosis and therapy. Annu Rev Med. 2014 ;65:33-48.
2013
Niu T, Smith DL, Yang Z, Gao S, Yin T, Jiang Z-H, You M, Gibbs RA, Petrosino JF, Hu M. Bioactivity and bioavailability of ginsenosides are dependent on the glycosidase activities of the A/J mouse intestinal microbiome defined by pyrosequencing. Pharm Res. 2013 ;30(3):836-46.
Weinstein JN, Collisson EA, Mills GB, Shaw KRMills, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 ;45(10):1113-20.
Wheeler DA, Wang L. From human genome to cancer genome: the first decade. Genome Res. 2013 ;23(7):1054-62.
Khurana E, Fu Y, Colonna V, Mu XJasmine, Kang HMin, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs RA, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny DM, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 ;342(6154):1235587.
2012
He J, Cui L, Zeng Y, Wang G, Zhou P, Yang Y, Ji L, Zhao Y, Chen J, Wang Z, Shi T, Zhang P, Chen R, Li X. REGγ is associated with multiple oncogenic pathways in human cancers. BMC Cancer. 2012 ;12:75.
2011
Plon SE, Wheeler DA, Strong LC, Tomlinson GE, Pirics M, Meng Q, Cheung HC, Begin PR, Muzny DM, Lewis L, Biegel JA, Gibbs RA. Identification of genetic susceptibility to childhood cancer through analysis of genes in parallel. Cancer Genet. 2011 ;204(1):19-25.
2009
Voidonikolas G, Kreml SS, Chen C, Fisher WE, F Brunicardi C, Gibbs RA, Gingras M-C. Basic principles and technologies for deciphering the genetic map of cancer. World J Surg. 2009 ;33(4):615-29.
2007
Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao M-S, Twomey D, Verhaak RGW, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007 ;450(7171):893-8.
2002
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LDW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, L Johnson S, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, W Kent J, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, W McCombie R, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang S-P, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 ;420(6915):520-62.