Publications

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2016
Eckstein OS, Wang L, Punia JN, Kornblau SM, Andreeff M, Wheeler DA, Goodell MA, Rau RE. Mixed-phenotype acute leukemia (MPAL) exhibits frequent mutations in DNMT3A and activated signaling genes. Exp Hematol. 2016 ;44(8):740-4.
Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny DM, Kang H, Lee J, Tamboli P, Reuter V, Shelley CSimon, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, A Hakimi A, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 ;14(10):2476-89.
Fan Y, Xi L, Hughes DST, Zhang J, Zhang J, P Futreal A, Wheeler DA, Wang W. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biol. 2016 ;17(1):178.
Becnel LB, Pereira S, Drummond JA, Gingras M-C, Covington KR, Kovar CL, Doddapaneni H, Hu J, Muzny DM, McGuire AL, Wheeler DA, Gibbs RA. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data. 2016 ;3:160010.
Potter SL, Venkatramani R, Wenderfer S, Graham BH, Vasudevan SA, Sher A, Wu H, Wheeler DA, Yang Y, Eng CM, Gibbs RA, Roy A, Plon SE, D Parsons W. Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia. Pediatr Blood Cancer. 2016 ;.
Davis CF, Ritter DI, Wheeler DA, Wang H, Ding Y, Dugan SP, Bainbridge MN, Muzny DM, Rao PH, Man T-K, Plon SE, Gibbs RA, Lau CC. SV-STAT accurately detects structural variation via alignment to reference-based assemblies. Source Code Biol Med. 2016 ;11:8.
Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JNath, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, Hendershot JM, Blenau W, Predel R, Johnston PR, Ioannidis P, Waterhouse RM, Nauen R, Schorn C, Ott M-C, Maiwald F, J Johnston S, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisén D, Crumière AJean Johan, Refki PNagui, Santos MEmilia, Sghaier E, Viala S, Khila A, Ahn S-J, Childers C, Lee C-Y, Lin H, Hughes DST, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler DA, Panfilio KA, Jentzsch IMVargas, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MAE, Jones JW, Mittapalli O, Zhao C, Zhou J-J, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JMC, Gibbs RA, Werren JH, Palli SR, Schal C, Richards S. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun. 2016 ;7:10165.
2015
English AC, Salerno WJ, Hampton OA, Gonzaga-Jauregui C, Ambreth S, Ritter DI, Beck CR, Davis CF, Dahdouli M, Ma S, Carroll A, Veeraraghavan N, Bruestle J, Drees B, Hastie A, Lam ET, White S, Mishra P, Wang M, Han Y, Zhang F, Stankiewicz P, Wheeler DA, Reid JG, Muzny DM, Rogers J, Sabo A, Worley KC, Lupski JR, Boerwinkle E, Gibbs RA. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics. 2015 ;16:286.
Peters TL, Kumar V, Polikepahad S, Lin FY, Sarabia SF, Liang Y, Wang W-L, Lazar AJ, Doddapaneni H, Chao H, Muzny DM, Wheeler DA, M Okcu F, Plon SE, M Hicks J, López-Terrada D, D Parsons W, Roy A. BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children. Mod Pathol. 2015 ;28(4):575-86.
Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier A-S, Patch A-M, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FCastro, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DTW, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 ;6:10001.
Mayle A, Yang L, Rodriguez B, Zhou T, Chang E, Curry CV, Challen GA, Li W, Wheeler DA, Rebel VI, Goodell MA. Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation. Blood. 2015 ;125(4):629-38.
Wang L, Ni X, Covington KR, Yang BY, Shiu J, Zhang X, Xi L, Meng Q, Langridge T, Drummond J, Donehower LA, Doddapaneni H, Muzny DM, Gibbs RA, Wheeler DA, Duvic M. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat Genet. 2015 ;47(12):1426-34.
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.
Smith MA, Hampton OA, C Reynolds P, Kang MH, Maris JM, Gorlick R, E Kolb A, Lock R, Carol H, Keir ST, Wu J, Kurmasheva RT, Wheeler DA, Houghton PJ. Initial testing (stage 1) of the PARP inhibitor BMN 673 by the pediatric preclinical testing program: PALB2 mutation predicts exceptional in vivo response to BMN 673. Pediatr Blood Cancer. 2015 ;62(1):91-8.
Zhao C, Escalante LNavarro, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM, Wheeler DA, Andersson MN, Bao R, Batterton M, Behura SK, Blankenburg KP, Caragea D, Carolan JC, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen CJP, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani SN, Johnson AJ, Kalra D, Korchina V, Kovar CL, Lara F, Lee SL, Liu X, Löfstedt C, Mata R, Mathew T, Muzny DM, Nagar S, Nazareth LV, Okwuonu G, Ongeri F, Perales L, Peterson BF, Pu L-L, Robertson HM, Schemerhorn BJ, Scherer SE, Shreve JT, Simmons DN, Subramanyam S, Thornton RL, Xue K, Weissenberger GM, Williams CE, Worley KC, Zhu D, Zhu Y, Harris MO, Shukle RH, Werren JH, Zdobnov EM, Chen M-S, Brown SJ, Stuart JJ, Richards S. A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. Curr Biol. 2015 ;25(5):613-20.
Walz AL, Ooms A, Gadd S, Gerhard DS, Smith MA, Auvil JMGuidry, Auvil JMGuidry, Meerzaman D, Chen Q-R, Hsu CHao, Yan C, Nguyen C, Hu Y, Bowlby R, Brooks D, Ma Y, Mungall AJ, Moore RA, Schein J, Marra MA, Huff V, Dome JS, Chi Y-Y, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Jafari N, Ross N, Gastier-Foster JM, Perlman EJ. Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. Cancer Cell. 2015 ;27(2):286-97.
Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, M Hicks J, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, D Parsons W. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun. 2015 ;6:8891.
Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni H, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen I-M, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Auvil JMGuidry, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015 ;6:6604.
2014
Parfenov M, Pedamallu CSekhar, 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, D Hayes N, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 ;111(43):15544-9.
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.
Takahashi Y, Pickering CR, Gelbard A, Drummond JA, Wheeler DA, Kupferman ME, Myers JN, Hanna EY. Genomic Characterization of Sinonasal Undifferentiated Carcinoma. J Neurol Surg B. 2014 ;75:A084.
Wang L, Wheeler DA. Genomic sequencing for cancer diagnosis and therapy. Annu Rev Med. 2014 ;65:33-48.
Pickering CR, Zhou JH, J Lee J, Drummond JA, S Peng A, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014 ;20(24):6582-92.