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DAVID A WHEELER

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
DivisionMolecular & Human Genetics
AddressOne Baylor Plaza
HGSC Room - N1619.01
Houston TX 77030
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentHuman Genome Sequencing Center
    DivisionHuman Genome Sequencing Center


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Lv J, Zhang H, Wong MG, Jardine MJ, Hladunewich M, Jha V, Monaghan H, Zhao M, Barbour S, Reich H, Cattran D, Glassock R, Levin A, Wheeler D, Woodward M, Billot L, Chan TM, Liu ZH, Johnson DW, Cass A, Feehally J, Floege J, Remuzzi G, Wu Y, Agarwal R, Wang HY, Perkovic V. Effect of Oral Methylprednisolone on Clinical Outcomes in Patients With IgA Nephropathy: The TESTING Randomized Clinical Trial. JAMA. 2017 Aug 01; 318(5):432-442. PMID: 28763548.
      View in: PubMed
    2. Moss TJ, Qi Y, Xi L, Peng B, Kim TB, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF. Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. Eur Urol. 2017 Jun 07. PMID: 28601352.
      View in: PubMed
    3. Chakraborty R, Hampton OA, Abhyankar H, Zinn DJ, Grimes A, Skull B, Eckstein O, Mahmood N, Wheeler DA, Lopez-Terrada D, Peters TL, Hicks MJ, Elghetany T, Krance R, Poulikakos PI, Merad M, McClain KL, Allen CE, Parsons DW. Activating MAPK1 (ERK2) mutation in an aggressive case of disseminated juvenile xanthogranuloma. Oncotarget. 2017 Apr 29. PMID: 28512266.
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    4. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 Mar 14; 18(11):2780-2794. PMID: 28297679.
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    5. Taneja N, Zofall M, Balachandran V, Thillainadesan G, Sugiyama T, Wheeler D, Zhou M, Grewal SI. SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication. Mol Cell. 2017 Mar 08. PMID: 28318821.
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    6. Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MC, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SH, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Davì MV, Landoni L, Malpaga A, Miotto M, Whitehall VL, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras MC, Fisher WE, Dagg RA, Lau LM, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature. 2017 Mar 02; 543(7643):65-71. PMID: 28199314.
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    7. Tagal V, Wei S, Zhang W, Brekken RA, Posner BA, Peyton M, Girard L, Hwang T, Wheeler DA, Minna JD, White MA, Gazdar AF, Roth MG. SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers. Nat Commun. 2017 Jan 19; 8:14098. PMID: 28102363.
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    8. Goschzik T, Gessi M, Dreschmann V, Gebhardt U, Wang L, Yamaguchi S, Wheeler DA, Lauriola L, Lau CC, Müller HL, Pietsch T. Genomic Alterations of Adamantinomatous and Papillary Craniopharyngioma. J Neuropathol Exp Neurol. 2017 Jan 09. PMID: 28069929.
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    9. 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, Parsons DW. Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia. Pediatr Blood Cancer. 2016 Oct 17. PMID: 27748010.
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    10. Chakraborty R, Burke TM, Hampton OA, Zinn DJ, Lim KP, Abhyankar H, Scull B, Kumar V, Kakkar N, Wheeler DA, Roy A, Poulikakos PI, Merad M, McClain KL, Parsons DW, Allen CE. Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis. Blood. 2016 Oct 11. PMID: 27729324.
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    11. Lanikova L, Babosova O, Swierczek S, Wang L, Wheeler DA, Divoky V, Korinek V, Prchal JT. Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera. Blood. 2016 Nov 03; 128(18):2266-2270. PMID: 27647865.
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    12. Lin FY, Bergstrom K, Person R, Bavle A, Ballester LY, Scollon S, Raesz-Martinez R, Jea A, Birchansky S, Wheeler DA, Berg SL, Chintagumpala MM, Adesina AM, Eng C, Roy A, Plon SE, Parsons DW. Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. Cold Spring Harb Mol Case Stud. 2016 Sep; 2(5):a001057. PMID: 27626068; PMCID: PMC5002928.
    13. Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016; 7:12601. PMID: 27574101.
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    14. Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, Futreal PA, 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. PMID: 27557938; PMCID: PMC4995747.
    15. Sim AD, Wheeler D. The venom gland transcriptome of the parasitoid wasp Nasonia vitripennis highlights the importance of novel genes in venom function. BMC Genomics. 2016; 17:571. PMID: 27503142; PMCID: PMC4977848.
    16. Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 08 08; 30(2):363. PMID: 27505681.
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    17. van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SC, Wells OS, Harakalova M, Chinn IK, Alt A, Vondrova L, Hochstenbach R, van Montfrans JM, Terheggen-Lagro SW, van Lieshout S, van Roosmalen MJ, Renkens I, Duran K, Nijman IJ, Kloosterman WP, Hennekam E, Orange JS, van Hasselt PM, Wheeler DA, Palecek JJ, Lehmann AR, Oliver AW, Pearl LH, Plon SE, Murray JM, van Haaften G. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. J Clin Invest. 2016 Jul 18. PMID: 27427983.
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    18. Davis CF, Ritter DI, Wheeler DA, Wang H, Ding Y, Dugan SP, Bainbridge MN, Muzny DM, Rao PH, Man TK, 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. PMID: 27330550; PMCID: PMC4913042.
    19. 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 May 18. PMID: 27208809.
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    20. Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 May 9; 29(5):723-36. PMID: 27165744; PMCID: PMC4864952 [Available on 05/09/17].
    21. Rustagi N, Hampton OA, Li J, Xi L, Gibbs RA, Plon SE, Kimmel M, Wheeler DA. ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. BMC Bioinformatics. 2016; 17:188. PMID: 27121965; PMCID: PMC4847212.
    22. Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Trevino LR, Alonzo TA, Guidry Auvil JM, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S. Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse. Cancer Res. 2016 Apr 15; 76(8):2197-205. PMID: 26941285; PMCID: PMC4873364 [Available on 04/15/17].
    23. Chen F, Zhang Y, ?enbabao?lu 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 D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, 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, Hakimi AA, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 Mar 15; 14(10):2476-89. PMID: 26947078; PMCID: PMC4794376.
    24. Saliba J, Zabriskie R, Ghosh R, Powell BC, Hicks S, Kimmel M, Meng Q, Ritter DI, Wheeler DA, Gibbs RA, Tsai FT, Plon SE. Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs. Pharmacogenet Genomics. 2016 Feb 22. PMID: 26906009.
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    25. Becnel LB, Pereira S, Drummond JA, Gingras MC, Covington KR, Kovar CL, Doddapaneni HV, Hu J, Muzny D, McGuire AL, Wheeler DA, Gibbs RA. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data. 2016; 3:160010. PMID: 26882539; PMCID: PMC4755126.
    26. Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, 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 MC, Maiwald F, Johnston JS, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisén D, Crumière AJ, Refki PN, Santos ME, Sghaier E, Viala S, Khila A, Ahn SJ, Childers C, Lee CY, Lin H, Hughes DS, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler D, Panfilio KA, Vargas Jentzsch IM, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MA, Jones JW, Mittapalli O, Zhao C, Zhou JJ, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JM, 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. PMID: 26836814; PMCID: PMC4740739.
    27. Parsons DW, Roy A, Yang Y, Wang T, Scollon S, Bergstrom K, Kerstein RA, Gutierrez S, Petersen AK, Bavle A, Lin FY, López-Terrada DH, Monzon FA, Hicks MJ, Eldin KW, Quintanilla NM, Adesina AM, Mohila CA, Whitehead W, Jea A, Vasudevan SA, Nuchtern JG, Ramamurthy U, McGuire AL, Hilsenbeck SG, Reid JG, Muzny DM, Wheeler DA, Berg SL, Chintagumpala MM, Eng CM, Gibbs RA, Plon SE. Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol. 2016 Jan 28. PMID: 26822237.
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    28. Gingras MC, Covington KR, Chang DK, Donehower LA, Gill AJ, Ittmann MM, Creighton CJ, Johns AL, Shinbrot E, Dewal N, Fisher WE. Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation. Cell Rep. 2016 Feb 2; 14(4):907-19. PMID: 26804919.
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    29. Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, Getz G. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell. 2016 Jan 28; 164(3):538-49. PMID: 26806129; PMCID: PMC4753048 [Available on 01/28/17].
    30. Liu Y, Kheradmand F, Davis CF, Scheurer ME, Wheeler D, Tsavachidis S, Armstrong G, Simpson C, Mandal D, Kupert E, Anderson M, You M, Xiong D, Pikielny C, Schwartz AG, Bailey-Wilson J, Gaba C, De Andrade M, Yang P, Pinney SM. Focused Analysis of Exome Sequencing Data for Rare Germline Mutations in Familial and Sporadic Lung Cancer. J Thorac Oncol. 2016 Jan; 11(1):52-61. PMID: 26762739.
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    31. Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, 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 FC, 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 DT, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015; 6:10001. PMID: 26647970.
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    32. Chang EC, Liu H, West JA, Zhou X, Dakhova O, Wheeler DA, Heslop HE, Brenner MK, Dotti G. Clonal Dynamics In Vivo of Virus Integration Sites of T Cells Expressing a Safety Switch. Mol Ther. 2015 Dec 7. PMID: 26639404.
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    33. Perlman EJ, Gadd S, Arold ST, Radhakrishnan A, Gerhard DS, Jennings L, Huff V, Guidry Auvil JM, Davidsen TM, Dome JS, Meerzaman D, Hsu CH, Nguyen C, Anderson J, Ma Y, Mungall AJ, Moore RA, Marra MA, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Gastier-Foster JM, Ross N, Smith MA. MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nat Commun. 2015; 6:10013. PMID: 26635203.
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    34. Wang L, Wheeler DA, Prchal JT. Acquired uniparental disomy of chromosome 9p in hematologic malignancies. Exp Hematol. 2016 Aug; 44(8):644-52. PMID: 26646991.
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    35. Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, John Hicks M, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, Parsons DW. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun. 2015; 6:8891. PMID: 26573325.
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    36. 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 Dec; 47(12):1426-34. PMID: 26551670.
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    37. 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, 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. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2015 Nov 4. PMID: 26536169.
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    38. 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. PMID: 25886820.
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    39. 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 IM, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Guidry Auvil JM, 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. PMID: 25790293; PMCID: PMC4377644.
    40. Walz AL, Ooms A, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, 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 YY, 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 Feb 9; 27(2):286-97. PMID: 25670082; PMCID: PMC4800737.
    41. Mayle A, Yang L, Rodriguez B, Zhou T, Chang E, Curry CV, Challen GA, Li W, Wheeler D, Rebel VI, Goodell MA. Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation. Blood. 2015 Jan 22; 125(4):629-38. PMID: 25416277; PMCID: PMC4304108.
    42. Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs R, 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 Oct; 17(10):831-5. PMID: 25569436.
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    43. 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. PMID: 25409906; PMCID: PMC4467577.
    44. Totoki Y, Tatsuno K, Covington KR, Ueda H, Creighton CJ, Kato M, Tsuji S, Donehower LA, Slagle BL, Nakamura H, Yamamoto S, Shinbrot E, Hama N, Lehmkuhl M, Hosoda F, Arai Y, Walker K, Dahdouli M, Gotoh K, Nagae G, Gingras MC, Muzny DM, Ojima H, Shimada K, Midorikawa Y, Goss JA, Cotton R, Hayashi A, Shibahara J, Ishikawa S, Guiteau J, Tanaka M, Urushidate T, Ohashi S, Okada N, Doddapaneni H, Wang M, Zhu Y, Dinh H, Okusaka T, Kokudo N, Kosuge T, Takayama T, Fukayama M, Gibbs RA, Wheeler DA, Aburatani H, Shibata T. Trans-ancestry mutational landscape of hepatocellular carcinoma genomes. Nat Genet. 2014 Dec; 46(12):1267-73. PMID: 25362482.
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    45. Peters TL, Kumar V, Polikepahad S, Lin FY, Sarabia SF, Liang Y, Wang WL, Lazar AJ, Doddapaneni H, Chao H, Muzny DM, Wheeler DA, Okcu MF, Plon SE, Hicks MJ, López-Terrada D, Parsons DW, Roy A. BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children. Mod Pathol. 2015 Apr; 28(4):575-86. PMID: 25360585; PMCID: PMC4385430.
    46. 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. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15544-9. PMID: 25313082; PMCID: PMC4217452.
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    48. Smith MA, Hampton OA, Reynolds CP, Kang MH, Maris JM, Gorlick R, Kolb EA, 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 Jan; 62(1):91-8. PMID: 25263539; PMCID: PMC4456187.
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    50. Fouquerel E, Goellner EM, Yu Z, Gagné JP, Barbi de Moura M, Feinstein T, Wheeler D, Redpath P, Li J, Romero G, Migaud M, Van Houten B, Poirier GG, Sobol RW. ARTD1/PARP1 negatively regulates glycolysis by inhibiting hexokinase 1 independent of NAD+ depletion. Cell Rep. 2014 Sep 25; 8(6):1819-31. PMID: 25220464; PMCID: PMC4177344.
    51. Chakraborty R, Hampton OA, Shen X, Simko SJ, Shih A, Abhyankar H, Lim KP, Covington KR, Trevino L, Dewal N, Muzny DM, Doddapaneni H, Hu J, Wang L, Lupo PJ, Hicks MJ, Bonilla DL, Dwyer KC, Berres ML, Poulikakos PI, Merad M, McClain KL, Wheeler DA, Allen CE, Parsons DW. Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis. Blood. 2014 Nov 6; 124(19):3007-15. PMID: 25202140; PMCID: PMC4224195.
    52. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol. 2014; 15(8):443. PMID: 25160522; PMCID: PMC4180956.
    53. Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 8; 26(3):319-30. PMID: 25155756; PMCID: PMC4160352.
    54. Wang L, Yamaguchi S, Burstein MD, Terashima K, Chang K, Ng HK, Nakamura H, He Z, Doddapaneni H, Lewis L, Wang M, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adekunle A, Sun J, Qiao Y, Marth G, Muzny DM, Gibbs RA, Leal SM, Wheeler DA, Lau CC. Novel somatic and germline mutations in intracranial germ cell tumours. Nature. 2014 Jul 10; 511(7508):241-5. PMID: 24896186; PMCID: PMC4532372.
    55. Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Ortega Alves MV, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers. Clin Cancer Res. 2014 Jul 15; 20(14):3842-8. PMID: 24874835; PMCID: PMC4102633.
    56. Tretiakova MS, Bond SD, Wheeler D, Contreras A, Kocherginsky M, Kroll TG, Hale TK. Heterochromatin protein 1 expression is reduced in human thyroid malignancy. Lab Invest. 2014 Jul; 94(7):788-95. PMID: 24840329.
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    57. 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 Apr; 232(5):522-33. PMID: 24374933; PMCID: PMC4362779.
    58. Wang L, Swierczek SI, Lanikova L, Kim SJ, Hickman K, Walker K, Wang K, Drummond J, Doddapaneni H, Reid JG, Muzny DM, Gibbs RA, Wheeler DA, Prchal JT. The relationship of JAK2(V617F) and acquired UPD at chromosome 9p in polycythemia vera. Leukemia. 2014 Apr; 28(4):938-41. PMID: 24463469; PMCID: PMC4532371.
    59. Wang L, Swierczek SI, Drummond J, Hickman K, Kim SJ, Walker K, Doddapaneni H, Muzny DM, Gibbs RA, Wheeler DA, Prchal JT. Whole-exome sequencing of polycythemia vera revealed novel driver genes and somatic mutation shared by T cells and granulocytes. Leukemia. 2014 Apr; 28(4):935-8. PMID: 24413320; PMCID: PMC4532385.
    60. Xiao JH, Yue Z, Jia LY, Yang XH, Niu LH, Wang Z, Zhang P, Sun BF, He SM, Li Z, Xiong TL, Xin W, Gu HF, Wang B, Werren JH, Murphy RW, Wheeler D, Niu LM, Ma GC, Tang T, Bian SN, Wang NX, Yang CY, Wang N, Fu YG, Li WZ, Yi SV, Yang XY, Zhou Q, Lu CX, Xu CY, He LJ, Yu LL, Chen M, Zheng Y, Wang SW, Zhao S, Li YH, Yu YY, Qian XJ, Cai Y, Bian LL, Zhang S, Wang JY, Yin Y, Xiao H, Wang GH, Yu H, Wu WS, Cook JM, Wang J, Huang DW. Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. Genome Biol. 2013; 14(12):R141. PMID: 24359812; PMCID: PMC4053974.
    61. Wang L, Wheeler DA. Genomic sequencing for cancer diagnosis and therapy. Annu Rev Med. 2014; 65:33-48. PMID: 24274147.
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    62. Benton CB, Ravandi F, Andreeff M, Kadia T, Ruvolo V, Qiu P, Wheeler DA, Garcia-Manero G, Cortes J, Kantarjian HM, Konopleva M. Case series of patients with acute myeloid leukemia receiving hypomethylation therapy and retrospectively found to have IDH1 or IDH2 mutations. Leuk Lymphoma. 2014 Jun; 55(6):1431-4. PMID: 24033106; PMCID: PMC4105975.
    63. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH. Function and evolution of DNA methylation in Nasonia vitripennis. PLoS Genet. 2013; 9(10):e1003872. PMID: 24130511; PMCID: PMC3794928.
    64. Wheeler DA, Wang L. From human genome to cancer genome: the first decade. Genome Res. 2013 Jul; 23(7):1054-62. PMID: 23817046; PMCID: PMC3698498.
    65. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat Genet. 2013 Jul; 45(7):767-75. PMID: 23708188; PMCID: PMC3821058.
    66. Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, Zhao M, Ortega Alves MV, Chang K, Drummond J, Cortez E, Xie TX, Zhang D, Chung W, Issa JP, Zweidler-McKay PA, Wu X, El-Naggar AK, Weinstein JN, Wang J, Muzny DM, Gibbs RA, Wheeler DA, Myers JN, Frederick MJ. Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov. 2013 Jul; 3(7):770-81. PMID: 23619168; PMCID: PMC3858325.
    67. Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne PH, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. J Pathol. 2013 Jan; 229(1):99-110. PMID: 22899370; PMCID: PMC3926301.
    68. Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun. 2013; 4:2730. PMID: 24220575; PMCID: PMC3868236.
    69. Powell BC, Jiang L, Muzny DM, Treviño LR, Dreyer ZE, Strong LC, Wheeler DA, Gibbs RA, Plon SE. Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing. Pediatr Blood Cancer. 2013 Jun; 60(6):E1-3. PMID: 23255406; PMCID: PMC3926299.
    70. Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature. 2012 Nov 15; 491(7424):399-405. PMID: 23103869; PMCID: PMC3530898.
    71. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71. PMID: 22745252; PMCID: PMC3656569.
    72. Crowley JJ, Hilliard CE, Kim Y, Morgan MB, Lewis LR, Muzny DM, Hawes AC, Sabo A, Wheeler DA, Lieberman JA, Sullivan PF, Gibbs RA. Deep resequencing and association analysis of schizophrenia candidate genes. Mol Psychiatry. 2013 Feb; 18(2):138-40. PMID: 22472875; PMCID: PMC3577417.
    73. Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012; 7(3):e34546. PMID: 22479643; PMCID: PMC3315571.
    74. Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011 Nov 15; 108(46):E1128-36. PMID: 22065754; PMCID: PMC3219132.
    75. Sano D, Xie TX, Ow TJ, Zhao M, Pickering CR, Zhou G, Sandulache VC, Wheeler DA, Gibbs RA, Caulin C, Myers JN. Disruptive TP53 mutation is associated with aggressive disease characteristics in an orthotopic murine model of oral tongue cancer. Clin Cancer Res. 2011 Nov 1; 17(21):6658-70. PMID: 21903770; PMCID: PMC3207013.
    76. Harring TR, Guiteau JJ, Nguyen NT, Cotton RT, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA. Building a comprehensive genomic program for hepatocellular carcinoma. World J Surg. 2011 Aug; 35(8):1746-50. PMID: 21225260; PMCID: PMC4137964.
    77. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 Aug 26; 333(6046):1154-7. PMID: 21798897; PMCID: PMC3162986.
    78. Butte NF, Voruganti VS, Cole SA, Haack K, Comuzzie AG, Muzny DM, Wheeler DA, Chang K, Hawes A, Gibbs RA. Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children. Physiol Genomics. 2011 Sep 22; 43(18):1029-37. PMID: 21771880; PMCID: PMC3180738.
    79. Klassen T, Davis C, Goldman A, Burgess D, Chen T, Wheeler D, McPherson J, Bourquin T, Lewis L, Villasana D, Morgan M, Muzny D, Gibbs R, Noebels J. Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Cell. 2011 Jun 24; 145(7):1036-48. PMID: 21703448; PMCID: PMC3131217.
    80. Hicks S, Wheeler DA, Plon SE, Kimmel M. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat. 2011 Jun; 32(6):661-8. PMID: 21480434; PMCID: PMC4154965.
    81. Sun T, Aceto N, Meerbrey KL, Kessler JD, Zhou C, Migliaccio I, Nguyen DX, Pavlova NN, Botero M, Huang J, Bernardi RJ, Schmitt E, Hu G, Li MZ, Dephoure N, Gygi SP, Rao M, Creighton CJ, Hilsenbeck SG, Shaw CA, Muzny D, Gibbs RA, Wheeler DA, Osborne CK, Schiff R, Bentires-Alj M, Elledge SJ, Westbrook TF. Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase. Cell. 2011 Mar 4; 144(5):703-18. PMID: 21376233.
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    82. Davis EE, Zhang Q, Liu Q, Diplas BH, Davey LM, Hartley J, Stoetzel C, Szymanska K, Ramaswami G, Logan CV, Muzny DM, Young AC, Wheeler DA, Cruz P, Morgan M, Lewis LR, Cherukuri P, Maskeri B, Hansen NF, Mullikin JC, Blakesley RW, Bouffard GG. TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. Nat Genet. 2011 Mar; 43(3):189-96. PMID: 21258341; PMCID: PMC3071301.
    83. 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 Jan; 204(1):19-25. PMID: 21356188; PMCID: PMC3075924.
    84. Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF. Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun. 2010; 1:131. PMID: 21119644.
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    85. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep 2; 467(7311):52-8. PMID: 20811451; PMCID: PMC3173859.
    86. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. PMID: 20393554; PMCID: PMC2902243.
    87. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, Muzny DM, Gibbs RA. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med. 2010 Apr 1; 362(13):1181-91. PMID: 20220177; PMCID: PMC4036802.
    88. Montemayor C, Montemayor OA, Ridgeway A, Lin F, Wheeler DA, Pletcher SD, Pereira FA. Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI. PLoS One. 2010; 5(1):e8910. PMID: 20111703; PMCID: PMC2811727.
    89. Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 Feb; 20(2):273-80. PMID: 20019143; PMCID: PMC2813483.
    90. Maheshwari M, Shi J, Badner JA, Skol A, Willour VL, Muzny DM, Wheeler DA, Gerald FR, Detera-Wadleigh S, McMahon FJ, Potash JB, Gershon ES, Liu C, Gibbs RA. Common and rare variants of DAOA in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet. 2009 Oct 5; 150B(7):960-6. PMID: 19194963; PMCID: PMC2753761.
    91. Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet. 2009 Jun; 41(6):739-45. PMID: 19430481; PMCID: PMC2783476.
    92. Guo DC, Papke CL, Tran-Fadulu V, Regalado ES, Avidan N, Johnson RJ, Kim DH, Pannu H, Willing MC, Sparks E, Pyeritz RE, Singh MN, Dalman RL, Grotta JC, Marian AJ, Boerwinkle EA, Frazier LQ, LeMaire SA, Coselli JS, Estrera AL, Safi HJ, Veeraraghavan S, Muzny DM, Wheeler DA, Willerson JT, Yu RK, Shete SS, Scherer SE, Raman CS, Buja LM, Milewicz DM. Mutations in smooth muscle alpha-actin (ACTA2) cause coronary artery disease, stroke, and Moyamoya disease, along with thoracic aortic disease. Am J Hum Genet. 2009 May; 84(5):617-27. PMID: 19409525; PMCID: PMC2680995.
    93. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24; 324(5926):522-8. PMID: 19390049; PMCID: PMC2943200.
    94. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24; 324(5926):528-32. PMID: 19390050; PMCID: PMC2735092.
    95. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23; 455(7216):1069-75. PMID: 18948947; PMCID: PMC2694412.
    96. Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One. 2008; 3(7):e2548. PMID: 18648548; PMCID: PMC2481296.
    97. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 Apr 17; 452(7189):872-6. PMID: 18421352.
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    98. 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 MS, Twomey D, Verhaak RG, 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 Dec 6; 450(7171):893-8. PMID: 17982442; PMCID: PMC2538683.
    99. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61. PMID: 17943122; PMCID: PMC2689609.
    100. Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007 Nov; 4(11):903-5. PMID: 17934467.
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    101. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816. PMID: 17571346; PMCID: PMC2212820.
    102. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun; 17(6):760-74. PMID: 17567995; PMCID: PMC1891336.
    103. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. PMID: 17431167.
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    104. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science. 2007 Apr 13; 316(5822):240-3. PMID: 17431170.
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    105. Mukherjee A, Soyal SM, Wheeler DA, Fernandez-Valdivia R, Nguyen J, DeMayo FJ, Lydon JP. Targeting iCre expression to murine progesterone receptor cell-lineages using bacterial artificial chromosome transgenesis. Genesis. 2006 Dec; 44(12):601-10. PMID: 17149722.
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    106. Zhao Y, Yang Z, Phelan JK, Wheeler DA, Lin S, McCabe ER. Zebrafish dax1 is required for development of the interrenal organ, the adrenal cortex equivalent. Mol Endocrinol. 2006 Nov; 20(11):2630-40. PMID: 16840536.
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    110. Gu P, LeMenuet D, Chung AC, Mancini M, Wheeler DA, Cooney AJ. Orphan nuclear receptor GCNF is required for the repression of pluripotency genes during retinoic acid-induced embryonic stem cell differentiation. Mol Cell Biol. 2005 Oct; 25(19):8507-19. PMID: 16166633; PMCID: PMC1265758.
    111. Cooper SJ, Wheeler D, Hope RM, Dolman G, Saint KM, Gooley AA, Holland RA. The alpha-globin gene family of an Australian marsupial, Macropus eugenii: the long evolutionary history of the theta-globin gene and its functional status in mammals. J Mol Evol. 2005 May; 60(5):653-64. PMID: 15983873.
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    112. Gu P, Goodwin B, Chung AC, Xu X, Wheeler DA, Price RR, Galardi C, Peng L, Latour AM, Koller BH, Gossen J, Kliewer SA, Cooney AJ. Orphan nuclear receptor LRH-1 is required to maintain Oct4 expression at the epiblast stage of embryonic development. Mol Cell Biol. 2005 May; 25(9):3492-505. PMID: 15831456; PMCID: PMC1084298.
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    125. Rendahl KG, Gaukhshteyn N, Wheeler DA, Fry TA, Hall JC. Defects in courtship and vision caused by amino acid substitutions in a putative RNA-binding protein encoded by the no-on-transient A (nonA) gene of Drosophila. J Neurosci. 1996 Feb 15; 16(4):1511-22. PMID: 8778301.
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    128. Guo W, Worley K, Adams V, Mason J, Sylvester-Jackson D, Zhang YH, Towbin JA, Fogt DD, Madu S, Wheeler DA, et al. Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene. Nat Genet. 1993 Aug; 4(4):367-72. PMID: 8401584.
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    131. Incerti B, Guioli S, Pragliola A, Zanaria E, Borsani G, Tonlorenzi R, Bardoni B, Franco B, Wheeler D, Ballabio A, et al. Kallmann syndrome gene on the X and Y chromosomes: implications for evolutionary divergence of human sex chromosomes. Nat Genet. 1992 Dec; 2(4):311-4. PMID: 1303285.
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    132. Peixoto AA, Costa R, Wheeler DA, Hall JC, Kyriacou CP. Evolution of the threonine-glycine repeat region of the period gene in the melanogaster species subgroup of Drosophila. J Mol Evol. 1992 Nov; 35(5):411-9. PMID: 1487825.
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    134. Hamblen M, Zehring WA, Kyriacou CP, Reddy P, Yu Q, Wheeler DA, Zwiebel LJ, Konopka RJ, Rosbash M, Hall JC. Germ-line transformation involving DNA from the period locus in Drosophila melanogaster: overlapping genomic fragments that restore circadian and ultradian rhythmicity to per0 and per- mutants. J Neurogenet. 1986 Sep; 3(5):249-91. PMID: 3097289.
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    135. Slagle BL, Wheeler DA, Hager GL, Medina D, Butel JS. Molecular basis of altered mouse mammary tumor virus expression in the D-2 hyperplastic alveolar nodule line of BALB/c mice. Virology. 1985 May; 143(1):1-15. PMID: 2414907.
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    136. Zehring WA, Wheeler DA, Reddy P, Konopka RJ, Kyriacou CP, Rosbash M, Hall JC. P-element transformation with period locus DNA restores rhythmicity to mutant, arrhythmic Drosophila melanogaster. Cell. 1984 Dec; 39(2 Pt 1):369-76. PMID: 6094014.
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    137. Reddy P, Zehring WA, Wheeler DA, Pirrotta V, Hadfield C, Hall JC, Rosbash M. Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms. Cell. 1984 Oct; 38(3):701-10. PMID: 6435882.
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    138. Wheeler DA, Nelson JM, Shulman IA, Okamoto M, Dave V, Yoshida A. Serologic and biochemical studies of a previously unclassified blood type B variant. Blood. 1984 Mar; 63(3):711-3. PMID: 6421345.
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    139. Wheeler DA, Butel JS, Medina D, Cardiff RD, Hager GL. Transcription of mouse mammary tumor virus: identification of a candidate mRNA for the long terminal repeat gene product. J Virol. 1983 Apr; 46(1):42-9. PMID: 6298469; PMCID: PMC255091.
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