Publications

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, A Robertson G, Wu H-T, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 ;29(5):723-736.

Zhdanova IV, Rogers J, González-Martínez J, Farrer LA. The ticking clock of Cayo Santiago macaques and its implications for understanding human circadian rhythm disorders. Am J Primatol. 2016 ;78(1):117-26.

Zhao C, Shukle R, Navarro-Escalante L, Chen M, Richards S, Stuart JJ. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family. J Insect Physiol. 2016 ;84:22-31.

Zhao L, Chen Y, Bajaj AOnkar, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SYun, He F, Li Y, Wensel TG, Qin J, Chen R. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes. Genome Res. 2016 ;26(5):660-9.

Zhao C, Escalante LNavarro, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM, Wheeler D, 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.

Zhao S, Zhang Y, Hallgrimsdottir S, Zuo Y, Li X, Batkovskyte D, Liu S, Lindelöf H, Wang S, Hammarsjö A, Yang Y, Ye Y, Wang L, Yan Z, Lin J, Yu C, Chen Z, Niu Y, Wang H, Zhao Z, Liu P, Qiu G, Posey JE, Wu Z, Lupski JR, Micule I, Anderlid B-M, Voss U, Sulander D, Kuchinskaya E, Nordgren A, Nilsson O, Zhang TJianguo, Grigelioniene G, Wu N. Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders. NPJ Genom Med. 2022 ;7(1):11.

Zhao S, Zhang Y, Chen W, Li W, Wang S, Wang L, Zhao Y, Lin M, Ye Y, Lin J, Zheng Y, Liu J, Zhao H, Yan Z, Yang Y, Huang Y, Lin G, Chen Z, Zhang Z, Liu S, Jin L, Wang Z, Chen J, Niu Y, Li X, Wu Y, Wang Y, Du R, Gao N, Zhao H, Yang Y, Liu Y, Tian Y, Li W, Zhao Y, Liu J, Yu B, Zhang N, Yu K, Yang X, Li S, Xu Y, Hu J, Liu Z, Shen J, Zhang S, Su J, Khanshour AM, Kidane YH, Ramo B, Rios JJ, Liu P, V Sutton R, Posey JE, Wu Z, Qiu G, Wise CA, Zhang F, Lupski JR, Zhang J, Wu N. Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS). J Med Genet. 2021 ;58(1):41-47.

Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAGagliano, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, L Cupples A, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, W Johnson C, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O'Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, R Barr G, Cho MH, Manichaikul A. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun. 2020 ;11(1):5182.

Zhao N, Teles F, Lu J, Koestler DC, Beck J, Boerwinkle E, Bressler J, Kelsey KT, Platz EA, Michaud DS. Epigenome-wide association study using peripheral blood leukocytes identifies genomic regions associated with periodontal disease and edentulism in the Atherosclerosis Risk in Communities study. J Clin Periodontol. 2023 ;50(9):1140-1153.

Zhao Z, Boerwinkle E. Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res. 2002 ;12(11):1679-86.

Zhao Z, Fu Y-X, Hewett-Emmett D, Boerwinkle E. Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene. 2003 ;312:207-13.

Zhao J, Boerwinkle E, Xiong M. An entropy-based statistic for genomewide association studies. Am J Hum Genet. 2005 ;77(1):27-40.

Zhao Y, Yang Z, Phelan JK, Wheeler DA, Lin S, McCabe ERB. Zebrafish dax1 is required for development of the interrenal organ, the adrenal cortex equivalent. Mol Endocrinol. 2006 ;20(11):2630-40.

Zhao J, Boerwinkle E, Xiong M. An entropy-based genome-wide transmission/disequilibrium test. Hum Genet. 2007 ;121(3-4):357-67.

Zhang Z, Lin L, Liu G, Wang M, Hill J, Wang Y, You M, Devereux TR. Fine mapping and characterization of candidate lung tumor resistance genes for the Par2 locus on mouse chromosome 18. Exp Lung Res. 2000 ;26(8):627-39.

Zhang Y, Dipple KM, Vilain E, Huang BL, Finlayson G, Therrell BL, Worley KC, Deininger P, McCabe ER. AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency. Hum Mutat. 2000 ;15(4):316-23.

Zhang Z, Futamura M, Vikis HG, Wang M, Li J, Wang Y, Guan K-L, You M. Positional cloning of the major quantitative trait locus underlying lung tumor susceptibility in mice. Proc Natl Acad Sci U S A. 2003 ;100(22):12642-7.

Zhang Z, Burch PE, Cooney AJ, Lanz RB, Pereira FA, Wu J, Gibbs RA, Weinstock G, Wheeler DA. Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome. Genome Res. 2004 ;14(4):580-90.

Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 ;1(5):e53.

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.

Zhang Y, Chen F, Creighton CJ. SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints. BMC Bioinformatics. 2021 ;22(1):135.

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.

Zhang Y, Chen F, Donehower LA, Scheurer ME, Creighton CJ. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun. 2021 ;12(1):937.

Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, 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, Li W, Park PJ, Kucherlapati R, Creighton CJ. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 ;24(2):515-527.

Zhang C, Mazzeu JF, Eisfeldt J, Grochowski CM, White J, Akdemir ZC, Jhangiani SN, Muzny DM, Gibbs RA, Lindstrand A, Lupski JR, V Sutton R, Carvalho CMB. Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome. Am J Med Genet A. 2021 ;185(12):3593-3600.