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Department of Genetics Heersink School of Medicine

Publications

2017

  • Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 Feb 23;168(5):830-842.e7. doi: 10.1016/j.cell.2017.01.037. PubMed PMID: 28235197.

  • Cancer Genome Atlas Research Network (including Chong Z as a coauthor). Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Jan 23. doi: 10.1038/nature21386. [Epub ahead of print] PubMed PMID: 28112728.

  • Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K. novoBreak: local assembly for breakpoint detection in cancer genomes. Nat Methods. 2017 Jan;14(1):65-67. doi: 10.1038/nmeth.4084. PubMed PMID: 27892959; PubMed Central PMCID: PMC5199621.

2016

  • Zhang K, Gao M, Chong Z, Li Y, Han X, Chen R, Qin L. Single-cell isolation by a modular single-cell pipette for RNA-sequencing. Lab Chip. 2016 Nov 29;16(24):4742-4748. PubMed PMID: 27841430.

  • Chen T, Wang Z, Zhou W, Chong Z, Meric-Bernstam F, Mills GB, Chen K. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics. 2016 Jun 23;17 Suppl 2:394. doi: 10.1186/s12864-016-2727-x. PubMed PMID: 27356755; PubMed Central PMCID: PMC4928158.

  • Tsang YH, Dogruluk T, Tedeschi PM, Wardwell-Ozgo J, Lu H, Espitia M, Nair N, Minelli R, Chong Z, Chen F, Chang QE, Dennison JB, Dogruluk A, Li M, Ying H, Bertino JR, Gingras MC, Ittmann M, Kerrigan J, Chen K, Creighton CJ, Eterovic K, Mills GB, Scott KL. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nat Commun. 2016 Jan 25;7:10500. doi: 10.1038/ncomms10500. PubMed PMID: 26806015; PubMed Central PMCID: PMC4737758.

2015

  • Dogruluk T, Tsang YH, Espitia M, Chen F, Chen T, Chong Z, Appadurai V, Dogruluk A, Eterovic AK, Bonnen PE, Creighton CJ, Chen K, Mills GB, Scott KL. Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations. Cancer Res. 2015 Dec 15;75(24):5341-54. doi: 10.1158/0008-5472.CAN-15-1654. PubMed PMID: 26627007; PubMed Central PMCID: PMC4681596.

  • Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multilevel variant annotator for precision genomics. Nat Methods. 2015 Nov;12(11):1002-3. doi: 10.1038/nmeth.3622. PubMed PMID: 26513549; PubMed Central PMCID: PMC4772859.

  • Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium., Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. PubMed PMID: 26432246; PubMed Central PMCID: PMC4617611.

  • 1000 Genomes Project Consortium., Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. PubMed PMID: 26432245; PubMed Central PMCID: PMC4750478.

  • Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K. ClinSeK: a targeted variant characterization framework for clinical sequencing. Genome Med. 2015 Mar 31;7(1):34. doi: 10.1186/s13073-015-0155-1. PubMed PMID: 25918555; PubMed Central PMCID: PMC4410453.

  • Wang XX, Sun BF, Jiao J, Chong ZC, Chen YS, Wang XL, Zhao Y, Zhou YM, Li D. Genome-wide 5-hydroxymethylcytosine modification pattern is a novel epigenetic feature of globozoospermia. Oncotarget. 2015 Mar 30;6(9):6535-43. PubMed PMID: 25762640; PubMed Central PMCID: PMC4466632.

  • Chen K, Meric-Bernstam F, Zhao H, Zhang Q, Ezzeddine N, Tang LY, Qi Y, Mao Y, Chen T, Chong Z, Zhou W, Zheng X, Johnson A, Aldape KD, Routbort MJ, Luthra R, Kopetz S, Davies MA, de Groot J, Moulder S, Vinod R, Farhangfar CJ, Shaw KM, Mendelsohn J, Mills GB, Eterovic AK. Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clin Chem. 2015 Mar;61(3):544-53. doi: 10.1373/clinchem.2014.231100. PubMed PMID: 25626406; PubMed Central PMCID: PMC4511273.

2014

  • Fan X, Zhou W, Chong Z, Nakhleh L, Chen K. Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinformatics. 2014 Sep 8;15:299. doi: 10.1186/1471-2105-15-299. PubMed PMID: 25201439; PubMed Central PMCID: PMC4165998.

  • Tapias A, Zhou ZW, Shi Y, Chong Z, Wang P, Groth M, Platzer M, Huttner W, Herceg Z, Yang YG, Wang ZQ. Trrap-dependent histone acetylation specifically regulates cell-cycle gene transcription to control neural progenitor fate decisions. Cell Stem Cell. 2014 May 1;14(5):632-43. doi: 10.1016/j.stem.2014.04.001. PubMed PMID: 24792116.

  • Gao M, Wei W, Li MM, Wu YS, Ba Z, Jin KX, Li MM, Liao YQ, Adhikari S, Chong Z , Zhang T, Guo CX, Tang TS, Zhu BT, Xu XZ, Mailand N, Yang YG, Qi Y, Rendtlew Danielsen JM. Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination. Cell Res. 2014 May;24(5):532-41. doi: 10.1038/cr.2014.36. PubMed PMID: 24662483; PubMed Central PMCID: PMC4011338.

  • Zhao B, Yang Y, Wang X, Chong Z, Yin R, Song SH, Zhao C, Li C, Huang H, Sun BF, Wu D, Jin KX, Song M, Zhu BZ, Jiang G, Rendtlew Danielsen JM, Xu GL, Yang YG, Wang H. Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism. Nucleic Acids Res. 2014 Feb;42(3):1593-605. doi: 10.1093/nar/gkt1090. PubMed PMID: 24214992; PubMed Central PMCID: PMC3919571.

2013

  • Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI. Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology. BMC Genomics. 2013 Oct 17;14:711. doi: 10.1186/1471-2164-14-711. PubMed PMID: 24134808; PubMed Central PMCID: PMC4046676.

  • Chong Z, Zhai W, Li C, Gao M, Gong Q, Ruan J, Li J, Jiang L, Lv X, Hungate E, Wu CI. The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster. Mol Biol Evol. 2013 Dec;30(12):2699-708. doi: 10.1093/molbev/mst167. PubMed PMID: 24077769.

  • Yin R, Mao SQ, Zhao B, Chong Z, Yang Y, Zhao C, Zhang D, Huang H, Gao J, Li Z, Jiao Y, Li C, Liu S, Wu D, Gu W, Yang YG, Xu GL, Wang H. Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals. J Am Chem Soc. 2013 Jul 17;135(28):10396-403. doi: 10.1021/ja4028346. PubMed PMID: 23768208.

2012

  • Chong Z, Ruan J, Wu CI. Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics. 2012 Nov 1;28(21):2732-7. doi: 10.1093/bioinformatics/bts482. PubMed PMID: 22942077.

2011

  • Tao Y, Ruan J, Yeh SH, Lu X, Wang Y, Zhai W, Cai J, Ling S, Gong Q, Chong Z, Qu Z, Li Q, Liu J, Yang J, Zheng C, Zeng C, Wang HY, Zhang J, Wang SH, Hao L, Dong L, Li W, Sun M, Zou W, Yu C, Li C, Liu G, Jiang L, Xu J, Huang H, Li C, Mi S, Zhang B, Chen B, Zhao W, Hu S, Zhuang SM, Shen Y, Shi S, Brown C, White KP, Chen DS, Chen PJ, Wu CI. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12042-7. doi: 10.1073/pnas.1108715108. PubMed PMID: 21730188; PubMed Central PMCID: PMC3141952.