See the updated full publication list here

2021

  • Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021 Feb 25:eabf7117. doi: 10.1126/science.abf7117. Epub ahead of print. PMID: 33632895.
  • Xu P, Chen Y, Gao M, Chong Z. ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules. NAR Genom Bioinform. 2021 Feb 1;3(1):lqab003. doi: 10.1093/nargab/lqab003. PMID: 33554118; PMCID: PMC7850140.

2020

  • Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium (including Chong Z). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y. Erratum in: Nat Commun. 2020 Nov 30;11(1):6232. PMID: 32958763; PMCID: PMC7505971.
  • Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium (including Chong Z). Sex differences in oncogenic mutational processes. Nat Commun. 2020 Aug 28;11(1):4330. doi: 10.1038/s41467-020-17359-2. PMID: 32859912; PMCID: PMC7455744.
  • Liu RM, Chong Z, Chen JC. Ozone and Particulate Matter Exposure and Alzheimer’s Disease: A Review of Human and Animal Studies. J Alzheimers Dis. 2020;76(3):807-824. doi: 10.3233/JAD-200435. PMID: 32568209.
  • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (including Chong Z). Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5. PMID: 32025007; PMCID: PMC7025898.
  • Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 Mar;52(3):306-319. doi:10.1038/s41588-019-0562-0. Epub 2020 Feb 5. PMID: 32024998; PMCID: PMC7058536.
  • Shanta O, Noor A; Human Genome Structural Variation Consortium (HGSVC, including Chong Z), Sebat J. The effects of common structural variants on 3D chromatin structure. BMC Genomics. 2020 Jan 30;21(1):95. doi: 10.1186/s12864-020-6516-1. PMID: 32000688;PMCID: PMC6990566.
  • Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O’Connell JR, Mitchell BD; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium (including Chong Z); TOPMed Population Genetics Working Group, O’Connor TD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2560-2569. doi: 10.1073/pnas.1902766117. Epub 2020 Jan 21. PMID: 31964835; PMCID: PMC7007577.
  • Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA; Human Genome Structural Variation Consortium (including Chong Z), Warren WC, Pollen AA, Chaisson MJP, Eichler EE. Human-specific tandem repeat expansion and differential gene expression during primate evolution. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23243-23253. doi: 10.1073/pnas.1912175116. Epub 2019 Oct 28. PMID: 31659027; PMCID: PMC6859368.

2019

  • Xu P, Kennell T, Gao M; Human Genome Structural Variation Consortium, Kimberly R, Chong Z. MRLR: unraveling high-resolution meiotic recombination by linked reads. Bioinformatics. 2019 Jun 19. pii: btz503. doi: 10.1093/bioinformatics/btz503. [Epub ahead of print] PubMed PMID: 31214684.
  • Guo G, Chen H, Yan D, Cheng J, Chen J, Chong Z. Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. IEEE/ACM Trans Comput Biol Bioinform. 2019 Jun 5. doi: 10.1109/TCBB.2019.2920912. [Epub ahead of print] PubMed PMID: 31180898.
  • Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z. PubMed PMID: 30992455; PubMed Central PMCID: PMC6467913.
  • Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 Mar 7;176(6):1310-1324.e10. doi: 10.1016/j.cell.2019.01.045. Epub 2019 Feb 28. PubMed PMID: 30827684; PubMed Central PMCID: PMC6438178.

2018

  • Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5. PubMed PMID: 30400818; PubMed Central PMCID:PMC6219177.
  • Chong Z, Chen K. Structural Variant Breakpoint Detection with novoBreak. Methods Mol Biol. 2018;1833:129-141. doi: 10.1007/978-1-4939-8666-8_10. PubMed PMID: 30039369.
  • Zhu W, Zhang E, Zhao M, Chong Z, Fan C, Tang Y, Hunter JD, Borovjagin AV, Walcott GP, Chen JY, Qin G, Zhang J. Regenerative Potential of Neonatal Porcine Hearts. Circulation. 2018 Jul 20. pii: CIRCULATIONAHA.118.034886. doi: 10.1161/CIRCULATIONAHA.118.034886. [Epub ahead of print] PubMed PMID: 30030418.
  • Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL. In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nat Commun. 2018 Jul 16;9(1):2732. doi: 10.1038/s41467-018-04572-3. PubMed PMID: 30013058; PubMed Central PMCID: PMC6048166.
  • Grochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Hum Mutat. 2018 Jul;39(7):939-946. doi: 10.1002/humu.23537. Epub 2018 May 11. PubMed PMID: 29696747; PubMed Central PMCID: PMC5995661.

2017

  •  Federico L, Chong Z, Zhang D, McGrail DJ, Zhao W, Jeong KJ, Vellano CP, Ju Z,  Gagea M, Liu S, Mitra S, Dennison JB, Lorenzi PL, Cardnell R, Diao L, Wang J, Lu Y, Byers LA, Perou CM, Lin SY, Mills GB. A murine preclinical syngeneic transplantation model for breast cancer precision medicine. Sci Adv. 2017 Apr 19;3(4):e1600957. doi: 10.1126/sciadv.1600957. eCollection 2017 Apr. PubMed PMID: 28439535; PubMed Central PMCID: PMC5397135.
  • 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 Mar 16;543(7645):378-384. doi: 10.1038/nature21386. Epub 2017 Jan 23. PubMed PMID: 28112728; PubMed Central PMCID: PMC5354998.
  • 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 (including Chong Z)., 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.