2025

• Guo Y, Song Y, Jiang L, Chen Y, Ceccarelli M, Gao M, Chong Z.

  Protocol: a detailed guide to assess genome assembly based on long-read sequencing data.
  Nature Protocol
  [Abstract]

2024

• Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Scholz S, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T.

  Complex genetic variation in nearly complete human genomes.
  Nature (Under Revision)
  [Abstract]

• He M, Sun Y, Huang F, Zhu Z, Velazquez-Miranda E, Chong Z, Chen Y.

  Smooth Muscle Cells–Expressed Bmal1 Regulates Vascular Calcification Independent of the Canonical Circadian Pathway.
  bioRxiv
  [Abstract]

• Huang F, Xu P, Yue Z, Song Y, Hu K, Zhao X, Gao M, Chong Z.

  Body Weight Correlates with Molecular Variances in Patients with Cancer.
  Cancer Res. 2024 Mar 4;84(5):757-770
  [Abstract]

• Hale AT, Boudreau H, Devulapalli R, Duy PQ, Atchley TJ, Dewan MC, Goolam M, Fieggen G, Spader HL, Smith AA, Blount JP, Johnston JM, Rocque BG, Rozzelle CJ, Chong Z, Strahle JM, Schiff SJ, Kahle KT.

  The genetic basis of hydrocephalus: genes, pathways, mechanisms, and global impact.
  Fluids Barriers CNS. 2024 Mar 4;21(1):24
  [Abstract]

• Chong Z, Huang F, McLeod MC, Irwin RK, Smithson M, Yue Z, Gao M, Hardiman KM.

  Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancer
  Res Sq. 2024 Jul 1:rs.3.rs-4456000
  [Abstract]

2023

• Chen Y, Wang AY, Barkley CA, Zhang Y, Zhao X, Gao M, Edmonds MD, Chong Z.

  Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak.
  Nat Commun. 2023 Jan 17;14(1):283
  [Abstract]

2022

• Huang F, Xiao L, Gao M, Vallely EJ, Dybvig K, Atkinson TP, Waites KB, Chong Z.

  B-assembler: a circular bacterial genome assembler.
  BMC Genomics. 2022 May 11;23(Suppl 4):361
  [Abstract]

• Wang J, Thomas HR, Chen Y, Percival SM, Waldrep SC, Ramaker RC, Thompson RG, Cooper SJ, Chong Z, Parant JM.

  Reduced sister chromatid cohesion acts as a tumor penetrance modifier.
  PLoS Genet. 2022 Aug 22;18(8):e1010341
  [Abstract]

• Shen H, Huang F, Zhang X, Ojo OA, Li Y, Trummell HQ, Anderson JC, Fiveash J, Bredel M, Yang ES, Willey CD, Chong Z, Bonner JA, Shi LZ.

  Selective suppression of melanoma lacking IFN-γ pathway by JAK inhibition depends on T cells and host TNF signaling.
  Nat Commun. 2022 Aug 25;13(1):5013
  [Abstract]

• Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E; Human Genome Structural Variation Consortium (including Chong Z), Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC.

  High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
  Cell. 2022 Sep 1;185(18):3426-3440.e19
  [Abstract]

• Zhao X, Chong Z, Chen Y, Zheng XL, Wang QF, Li Y.

  Protein arginine methyltransferase 1 in the generation of immune megakaryocytes: A perspective review.
  Biol Chem. 2022 Sep 21;298(11):102517
  [Abstract]

• Chen Y, Wang Y, Chen W, Tan Z, Song Y, Human Genome Structural Variation Consortium N, Chen H, Chong Z.

  Gene fusion detection and characterization in long-read cancer transcriptome sequencing data with FusionSeeker.
  Cancer Res. 2022 Nov 1:CAN-22-1628
  [Abstract]

2021

• 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
  [Abstract]

• 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
  [Abstract]

• Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C; Human Genome Structural Variation Consortium (including Chong Z), Lee C, Devine SE, Eichler EE, Ye K.

  Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. Genomics Proteomics Bioinformatics.
  2021 Jul 3:S1672-0229(21)00143-1
  [Abstract]

• Zhang Z, Luo L, Xing C, Chen Y, Xu P, Li M, Zeng L, Li C, Ghosh S, Della Manna D, Townes T, Britt WJ, Wajapeyee N, Sleckman BP, Chong Z, Leavenworth JW, Yang ES.

  RNF2 ablation reprograms the tumor-immune microenvironment and stimulates durable NK and CD4+ T-cell-dependent antitumor immunity.
  Nat Cancer. 2021 Oct;2(10):1018-1038
  [Abstract]

• Chen Y, Zhang Y, Wang AY, Gao M, Chong Z.

  Accurate long-read de novo assembly evaluation with Inspector.
  Genome Biol. 2021 Nov 14;22(1):312
  [Abstract]

2020

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2019

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2018

• 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.
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• Chong Z, Chen K.

  Structural Variant Breakpoint Detection with novoBreak.
  Methods Mol Biol. 2018;1833:129-141
  [Abstract]

• 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
  [Abstract]

2017

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2016

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2015

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2014

• 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
  [Abstract]

• 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.
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

2013

• 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
  [Abstract]

• 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
  [Abstract]

• 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
  [Abstract]

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
  [Abstract]

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
  [Abstract]

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