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Faculty Detail    
Name ZECHEN CHONG
Assistant Professor
 
Campus Address THT 134 Zip 0024
Phone  (20-5) -590
E-mail  zchong@uab.edu
Other websites Chong Lab
Publications in Google Scholar
     

Education
Undergraduate  Harbin Institute of Technology    2007  B.E. in Computer Science 
Graduate  Beijing Institute of Genomics, Chinese Academy of Sciences    2010  M.S. in Bioinformatics 
Graduate  Beijing Institute of Genomics, Chinese Academy of Sciences     2013  Ph.D. in Genomics 


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Genetics   Genetics Chair Office Assistant Professor
Center  General Clinical Research Center  Ctr for Clinical & Translational Sci Assistant Professor
Center  Informatics Institute  Informatics Institute Assistant Professor
Center  General Clinical Research Center  Minority Health & Research Center Assistant Professor

Biographical Sketch 
After obtaining a PhD degree in Genomics in 2013, I worked with Dr. Ken Chen at MD Anderson Cancer Center as a postdoc fellow until Feb. 2017. Honors: Fellow of Computational Cancer Biology Training Program (CCBTP) of CPRIT, 2016 Best Performer of ICGC-TCGA Somatic Mutation Calling DREAM SV Sub-Challenges, 2015 Best Performer of ICGC-TCGA Somatic Mutation Calling DREAM SV Sub-Challenges, 2014 First-Class National Scholarship, 2013, GUCAS Hao Bolin Scholarship, 2013, GUCAS CAS Merit Student, 2011-2012, GUCAS CAS Second-Class PhD candidate Scholarship, 2010, GUCAS



Research/Clinical Interest
Title
Description
1. Develop algorithms for sequencing data analysis. Although there are many tools available for next-generation sequencing data analysis, the vast volumes of sequencing data which are being generated at a decreasing cost still require more sensitive and specific algorithms to analyze in an efficient manner. The third-generation sequencing (TGS) platforms (PacBio, Oxford nanopore, etc.) can generate reads of thousands of basepairs, which can cover a large proportion of the genome in a haplotype. However, the error rates of the TGS platforms are very high (e.g. ~15% for PacBio), which is extremely challenging for data analysis. But there are many open questions for Bioinformaticians to develop novel methods to overcome the drawbacks and fully exploit the properties of the TGS data. Besides, there are newly developed biotechniques, such as 10X genomics, strand-seq, improved single cell sequencing, etc., which are generating miscellaneous of sequencing data types. We are also interested in providing efficient solutions to deal with these types of data. 2. Functions and mechanisms of genomic rearrangements. Compared to single nucleotide variants and short indels, genomic rearrangements or structural variations (SVs) can contribute more polymorphisms within species and more divergence between species. However, it is still an open question in terms of the functions and mechanisms of SVs. For example, the observation and hypothesis of chromothripsis is still mysterious. We are interested in in-depth analysis of SVs in a hypothesis-driven manner. 3. Disease genomics. Disease is an abnormal phenotype. There is a long-lasting complex problem regarding how the genotype (mixing with epigenetic alterations and modifications and environment) determines the phenotype. We are interested in a wide range of questions, for examples, discovering the causing variants, pan-cancer/disease genomics data analysis, integrated data analysis, etc. 4. Collaborations. We have extensive collaborations around UAB campus, around the country and abroad.

Selected Publications 
Publication PUBMEDID
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.  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. PubMed PMID: 28112728.  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.  27892959 
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.  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.  27356755 
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.  26806015 
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.  26627007 
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.  26513549 
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.  26432246 
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.  26432246 
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.  26432245 
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.  25918555 
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.  25918555 
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.  25762640 
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.   25626406 
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.   25201439 
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.  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.   24662483 
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.  24214992 
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.   24134808 
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.   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.   23768208 
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.   22942077 
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.   21730188 

Keywords
Bioinformatics; Genomics; Computational Biology