Search
About us
Research Centers
Key Laboratories
Research
Faculty
CAS Members
Center for Genome Biology
Molecular Agrobiology
Developmental Biology
Molecular Systems Biology
Agro-Resources Research
International Cooperation
News
Resources
Education & Training
Join Us
Societies & Publications
Papers
Links
  Location: Home >> Faculty >> Center for Genome Biology
  Center for Genome Biology


Chengzhi Liang


Education
 
Master of Mathematics in Computer Science, University of Waterloo, Canada, 2001
Doctor of Science in Genetics, Institute of Genetics, Chinese Academy of Sciences, China, 1995
Bachelor of Science in Genetics, Wuhan University, China, 1989
 
Professional Experience
 
2012 –, Principle Investigator and Director of Genomics and Bioinformatics Facility, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
2009 – 2012, Scientist II, Crop Information Systems Specialist, International Rice Research Institute
2004 – 2009, Scientific Informatics Manager I, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
2001 – 2003, Bioinformatics Scientist, Bioinformatics Solutions Inc., Waterloo, ON
 


major research areas
 
1) Genome sequencing and analysis: genome de novo sequencing or re-sequecing, RNAseq, population sequencing, genome assembly, population genetic analysis, gene or QTL mapping;
2) Bioinformatics development: algorithm and software for genome annotation and gene regulatory network construction, and databases for genotypic and phenotypic data management and integration.
 

Publications
(Genome annotation, database and software development)
 
1.Du H and Liang C*, Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads". Nature Comm. (Accepted)
 
2.Peng H, Wang K, Chen Z, Cao Y, Gao Q, Li Y, Li X, Lu H, Du H, Lu M, Yang X, Liang C*, MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Res. doi: 10.1093/nar/gkz921. (2019)
 
3.Jin S#, Zong Y#, Gao Q#, Zhu Z, Wang Y, Qin P, Liang C, Wang D, Qiu JL, Zhang F, Gao C, Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:292–295. doi: 10.1126/science.aaw7166 (2019)
 
4.Li M#, Zhang D#, Gao Q#, Luo Y#, Zhang H#, Ma B#, Chen C, Whibley A, Zhang Y, Cao Y, Li Q, Guo H, Li J, Song Y, Zhang Y, Copsey L, Li Y, Li X, Qi M, Wang J, Chen Y, Wang D, Zhao J, Liu G, Wu B, Yu L, Xu C, Li J, Zhao S, Zhang Y, Hu S, Liang C*, Yin Y*, Coen E*, Xue Y*, Genome structure and evolution of Antirrhinum majus L. Nat Plants 5:174–183. doi: 10.1038/s41477-018-0349-9 (2019)
 
5.Yu H*, Lu L, Jiao B, Liang C*, Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics 35:361–364. doi: 10.1093/bioinformatics/bty642 (2019)
 
6.Ling H-Q*#, Ma B#, Shi X#, Liu H#, Dong L#, Sun H#, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A*, Wang D*, Liang C*, Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557:424–428. doi: 10.1038/s41586-018-0108-0 (2018)
 
7.Liu L, Lu Y, Wei L, Yu H, Cao Y, Li Y, Yang N, Song Y, Liang C*, Wang T*, Transcriptomics analyses reveal the molecular roadmap and long noncoding RNA landscape of sperm cell lineage development. Plant J doi: 10.1111/tpj.14041 (2018)
 
8.Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J, Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 50:1289–1295. doi: 10.1038/s41588-018-0182-0 (2018)
 
9.Wu Z, Fang D, Yang R, Gao F, An X, Zhuo X, Li Y, Yi C, Zhang T, Liang C, Cui P, Cheng Z, Luo Q, De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Commun Biol 1:84. doi: 10.1038/s42003-018-0089-4 (2018)
 
10.  Wang S, Ma B, Gao Q, Jiang G, Zhou L, Tu B, Qin P, Tan X, Liu P, Kang Y, Wang Y, Chen W, Liang C*, Li S*, Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes. Theor Appl Genet 131:1391–1403. doi: 10.1007/s00122-018-3085-7 (2018)
 
11.  Xiao N, Gao Y, Qian H, Gao Q, Wu Y, Zhang D, Zhang X, Yu L, Li Y, Pan C, Liu G, Zhou C, Jiang M, Huang N, Dai Z, Liang C, Chen Z, Chen J, Li A, Identification of genes related to cold tolerance and a functional allele that confers cold tolerance. Plant Physiol 177:1108–1123. doi: 10.1104/pp.18.00209 (2018)
 
12.  Xiao N, Wu Y, Pan C, Yu L, Chen Y, Liu G, Li Y, Zhang X, Wang Z, Dai Z, Liang C*, Li A*, Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes. Front Plant Sci 7:1918. doi: 10.3389/fpls.2016.01918 (2017)
 
13.  Zhang L#, Li X#, Ma B#, Gao Q#, Du H#, Han Y, Li Y, Cao Y, Qi M, Zhu Y, Lu H, Ma M, Liu L, Zhou J, Nan C, Qin Yn, Wang J*, Cui L*, Liu H*, Liang C*, Qiao Z*. The Tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance. Molecular Plant 10(9): 1224-1237 (2017)
 
14.  Du H#, Yu Y#, Ma Y#, Gao Q#, Cao Y#, Chen Z, Ma B, Qi M, Li Y, Zhao X, Wang J, Liu K, Qin P, Yang X, Zhu L, Li S*, Liang C*. Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications 8:15324 (2017)
 
15.  Wu Y, Chen Y, Pan C, Xiao N, Yu L, Li Y, Zhang X, Pan X, Chen X, Liang C, Dai Z, Li A, Development and evaluation of near-isogenic lines with different blast resistance alleles at the Piz Locus in Japonica rice from the lower region of the Yangtze River, China. Plant Dis 101:1283–1291. doi: 10.1094/PDIS-12-16-1855-RE (2017)
 
16.  Wu Y, Yu L, Pan C, Dai Z, Li Y, Xiao N, Zhang X, Ji H, Huang N, Zhao B, Zhou C, Liu G, Liu X, Pan X, Liang C, Li A, Development of near-isogenic lines with different alleles of Piz locus and analysis of their breeding effect under Yangdao 6 background. Mol Breed 36:12. doi: 10.1007/s11032-016-0433-7 (2016)
 
17.  Chengzhen Liang, Aifu Li, Hua Yu, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, and Chengcai Chu, (2017) Melatonin regulates root architecture by modulating auxin response in rice. Frontiers in Plant Science 8: 134.
 
18.  Li D, Huang Z, Song S, Xin Y, Mao D, Lv Q, Zhou M, Tian D, Tang M, Wu Q, Liu X, Chen T, Song X, Fu X, Zhao B, Liang C, Li A, Liu G, Li S, Hu S, Cao X, Yu J, Yuan L, Chen C, Zhu L, Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase. Proc Natl Acad Sci 113:201610115. doi: 10.1073/pnas.1610115113 (2016)
 
19.  Li D#, Zeng R#, Li Y#, Zhao M, Chao J, Li Y, Wang K, Zhu L*, Tian W-M*, Liang C*. Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids. Scientific Reports 6: 24984 (2016)
 
20.  Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Goicoechea LJ, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y, Yin Y, Song W, Jiang J, Jackson SA, Wing RA*, Wang Jun*, Chen M*. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications 4:1595 (2013)
 
21.  Xie W, Liang C, Birchler JA, Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 188, 823-34  (2011)
 
22.  Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, et al. Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet 5(11): e1000728 (2009)
 
23.  Liang C*, Mao L, Ware D, Stein L, Evidence-based gene predictions in plant genomes. Genome Res 19, 1912-23 (2009)
 
24.  Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, …, McCombie WR, Wing RA, Wilson RK, The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–5. doi: 10.1126/science.1178534 (2009)
 
25.  Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung C-W, Wei X, Yap I, Youens-Clark K, Ware D, Stein L*; Gramene: a growing plant comparative genomics resource, Nucleic Acids Research 36: D947-D953 (2008)
 
26.  Hladish T, Gopalan V, Liang C, Qiu W, Yang P and Stoltzfus A, Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8, 191 (2007)
 
27.  Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S, Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34:D717-23. doi: 10.1093/nar/gkj154 (2006)
 
28.  Ma B, Zhang K, and Liang C,  An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. J Computer and System Sciences 70, 418-430 (2005)
 
29.  Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G, PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS. Rapid Comm Mass Spec 17, 2337-2342 (2003)
 
30.  Williams CE, Collier CC, Nemacheck, JA, Liang C and Cambron SE, A lection-like wheat gene responds systemically to attempted feeding by virulent first-instar Hessian fly larvae. J Chem Ecol 28, 1411-1428 (2002)
 
31.  Li XB, Liang CZ, Wu HG, Zhai WX, Huang N, Zhu LH, Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species. Theor Appl Genet 92, 702-708 (1996)
 
32.  Liang CZ, Gu MH, Pan XB, Liang GH, Zhu LH, RFLP tagging a semi-dwarfing gene in rice. Theor Appl Genet 88, 898-900 (1994)