Chaochun Wei

Professor

  • Tel: +86-021-34204083
  • Email: ccwei@sjtu.edu.cn
  • Address:
  • Lab Web: http://cgm.sjtu.edu.cn/index/index.php
  • Professor. BS from Peking University, ScD from Washington University (US). Research areas: Genomics and Evolutionary Genomics, including functional element identification and their evolution analysis, eukaryote pan-genomics, cancer genomics and metagenomics. Published ~50 papers in Nature et al, with citations > 5500. Chancellor's Award.

Education and Research Experience

  • 2015-                     Professor, Department of Bioinformatics & Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
  • 2008-2015              Associate Professor, Department of Bioinformatics & Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
  • 2006-2007              Software Engineer, Microsoft, USA
  • 2000-2006              Sc.D in Computer Science, Washingtong University in St. Louis, MO, USA
  • 1996-1999              Master in Signal and Information Processing, Center for Information Science, Beijing University, China
  • 1991-1996              BS in Mathematics, Department of Mathematics, Beijing University, China

Research Interests

Genomics

Functional element finding, alternative splicing prediction, evolutiaonary genomics, comparative genomics, pangenomics and metagenomics. 

Selected Publications

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    Yu, Y.* #, Zhang, Z. #, Dong, X. #, Yang, R. #, Duan, Z. #, Xiang, Z., Li, J., Li, G., Yan, F., Xue, H., Jiao, D., Lu, J., Lu, H., Zhang, W., Wei, Y., Fan, S., Li, J., Jia, J., Zhang, J., Ji, J., Liu, P., Lu, H., Zhao, H., Chen, S., Wei, C.*, Chen, H.*, Zhu, Z.*, “Pangenomic analysis of Chinese gastric cancer”, Nature Communications, 2022, 13:5412.

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    Li, K., Yan, F., Duan, Z., Adelson, D., Wei, C.*, “Widespread of horizontal gene transfer regions in eukaryotes”, bioRxiv, doi: https://doi.org/10.1101/2022.07.26.501571.

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    Zhang, F., Xue, H., Dong, X., Li, M., Zheng, X., Li, Z., Xu, J., Wang, W., and Wei, C. *, “Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes”, Genome Research, 2022,32:853-863.

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    Duan, Z., Qiao, Y., Lu, J., Lu, H., Zhang, W., Yan, F., Sun, C., Hu, Z., Zhang, Z., Li, G., Chen, H., Xiang, Z., Zhu, Z., Zhao, H., Yu, Y.*, Wei, C.*, HUPAN: a pan-genome analysis pipeline for human genomes, Genome Biology, 2019, 20:149

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    Wang, W., et al., "Genomic variation in 3,010 diverse accessions of Asian cultivated rice", Nature, 2018, 557:43-49 (co-corresponding author)

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    Hu, Z., Sun, C., Lu, K., Chu, X., Zhao, Y., Lu, J., Shi, J.*, Wei, C.*, “EUPAN enables pan-genome studies of a large number of eukaryotic genomes”, Bioinformatics, 2017, btx170.

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    Sun, C., Hu, Z., Lu, K., Zhao, Y., Lu, J., Zheng, T., Wang, W., Shi, J., Zhang, D., Li, Z.*, Wei, C.*, “RPAN: Rice Pan-genome Browser for ~3,000 rice genomes”, Nucleic Acids Research, 2017, 45(2): 597-605.

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    Hu, Z., Scott, H., Qin, G., Zheng, G, Chu, X., Xie, L., Adelson, D., Oftedal, B., Venugopal, P., Babic, M., Hahn, C., Zhang, B., Wang, X., Li, N., Wei, C.*, "Revealing missing human protein isoforms based on ab initio prediction, RNA-sesq and proteomics", Scientific Reports, 2015, 5:10940 

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    Wei, C., Lamesch, P., Arumugam M., Rosenberg, J., Hu, P., Vidal, M., and Brent, M. R. “Closing in on the C.elegans ORFeome by Cloning TWINSCAN predictions”, Genome Research, 2005, 15:577-582.

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    Yang, X., Xie, L., Li, Y., Wei, C*. “More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body”, PLoS ONE, 2009, 4(6): e6074.

Teaching Experiences

  • “Omics big data”, Credit 3, Spring 2017, 2018, 2019, Fall 2020, Spring 2021-2023
  • "Advanced Bioinformatics", Credit 3, Spring 2012-2015
  • “Programming languages for Bioinformatics”, Credit 3, Spring 2013-2016, Credit 2, Spring 2017, 2018, 2019, 2020
  • “Matlab programming”, Credit 2, Spring 2012
  • “Computational Biology”, Bioinformatics session, Credit 3, Fall 2011- 2016
  • “Algorithms in Bioinformatics”, Credit 3, Fall 2011 – 2016, Spring 2018, 2021-2023
  • “Genomics and Proteomics”, Credit 3, Fall 2010
  • “Digital Signal Processing”, Credit 3, Fall 2009
  •  “Frontier topics in Bioinformatics”, Biological Sequence Analysis session, Spring 2009
  • NSFC Project  (32170643, PI, ¥580K), 2022.1-2025.12 "A third-generation-sequencing-based pan-genome construction method and its application in rice genome analysis"
  • Science and Technology Commission of Shanghai Municipality (22ZR1433600, ¥200K) 2022.4-2025.3 “Identification and characterization of horizontal gene transfer in bat genomes”
  • Science and Technology Commission of Shanghai Municipality (20ZR1428200, ¥200K) 2020.7-2023.6“Construction of rice pan-genome browser 2.0”
  • Medicine and Engineering joint project (YG2017ZD01, co-PI, ¥750K) 2018.1-2020.12“Data analysis platform for big omics data from gastric cancer considering complex cancer phenotypes and microbiome diversity”
  • NSFC Project  (61472246, PI, ¥800K), 2015.1-2018.12 " Finding and characterizing complex structure sequence modules in metagenomes"
  • National High-Tech R&D Program (863) (2014AA02502, Co-PI,  budget ¥650K,total budget¥7.2M),  2014.1-2017.12“Key technologies for microbial genomic data integration and analysis”
  • National Basic Research Program of China (973) (2013CB956103, Co-PI, budget ¥1.04M,  total budget ¥26M), 2013.1 – 2017.12“The degeneration mechanism and recovery potential of coral reefs in South China sea”
  • NSFC Project  (61272250, PI, ¥800K),  (2013.1-2016.12)“Finding and characterization of genes containing repeat regions”
  • NSFC Project  (60970050, PI, ¥300K),  (2010.1-2012.12)“An index measuring gene structure variation and its application on the study of disease susceptibility of genes”
  • National High-Tech R&D Program (863) (2009AA02Z310, PI, ¥1.6 1million),  2009.1-2011.12“Metagenomics data collection and analysis system based on the next-generation sequencing technologies”
  • Shanghai Pujiang Program  (09PJ1407900, PI, ¥200K), (2009.8-2011.7)“Conditional random field theory and its applications in Bioinformatics”
  • Science and Technology Innovation Program of Basic Science Foundation of Shanghai (08JC1416700, PI,¥250K), 2008.10-2010.9“Algorithms and system for complex sequence module finding”

Selected Grants