Chaochun Wei

  • 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 ~60 papers in Nature et al, with citations > 7000. Chancellor's Award.
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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

Genomics, Comparative Genomics and Evolutionary Genomics.  Pangenomics, Metagenomics, functional element finding including alternative splicing prediction, 

Selected Publications

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    Zhao K.#, Xue H.#, Li G.#, Chitkineni A, Fan, Y, Cao Z., Dong X., Lu H., Zhao K, Zhang L, Qiu D, Ren R, Gong F., Li Z., Ma X., Wan S., Varshney R*, Wei C.* and Yin D.*, “Pangenome reveals genomic variations associated with seed size/weight traits in peanut”, Nature Genetics, 2025, 57:1250-1261.

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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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    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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    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.

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Teaching Experiences

  • “Omics big data”, Credit 3, Spring 2017, 2018, 2019, Fall 2020, Spring 2021-2025
  • “Algorithms in Bioinformatics”, Credit 3, Fall 2011 – 2016, Spring 2018, 2021-2025
  • “Programming languages for Bioinformatics”, Credit 3, Spring 2013-2016, Credit 2, Spring 2017, 2018, 2019, 2020
  • “Matlab programming”, Credit 2, Spring 2012
  • "Advanced Bioinformatics", Credit 3, Spring 2012-2015
  • “Computational Biology”, Bioinformatics session, Credit 3, Fall 2011- 2016
  • “Genomics and Proteomics”, Credit 3, Fall 2010
  • “Digital Signal Processing”, Credit 3, Fall 2009
  •  “Frontier topics in Bioinformatics”, Biological Sequence Analysis session, Spring 2009

  • National Key R&D Program (2023YFF1001600, PI), 2023.12-2027.11, "Validation and evaluation of genome editing in agricultural plants and animals"

  •  Science and Technology Commission of Shanghai Municipality (24JS2840300, PI), 2024.12-2027.11, "Cancer pan-genomics-based mutation identification and application in precision diagnosis and therapy"

  • NSFC Project  (32170643, PI), 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), 2022.4-2025.3, "Identification and characterization of horizontal gene transfer in bat genomes"
  • Science and Technology Commission of Shanghai Municipality (20ZR1428200) 2020.7-2023.6, "Construction of rice pan-genome browser 2.0"
  • Medicine and Engineering joint project (YG2017ZD01, co-PI), 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), 2015.1-2018.12, "Finding and characterizing complex structure sequence modules in metagenomes"
  • National High-Tech R&D Program (863) (2014AA02502, Co-PI),  2014.1-2017.12, "Key technologies for microbial genomic data integration and analysis"
  • National Basic Research Program of China (973) (2013CB956103, Co-PI), 2013.1 – 2017.12,“The degeneration mechanism and recovery potential of coral reefs in South China sea"
  • NSFC Project  (61272250, PI),  2013.1-2016.12, "Finding and characterization of genes containing repeat regions"
  • NSFC Project  (60970050, PI),  (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),  2009.1-2011.12, "Metagenomics data collection and analysis system based on the next-generation sequencing technologies"
  • Shanghai Pujiang Program  (09PJ1407900, PI), (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), 2008.10-2010.9, "Algorithms and system for complex sequence module finding"

Selected Grants