Chaochun Wei

Professor (Information and computing sciences)

Shanghai, China

Dr. Chaochun Wei is currently Professor in the Department of Bioinformatics and Biostatistics at Shanghai Jiao Tong University, China. He obtained his Sc.D. in Computer Science from Washington University in St. Louis, USA, and B.S. in Mathematics from Peking University, China. His research interests focus on genomics, comparative genomics and metagenomics. His work on C.elegans gene prediction was the first gene prediction system to achieve 60% sensitivity in the exact prediction of proteins in a multi-cellular organisms. He identified and characterized ~30,000 novel human protein-coding transcripts. In metagenomics, Dr. Wei estimated that there are more than 9 million unique genes in the human gut, which is more than 400 times of the number of human genes. He has published in PLoS Biology, Genome Research, Nucleic Acids Research, Bioinformatics, etc.


  • Li, X., Hu, Z., Yu, X., Ma, B., Zhang, C., Wei, C.*, and Wu, J.*, “RNA-seq of embryonic cells and germ cells shows direct evidence for dosage compensation in mammals”, Scientific Reports, 2017 (accepted), 10.1038/s41498-017-03829-z (SREP-16-42-20).
  • 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.
  • Huang, W., Tsai L., Li, Y., Hua, N., Sun, C., Wei, C.*, “Widespread of horizontal gene transfer in the human genome”, BMC Genomics, 2017, 18:274
  • Zhu, H., Xu, W., Hu, Z., Zhang, H., Shen, Y., Lu, S., Wei, C.*, Wang, Z.*, “RNA virus receptor Rig-I monitors gut microbiota and inhibits colitis-associated colorectal cancer”, J. of Experimental & Clinical Cancer Research, 2017, 36:2.
  • 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
  • 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-seq and proteomics", Scientific Reports, 2015, 5:10940
  • Zhang, Y., He, Y., Zheng, G., Wei, C.*, "MOST+: A de novo motif finder combining genomic sequence and heterogeneous genome-wide signatures", BMC Genomics, 2015, 16(Suppl 7):S13
  • Hou, T., Zheng, G., Zhang P., Jia, J., Li, J., Xie, L., Wei, C.*, Li, Y., " LAceP: lysine acetylation sites prediction using logistic regression classifier", PLoS ONE, 2014, 9(2): e89575
  • Jia, B., Cai, K., Xuan, L., Wei, C.*, “NeSSM: a Next-generation Sequencing Simulator for Metagenomics”, PLoS ONE, 2013, 8(10):e75448.
  • Zheng, G., Liu, Q., Ding, G., Wei, C.*, Li, Y., “Towards biological characters of interactions between transcription factors and their DNA targets in Mammals”, 2012, BMC Genomics, 13:388
  • He, Y., Zhang, Y., Zheng, G., Wei, C.*, “CTF: a CRF-based transcription factor binding sites finding system”, BMC Genomics, 2012, 13(Suppl 8):S18
  • Zheng, G., Wang, H., Wei, C.*, Li, Y., “iGepros: An integrated gene and protein annotation server for biological nature exploration”, BMC Bioinformatics, 2011, 12(Suppl 14):S6
  • Jia, P., Xuan, L., Liu, L., Wei, C.*, “MetaBinG: Using GPUs to accelerate metagenomic sequence classification”. PLoS ONE, 2011, 6(11): e25353.
  • The MGC Project Team, “The Completion of the Mammalian Gene Collection (MGC)”, Genome Research, 2009, 19:2324-2333
  • 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
  • Zheng, G., Tu, K., Yang, Q., Xiong, Y., Wei, C., Xie, L., Zhu, Y. and Li, Y. “ITFP: an integrated platform of mammalian transcription factors”, Bioinformatics, 2008, 24(20):2416-2417
  • Zheng, G., Qian, Z., Yang, Q., Wei, C., Xie, L., Zhu, Y. and Li, Y. “The Combination Approach of SVM and ECOC for Powerful Identification and Classification of Transcription Factor”, BMC Bioinformatics, 2008 Jun 16;9(1):282.
  • Arumugam, M., Wei, C., Brown, R. H. and Brent, M. R. “PAIRAGON + N-SCAN_EST: A Model-Based Gene Annotation Pipeline”, Genome Biology, 2006, 7(Suppl I):S5.
  • Wei, C. and Brent, M. R. “Using ESTs to Improve the Accuracy of de novo Gene Prediction”, BMC Bioinformatics, 2006, 7:327.
  • 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.
  • Stein, L. D. Z. Bao, ..., Wei, C., ..., Waterston, R. H. “The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics”, PLoS Biology, 2003, 1(2): E45

Chaochun Wei's public data