Dr. Chaochun Wei, Department of Bioinformatics and Biostatistics

Research

Research interests:

• functional element finding in genomes, such as
• alternative splicing prediction
• regulatory element finding
• metagenomics
• pan-genomics
• high performance computing for bioinformatics

Major research contents are comparative-genomics and biological sequence analysis methods and systems for data generated by the next-generation sequencing technologies. These methods and systems can improve the understanding of some biological processes by sequence information, such as the impact of genome sequence mutations on pathogenicity of microbes, alternative splicing, gene expression regulation and host-environment interactions. The final goal is to apply these knowledge to medical diagnose, disease therapy and disease prevention.

Grants:
• Shanghai Science and Technology Innovation Action Plan
• "Cancer pangenome based structural variation identification and its application in precision diagonosis and therapy",(24JS2840300, PI, RMB 3M)(2024.12-2027.11)
• National Key R&D Program of China
• "Validation and evaluation tehcnologies for genome editing agriculture animals and plants" (2023YFF1001600, PI, RMB 25M)(2023.12-2027.11)
• National Natural Science Foundation of China(NSFC)
• "A third-generation-sequencing-based pan-genome construction method and its application in rice genome analysis" (32170643, PI, RMB 580K)(2022.1-2025.12)
• Natural Science Foundation of Shanghai
• "Horizontal gene transfer in bat genomes", (22ZR1433600, PI, RMB 200K) (2022.4-2025.3)

Finished grants:
• Natural Science Foundation of Shanghai
• "Construction of the rice pangenome browser 2.0", (20ZR1428200, PI, RMB 200K) (2020.7-2023.6)
• National Natural Science Foundation of China(NSFC)
• "Finding and characterizing complex structure sequence modules in metagenomes"(61472246, PI, RMB 800K ) (2015.1-2018.12)
• "Finding and characterizing of genes containing repeat regions"(61272250, PI, RMB 800K ) (2012.1-2016.12)
• "An index measuring the gene structure variations and its application in the study of disease susceptibilities of genes"(60970050, PI, RMB 300k)(2010.1-2012.12)
• National High-Tech R&D Program (863)
• "A Next-generation-sequencing-based system for metagenome data collection and analysis"(2009AA02Z310, PI, RMB 1.61M)(2009.1 - 2011.12)
• "Integration and analysis of omics data for microbes" (2014AA021502, Co-PI, RMB 650K)(2014.1 - 2016.12)
• National Basic Research Program of China(973)
• "The degradation methanism of coral reefs in South China Sea and their restoration potential" (2013CB956103, RMB 1.04M(total 5.72M))(2013.1-2017.12)
• Shanghai Pujiang Program
• "CRF theory and its application in Bioinformatics"(09PJ1407900, PI, RMB 200k)(2009.8-2011.7)
• Science and Technology Innovation Program of Basic Science Foundation of Shanghai
• "Algorithms and system for complex sequence module finding"(08JC1416700, PI, RMB 250K) (2008.10-2010.9)
• Cross-Institute Research Fund of Shanghai Jiao Tong University
• "Construction of big data platform for complex phenotypes and diverse microbes of gastric cancer", (YG2017ZD01, RMB 750K, Co-PI, PI:Yanying Yu) (2018.1-2020.12)
• "The impact of genes Kiss1, CUX1 and ER on precocious puberty", (YG2015MS39, RMB 210K, Co-PI, PI: Yongfen Lv) (2016.1-2018.12)

 

©2010 Chaochun Wei