Jianlin (Jack) Cheng

Research

My group focuses on developing computational tools to tackle biological problems, such as protein structure prediction, protein interaction, protein function prediction, biological sequence alignments, inference and simulation of biological networks, and genomics. Currently, my group is actively working to

predict protein structure from protein sequence;
evaluate the quality of protein structure models;
develop tools to simulate and infer biological pathways with applications to plant development (iPlant collaborative project);
apply systems biology techniques to epigenomics and cancer research (collaborative project);
develop a protein structure and function database for the soybean genome (collaborative project);
apply bioinformatics methods to analyze the maize genome (collaborative project)
predict and analyze protein domain structure and domain evolution (collaborative project);
predict protein interaction;
build a computer-aided protein design (collaborative project);
develop tools to integrate multi-source data, including gene expression, SNP, protein structure, protein interaction, protein function, and biological pathway to discover the mechanism of a disease (collaborative project).
The bioinformatics tools produced by our group are used in a variety of biomedical research by life scientists from around the world.

Awards & Honors

• National Science Foundation CAREER Award (2012)
• 2nd in Automated High-Accuracy 3D Protein Structure Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006
• 1st in Automated Protein Domain Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006.
• 2nd in Automated Residue Contact Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006
• 2nd in Automated Protein Disorder Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006.
• Two campus awards during 2005 University of California Data Mining Contests
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008)
• Panelist, National Science Foundation Cyber-Enabled Discovery and Innovation (CDI) program (2008)
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM, 2008)
• Program Committee, International Joint Conference on Neural Networks (IJCNN) (2008)
• Program Committee, International Conference on Biomedical Engineering and Informatics (BMEI 2008)
• Editorial Board Member, Journal of Computational Intelligence in Bioinformatics and Systems Biology (since 2007)
• Editorial Board Member, International Journal of Computational Biology and Drug Design (since 2007)
• Program Committee and Session Chair, IEEE 7th Symposium on Bioinformatics and Bioengineering (BIBE 2007)
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)
• Chair of the Genomics Session, International Conference on Bioinformatics and Computational Biology (BIOCOMP 2007)