[Colloquium] 9/17 Thesis Defense : Jianzhu Ma

[Mary Marre]

When:     Thursday, September 17th, 2015 at 9:00 am

Where:    TTIC, 6045 S Kenwood Avenue, Room #526

Who:       Jianzhu Ma

Title:       Protein Structure Prediction by Protein Alignments

Abstract:

My thesis is aimed to solve the template-based protein structure prediction
problem from two directions: creating accurate protein alignments and
predicting accurate protein contact map. In this talk I will introduce a
new alignment framework MRFalign which goes beyond original HMM and CRF
methods and uses Markov Random Field (MRf) to model a protein family and
align two proteins by aligning two MRF together. Compared to HMM and CRF,
that can only model local-range residue correlation, MRFs can model
long-range residue interactions (e.g., residue co-evolution) and thus,
encodes global information in a protein. MRFalign formulizes the problem as
an integer programming problem and use an ADMM algorithm to quickly find a
suboptimal alignment of two MRFs. In addition I will also introduce a group
graphical lasso (GGL) method for contact prediction that integrates joint
multi-family EC analysis and supervised learning to improve accuracy on
proteins without many sequence homologs. Different from existing
single-family EC analysis that uses residue co-evolution information in
only the target protein family, our joint EC analysis uses residue
co-evolution in both the target family and its related families, which may
have divergent sequences but similar folds. The new GGL method can also
integrate supervised learning methods to further improve accuracy. We
evaluate the performance of both methods including each of its components
on large public benchmarks and show it our methods can achieve better
accuracy comparing with other state-of-the-art methods under all the
measurements on nearly most of the protein classes.

Thesis Advisor: Prof. Jinbo Xu






Mary C. Marre
Administrative Assistant
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 504*
*Chicago, IL  60637*
*p:(773) 834-1757 <%28773%29%20834-1757>*
*f: (773) 357-6970 <%28773%29%20357-6970>*
*mmarre at ttic.edu <mmarre at ttic.edu>*
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