Dr. Shoudan Liang

Regular Member

The University of Texas M. D. Anderson Cancer Center
Department of Bioinformatics and Computational Biology

Research Interests:

• Developing algorithms to analyze DNA sequences, especially the DNA motifs that bind to proteins
• Designing DNA microarray probes to increase data quality
• Identifying minor histo-compatibility antigens from SNP data to search for a leukemia vaccine
• Mathematical modeling of immune systems

We develop algorithms and tools to analyze microarray data with the aim of understanding the genetic circuitry that underlies diverse systems such as stem cell differentiation, development in animals, proliferation and apoptosis in immune and cancer cells. These algorithms combine several types of data, mRNA expression, high-throughput microarray assay on protein-DNA binding (chIP-chip), and conservation across species.

In collaboration with Dr. Molldrem of the Department of Blood and Marrow Transplantation, we are genotyping bone marrow transplant patients and their donors. By correlating these data with the corresponding clinical outcomes, we search for potential leukemia vaccines.

In my laboratory, students will gain familiarity with computational techniques for analyzing protein-binding DNA motifs and gene expression data, high-performance computing, and mathematical modeling of immune responses.

Selected Publications:

MP Samanta, S Liang (2003) Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 100: 12579-12583.

S Liang, MP Samanta, BA Biegel (2004) cWINNOWER algorithm for finding fuzzy DNA motifs. J Bioinform and Comput Biol 2: 47-60.

R Nigam, S Liang (2005) Perturbing Thermodynamically Unfeasible Metabolic Networks. Lecture Notes in Computer Science, Aug 2005, 3594: 30-41.

Additional Publications

Program Affiliation:

Program in Biomathematics and Biostatistics