Research

The Xia lab develops computational techniques to model complex bio-molecular systems, such as proteins and protein networks.  Representative publications are grouped into the following research areas.

Protein Network Reconstruction

• Integrated prediction of the helical membrane protein interactome in yeast. J. Mol. Biol. 357: 339-349 (2006).
• Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 15: 945-953 (2005).
• Analyzing cellular biochemistry in terms of molecular networks. Annu. Rev. Biochem. 73: 1051-1087 (2004).
  
• Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14: 1107-1118 (2004).
  

Protein Network Analysis

• The role of disorder in interaction networks: a structural analysis. Mol. Syst. Biol. 4: 179 (2008).
• Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell 131: 121-135 (2007).
• Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1938-1941 (2006).
• Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol. 7: R55 (2006).

Protein Function Prediction

• High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics 9: 119 (2008).

Protein Structure Prediction

• Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model. J. Chem. Phys. 113: 9318-9330 (2000).
  

• Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300: 171-185 (2000).
  
• Ab initio protein structure prediction using a combined hierarchical approach. Proteins 3S: 194-198 (1999).

• Molecular modelling and design of invariant chain peptides with altered dissociation kinetics from class II MHC. Biochemistry 35: 14734-14742 (1996).
  

Protein Evolution

• Simulating protein evolution in sequence and structure space. Curr. Opin. Struct. Biol. 14: 202-207 (2004).
  

• Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins 55: 107-114 (2004).
• Roles of mutation and recombination in the evolution of protein thermodynamics. Proc. Natl. Acad. Sci. USA 99: 10382-10387 (2002).