Research

Research in the Xia lab focuses on computer modeling of complex biomolecular systems such as proteins and protein networks.  Our goal is to understand the relationship between structure, function, and evolution at the level of proteins and protein networks.  The tools we use include informatics, modeling, and simulation.  Our research combines prediction and analysis in modeling proteins and protein networks.

Ongoing projects in the lab include: reconstruction of protein interaction and regulatory networks by genomic data integration, modeling dynamics and evolution of protein interaction and regulatory networks, prediction of protein three-dimensional structure and function, protein evolution.

Recent Publications

1)  "Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data," Y. Wang, X.S. Zhang, and Y. Xia, Nucleic Acids Res., 37, 5943-5958 (2009).

2)  "Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network," B. Linghu, E.S. Snitkin, Z. Hu, Y. Xia, and C. DeLisi, Genome Biol., 10, R91 (2009).

3)  "Structural determinants of protein evolution are context-sensitive at the residue level," E.A. Franzosa and Y. Xia, Mol. Biol. Evol., 26, 2387-2395 (2009).

4)  "Integrated assessment of genomic correlates of protein evolutionary rate," Y. Xia, E.A. Franzosa, and M.B. Gerstein, PLoS Comput. Biol., 5, e1000413 (2009).

5)  "Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies," A.Y. Yam, Y. Xia, H.T.J. Lin, A. Burlingame, M. Gerstein, and J. Frydman, Nat. Struct. Mol. Biol., 15, 1255-1262 (2008).

6)  "The role of disorder in interaction networks: a structural analysis," P.M. Kim, A. Sboner, Y. Xia, and M. Gerstein, Mol. Syst. Biol., 4, 179 (2008).

7)  "Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches," A.J. McClellan, Y. Xia, A.M. Deutschbauer, R.W. Davis, M. Gerstein, and J. Frydman, Cell, 131, 121-135 (2007).

8)  "Relating three-dimensional structures to protein networks provides evolutionary insights," P.M. Kim, L.J. Lu, Y. Xia, and M.B. Gerstein, Science, 314, 1938-1941 (2006).