Yu (Brandon) Xia, Ph.D.
Assistant Professor, Biomedical Engineering
Assistant Professor, Bioinformatics
Assistant Professor, Chemistry
Ph.D., Chemistry/Computational Biology, Stanford University
B.S., Chemistry, Minor in Computer Science, Peking University
Phone: (617) 358-2302
Office: LSEB 911
Office hours: By appointment
Our research focuses on computational structural and systems biology. We develop computational methods to model complex biomolecular systems such as proteins and protein networks. Our goal is to understand the relationship between sequence, 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.
- Computational Structural Biology focuses on computer modeling and analysis of protein structures. Ongoing projects in the lab include: prediction of protein three-dimensional structure and function, modeling protein sequence-structure-function relationships, comparative and evolutionary analysis of proteins.
- Computational Systems Biology focuses on computer modeling and analysis of protein networks. Ongoing projects in the lab include: reconstruction of protein-protein interaction and regulatory networks by genomic data integration, modeling dynamics and evolution of protein-protein interaction and regulatory networks, comparative and evolutionary analysis of protein networks.
Selected Recent Publications
Franzosa EA, Xia Y. “Structural principles within the human-virus protein-protein interaction network” Proceedings of the National Academy of Sciences USA. 108: 10538-10543. (2011)
Wang Y, Franzosa EA, Zhang XS, Xia Y. “Protein evolution in yeast transcription factor subnetworks” Nucleic Acids Research. 38: 5959-5969. (2010)
Wang Y, Zhang XS, Xia Y. “Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data” Nucleic Acids Research. 37: 5943-5958. (2009)
Linghu B, Snitkin ES, Hu Z, Xia Y, DeLisi C. “Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network” Genome Biology. 10: R91. (2009)
Franzosa EA, Xia Y. “Structural determinants of protein evolution are context-sensitive at the residue level” Molecular Biology and Evolution. 26: 2387-2395. (2009)
Xia Y, Franzosa EA, Gerstein MB. “Integrated assessment of genomic correlates of protein evolutionary rate” PLoS Computational Biology. 5: e1000413. (2009)
Yam AY, Xia Y, Lin HTJ, Burlingame A, Gerstein M, Frydman J. “Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies” Nature Structural & Molecular Biology. 15: 1255-1262. (2008)
Kim PM, Sboner A, Xia Y, Gerstein M. “The role of disorder in interaction networks: a structural analysis” Molecular Systems Biology. 4: 179. (2008)
McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. “Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches” Cell. 131: 121-135. (2007)
Kim PM, Lu LJ, Xia Y, Gerstein MB. “Relating three-dimensional structures to protein networks provides evolutionary insights” Science. 314: 1938-1941. (2006)