Publications

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	Spectral affinity in protein networks. Voevodski K, Teng SH, Xia Y. BMC Systems Biology, in press.
	Precipitation patterns with polygonal boundaries between electrolytes. Pan C, Gao Q, Xie J, Xia Y, Epstein IR. Physical Chemistry Chemical Physics 11: 11033-11039 (2009).
	A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Wang Y, Wang RS, Joshi T, Xu D, Zhang XS, Chen L, Xia Y. Handbook of Research on Computational Methodologies in Gene Regulatory Networks 450-475 (2009).
	Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Wang Y, Zhang XS, Xia Y. Nucleic Acids Research 37: 5943-5958 (2009).
	Finding local communities in protein networks. Voevodski K, Teng SH, Xia Y. BMC Bioinformatics 10: 297 (2009).
	Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Linghu B, Snitkin ES, Hu Z, Xia Y, DeLisi C. Genome Biology 10: R91 (2009).
	Structural determinants of protein evolution are context-sensitive at the residue level. Franzosa EA, Xia Y. Molecular Biology and Evolution 26: 2387-2395 (2009).
	Integrated assessment of genomic correlates of protein evolutionary rate. Xia Y, Franzosa EA, Gerstein MB. PLoS Computational Biology 5: e1000413 (2009).
	Computational reconstruction of protein-protein interaction networks: algorithms and issues. Franzosa E, Linghu B, Xia Y. Methods in Molecular Biology 541: 89-100 (2009).
	Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Yam AY, Xia Y, Lin HTJ, Burlingame A, Gerstein M, Frydman J. Nature Structural & Molecular Biology 15: 1255-1262 (2008).
	Condition specific subnetwork identification using an optimization model. Wang Y, Xia Y. Lecture Notes in Operations Research 9: 333-340 (2008).
	Structural perspectives on protein evolution. Franzosa E, Xia Y. Annual Reports in Computational Chemistry 4: 3-21 (2008).
	The role of disorder in interaction networks: a structural analysis. Kim PM, Sboner A, Xia Y, Gerstein M. Molecular Systems Biology 4: 179 (2008).
	High-precision high-coverage functional inference from integrated data sources. Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. BMC Bioinformatics 9: 119 (2008).
	Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. Cell 131: 121-135 (2007).
	Relating three-dimensional structures to protein networks provides evolutionary insights. Kim PM, Lu LJ, Xia Y, Gerstein MB. Science 314: 1938-1941 (2006).
	Design principles of molecular networks revealed by global comparisons and composite motifs. Yu H, Xia Y, Trifonov V, Gerstein M. Genome Biology 7: R55 (2006).
	Integrated prediction of the helical membrane protein interactome in yeast. Xia Y, Lu LJ, Gerstein M. Journal of Molecular Biology 357: 339-349 (2006).
	Assessing the limits of genomic data integration for predicting protein networks. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Genome Research 15: 945-953 (2005).
	Protein interaction prediction by integrating genomic features and protein interaction network analysis. Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F, Gerstein M. Data Analysis and Visualization in Genomics and Proteomics 61-81 (2005).
	*Use of thioredoxin as a reporter to identify a subset of Escherichia coli* signal sequences that promote signal recognition particle-dependent translocation.** Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J. Journal of Bacteriology 187: 2983-2991 (2005).
	Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Nucleic Acids Research 33: 1710-1721 (2005).
	Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Quarterly Reviews of Biophysics 37: 121-146 (2004).
	Analyzing cellular biochemistry in terms of molecular networks. Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Annual Review of Biochemistry 73: 1051-1087 (2004).
	Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Genome Research 14: 1107-1118 (2004).
	Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor ß receptor. Freeman-Cook LL, Dixon AM, Frank JB, Xia Y, Ely L, Gerstein M, Engelman DM, DiMaio D. Journal of Molecular Biology 338: 907-920 (2004).
	Simulating protein evolution in sequence and structure space. Xia Y, Levitt M. Current Opinion in Structural Biology 14: 202-207 (2004).
	Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Xia Y, Levitt M. Proteins: Structure, Function, Bioinformatics 55: 107-114 (2004).
	Roles of mutation and recombination in the evolution of protein thermodynamics. Xia Y, Levitt M. Proceedings of the National Academy of Sciences USA 99: 10382-10387 (2002).
	Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Fain B, Xia Y, Levitt M. Protein Science 11: 2010-2021 (2002).
	Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins. Fain B, Xia Y, Levitt M. IBM Journal of Research and Development 45: 525-532 (2001).
	Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model. Xia Y, Levitt M. Journal of Chemical Physics 113: 9318-9330 (2000).
	Ab initio construction of protein tertiary structures using a hierarchical approach. Xia Y, Huang ES, Levitt M, Samudrala R. Journal of Molecular Biology 300: 171-185 (2000).
	Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Pacific Symposium on Biocomputing 5: 176-187 (2000).
	Ab initio protein structure prediction using a combined hierarchical approach. Samudrala R, Xia Y, Huang E, Levitt M. Proteins: Structure, Function, Genetics 3S: 194-198 (1999).
	*A combined approach for ab initio* construction of low resolution protein tertiary structures from sequence.** Samudrala R, Xia Y, Levitt M, Huang ES. Pacific Symposium on Biocomputing 4: 505-516 (1999).
	Molecular modelling and design of invariant chain peptides with altered dissociation kinetics from class II MHC. Liang MN, Lee C, Xia Y, McConnell HM. Biochemistry 35: 14734-14742 (1996).
	Photodissociation of methylazide: Observation of triplet methylnitrene radical. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Journal of Chemical Physics 105: 5798-5805 (1996).
	Photodissociation of CH₃N₃ - Spectral evidences for the formation of triplet CH₃N radical. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Acta Physico-Chimica Sinica 11: 961-964 (1995).

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