Publications

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	Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. Franzosa EA, Xue R, Xia Y. Genome Biology and Evolution 5: 734-744 (2013).
	Construction of functional linkage gene networks by data integration. Linghu B, Franzosa EA, Xia Y. Methods in Molecular Biology 939: 215-232 (2013).
	Toward a three-dimensional view of protein networks between species. Franzosa EA, Garamszegi S, Xia Y. Frontiers in Microbiology 3: 428 (2012).
	Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. Coulombe-Huntington J, Xia Y. PLoS Computational Biology 8: e1002734 (2012).
	Independent effects of protein core size and expression on residue-level structure-evolution relationships. Franzosa EA, Xia Y. PLoS ONE 7: e46602 (2012).
	Multi-edge gene set networks reveal novel insights into global relationships between biological themes. Parikh JR, Xia Y, Marto JA. PLoS ONE 7: e45211 (2012).
	Active clustering of biological sequences. Voevodski K, Balcan MF, Röglin H, Teng SH, Xia Y. Journal of Machine Learning Research 13: 203-225 (2012). Preliminary version published as: Efficient clustering with limited distance information. Voevodski K, Balcan MF, Röglin H, Teng SH, Xia Y. Proceedings of the 26th Conference on Uncertainty in Artificial Intelligence 632-641 (2010).
	Structural models for host-pathogen protein-protein interactions: assessing coverage and bias. Franzosa EA, Xia Y. Pacific Symposium on Biocomputing 17: 287-298 (2012).
	Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. Franzosa EA, Albanèse V, Frydman J, Xia Y, McClellan AJ. PLoS ONE 6: e28211 (2011).
	*Production of a reference transcriptome and a transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis.* Traylor-Knowles N, Granger BR, Lubinski T, Parikh JR, Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR. BMC Genomics 12: 585 (2011).
	Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation. Yen JY, Garamszegi S, Geisbert JB, Rubins KH, Geisbert TW, Honko A, Xia Y, Connor JH, Hensley LE. Journal of Infectious Diseases 204: S1043-S1052 (2011).
	Structural principles within the human-virus protein-protein interaction network. Franzosa EA, Xia Y. Proceedings of the National Academy of Sciences USA 108: 10538-10543 (2011). *[Highlighted in "This Week in PNAS" and Frontiers in Microbiology]*
	Min-sum clustering of protein sequences with limited distance information. Voevodski K, Balcan MF, Röglin H, Teng SH, Xia Y. Proceedings of the 1st International Workshop on Similarity-Based Pattern Recognition 192-206 (2011). Published as Lecture Notes in Computer Science 7005: 192-206 (2011).
	Using functional linkage gene networks to study human diseases. Linghu B, Liu G, Xia Y. Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications 275-293 (2011).
	*Bioinformatics analysis of macrophages exposed to Porphyromonas gingivalis: implications in acute vs. chronic infections.* Yu WH, Hu H, Zhou Q, Xia Y, Amar S. PLoS ONE 5: e15613 (2010).
	Protein evolution in yeast transcription factor subnetworks. Wang Y, Franzosa EA, Zhang XS, Xia Y. Nucleic Acids Research 38: 5959-5969 (2010).
	Discovering causal signaling pathways through gene-expression patterns. Parikh JR, Klinger B, Xia Y, Marto JA, Blüthgen N. Nucleic Acids Research 38: W109-W117 (2010).
	Spectral affinity in protein networks. Voevodski K, Teng SH, Xia Y. BMC Systems Biology 3: 112 (2009).
	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).
	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). *[Highlighted in Current Opinion in Structural Biology]*
	Integrated assessment of genomic correlates of protein evolutionary rate. Xia Y, Franzosa EA, Gerstein MB. PLoS Computational Biology 5: e1000413 (2009). *[Highlighted in Current Opinion in Structural Biology]*
	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).
	Computational reconstruction of protein-protein interaction networks: algorithms and issues. Franzosa E, Linghu B, Xia Y. Methods in Molecular Biology 541: 89-100 (2009).
	Structural correlates of protein melting temperature. Franzosa EA, Lynagh KJ, Xia Y. Proceedings of the 4th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations 99-106 (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. Proceedings of the 2nd International Symposium on Optimization and Systems Biology 333-340 (2008). Published as Lecture Notes in Operations Research 9: 333-340 (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).
	Structural perspectives on protein evolution. Franzosa E, Xia Y. Annual Reports in Computational Chemistry 4: 3-21 (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). *[Highlighted in Nature Structural & Molecular Biology* and Faculty of 1000]**
	Relating three-dimensional structures to protein networks provides evolutionary insights. Kim PM, Lu LJ, Xia Y, Gerstein MB. Science 314: 1938-1941 (2006). *[Highlighted in Science, Nature Genetics, Chemical & Engineering News,* and Faculty of 1000]**
	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). *[Highlighted in Faculty of 1000]*
	*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).
	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).
	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). *[Highlighted in Current Opinion in Genetics & Development]*
	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).
	Physical, organizational and evolutionary principles of protein sequence-structure relationships. Xia Y. Ph.D. Thesis, Stanford University (2003).
	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). *[Highlighted in Faculty of 1000]*
	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). *[Highlighted in Modern Drug Discovery]*
	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 modeling 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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