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Publications

    1. Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis. Molecular Systems Biology 4: 179 (2008). [PDF]
    2. Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics 9: 119 (2008). [PDF]
    3. 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). [PDF] [Highlighted in Nature Structural & Molecular Biology, Faculty of 1000]
    4. Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1938-1941 (2006). [PDF] [Highlighted in Science, Nature Genetics, C&EN, Faculty of 1000]
    5. Yu H, Xia Y, Trifonov V, Gerstein M. Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biology 7: R55 (2006). [PDF]
    6. Xia Y, Lu LJ, Gerstein M. Integrated prediction of the helical membrane protein interactome in yeast. Journal of Molecular Biology 357: 339-349 (2006). [PDF]
    7. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Research 15: 945-953 (2005). [PDF] [Highlighted in Faculty of 1000]
    8. Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F, Gerstein M. Protein interaction prediction by integrating genomic features and protein interaction network analysis. Data Analysis and Visualization in Genomics and Proteomics 61-81 (2005). [PDF]
    9. Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J. Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation. Journal of Bacteriology 187: 2983-2991 (2005). [PDF]
    10. Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Research 33: 1710-1721 (2005). [PDF]
    11. Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Quarterly Reviews of Biophysics 37: 121-146 (2004). [PDF]
    12. Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annual Review of Biochemistry 73: 1051-1087 (2004). [PDF]
    13. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Research 14: 1107-1118 (2004). [PDF]
    14. Freeman-Cook LL, Dixon AM, Frank JB, Xia Y, Ely L, Gerstein M, Engelman DM, DiMaio D. Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor ß receptor. Journal of Molecular Biology 338: 907-920 (2004). [PDF]
    15. Xia Y, Levitt M. Simulating protein evolution in sequence and structure space. Current Opinion in Structural Biology 14: 202-207 (2004). [PDF] [ COSB Editorial]
    16. Xia Y, Levitt M. Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins: Structure, Function, Bioinformatics 55: 107-114 (2004). [PDF]
    17. Xia Y. Physical, organizational and evolutionary principles of protein sequence-structure relationships. Ph.D. Thesis, Stanford University (2002). [PDF]
    18. Xia Y, Levitt M. Roles of mutation and recombination in the evolution of protein thermodynamics. Proceedings of the National Academy of Sciences of the United States of America 99: 10382-10387 (2002). [PDF] [Highlighted in Faculty of 1000]
    19. Fain B, Xia Y, Levitt M. Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Protein Science 11: 2010-2021 (2002). [PDF]
    20. Fain B, Xia Y, Levitt M. Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins. IBM Journal of Research and Development 45: 525-532 (2001). [PDF]
    21. Xia Y, Levitt M. Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model. Journal of Chemical Physics 113: 9318-9330 (2000). [PDF]
    22. Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology 300: 171-185 (2000). [PDF]
    23. Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. Pacific Symposium on Biocomputing 5: 176-187 (2000). [PDF]
    24. Samudrala R, Xia Y, Huang E, Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins: Structure, Function, Genetics 3S: 194-198 (1999). [PDF] [Highlighted in Modern Drug Discovery]
    25. Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symposium on Biocomputing 4: 505-516 (1999). [PDF]
    26. Liang MN, Lee C, Xia Y, McConnell HM. Molecular modelling and design of invariant chain peptides with altered dissociation kinetics from class II MHC. Biochemistry 35: 14734-14742 (1996). [PDF]
    27. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Photodissociation of methylazide: Observation of triplet methylnitrene radical. Journal of Chemical Physics 105: 5798-5805 (1996). [PDF]
    28. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Photodissociation of CH3N3 - Spectral evidences for the formation of triplet CH3N radical. Acta Physico-Chimica Sinica 11: 961-964 (1995). [PDF]
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