| Year |
Citation |
Score |
| 2023 |
Li Y, Yao Y, Xia Y, Tang M. Searching for protein variants with desired properties using deep generative models. Bmc Bioinformatics. 24: 297. PMID 37480001 DOI: 10.1186/s12859-023-05415-9 |
0.306 |
|
| 2020 |
Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, ... ... Xia Y, et al. A reference map of the human binary protein interactome. Nature. 580: 402-408. PMID 32296183 DOI: 10.1038/S41586-020-2188-X |
0.344 |
|
| 2017 |
Ghadie MA, Coulombe-Huntington J, Xia Y. Interactome evolution: insights from genome-wide analyses of protein-protein interactions. Current Opinion in Structural Biology. 50: 42-48. PMID 29112911 DOI: 10.1016/j.sbi.2017.10.012 |
0.347 |
|
| 2017 |
Ghadie MA, Lambourne L, Vidal M, Xia Y. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. Plos Computational Biology. 13: e1005717. PMID 28846689 DOI: 10.1371/Journal.Pcbi.1005717 |
0.359 |
|
| 2017 |
Sharir-Ivry A, Xia Y. The Impact of Native State Switching on Protein Sequence Evolution. Molecular Biology and Evolution. PMID 28333346 DOI: 10.1093/molbev/msx071 |
0.325 |
|
| 2016 |
Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, ... ... Xia Y, et al. An inter-species protein-protein interaction network across vast evolutionary distance. Molecular Systems Biology. 12: 865. PMID 27107014 DOI: 10.15252/Msb.20156484 |
0.303 |
|
| 2016 |
Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, ... ... Xia Y, et al. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 164: 805-817. PMID 26871637 DOI: 10.1016/J.Cell.2016.01.029 |
0.325 |
|
| 2016 |
Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, ... ... Xia Y, et al. A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell. 164: 310-323. PMID 26771498 DOI: 10.1016/J.Cell.2015.11.037 |
0.634 |
|
| 2010 |
Wang Y, Franzosa EA, Zhang XS, Xia Y. Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Research. 38: 5959-69. PMID 20466810 DOI: 10.1093/nar/gkq353 |
0.338 |
|
| 2009 |
Voevodski K, Teng SH, Xia Y. Spectral affinity in protein networks. Bmc Systems Biology. 3: 112. PMID 19943959 DOI: 10.1186/1752-0509-3-112 |
0.32 |
|
| 2009 |
Xia Y, Franzosa EA, Gerstein MB. Integrated assessment of genomic correlates of protein evolutionary rate. Plos Computational Biology. 5: e1000413. PMID 19521505 DOI: 10.1371/Journal.Pcbi.1000413 |
0.654 |
|
| 2009 |
Franzosa E, Linghu B, Xia Y. Computational reconstruction of protein-protein interaction networks: algorithms and issues. Methods in Molecular Biology (Clifton, N.J.). 541: 89-100. PMID 19381528 DOI: 10.1007/978-1-59745-243-4_5 |
0.339 |
|
| 2008 |
Yam AY, Xia Y, Lin HT, 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: 1255-62. PMID 19011634 DOI: 10.1038/Nsmb.1515 |
0.611 |
|
| 2008 |
Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis. Molecular Systems Biology. 4: 179. PMID 18364713 DOI: 10.1038/Msb.2008.16 |
0.557 |
|
| 2007 |
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: 121-35. PMID 17923092 DOI: 10.1016/J.Cell.2007.07.036 |
0.501 |
|
| 2006 |
Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating three-dimensional structures to protein networks provides evolutionary insights. Science (New York, N.Y.). 314: 1938-41. PMID 17185604 DOI: 10.1126/Science.1136174 |
0.657 |
|
| 2006 |
Yu H, Xia Y, Trifonov V, Gerstein M. Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biology. 7: R55. PMID 16859507 DOI: 10.1186/Gb-2006-7-7-R55 |
0.686 |
|
| 2006 |
Xia Y, Lu LJ, Gerstein M. Integrated prediction of the helical membrane protein interactome in yeast. Journal of Molecular Biology. 357: 339-49. PMID 16413578 DOI: 10.1016/J.Jmb.2005.12.067 |
0.647 |
|
| 2005 |
Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Research. 15: 945-53. PMID 15998909 DOI: 10.1101/Gr.3610305 |
0.74 |
|
| 2005 |
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. PMID 15838024 DOI: 10.1128/Jb.187.9.2983-2991.2005 |
0.511 |
|
| 2005 |
Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Research. 33: 1710-21. PMID 15784611 DOI: 10.1093/Nar/Gki311 |
0.558 |
|
| 2005 |
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. DOI: 10.1002/0470094419.ch5 |
0.666 |
|
| 2004 |
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: 121-46. PMID 15999419 DOI: 10.1017/S003358350400397X |
0.746 |
|
| 2004 |
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: 1051-87. PMID 15189167 DOI: 10.1146/Annurev.Biochem.73.011303.073950 |
0.691 |
|
| 2004 |
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: 1107-18. PMID 15173116 DOI: 10.1101/Gr.1774904 |
0.728 |
|
| 2004 |
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 beta receptor. Journal of Molecular Biology. 338: 907-20. PMID 15111056 DOI: 10.1016/J.Jmb.2004.03.044 |
0.554 |
|
| 2004 |
Xia Y, Levitt M. Simulating protein evolution in sequence and structure space Current Opinion in Structural Biology. 14: 202-207. PMID 15093835 DOI: 10.1016/J.Sbi.2004.03.001 |
0.607 |
|
| 2004 |
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 and Genetics. 55: 107-114. PMID 14997545 DOI: 10.1002/Prot.10563 |
0.563 |
|
| 2002 |
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. PMID 12149452 DOI: 10.1073/Pnas.162097799 |
0.57 |
|
| 2002 |
Fain B, Xia Y, Levitt M. Design of an optimal Chebyshev-expanded discrimination function for globular proteins Protein Science. 11: 2010-2021. PMID 12142455 DOI: 10.1110/Ps.0200702 |
0.536 |
|
| 1999 |
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. Pacific Symposium On Biocomputing. 505-16. PMID 10380223 DOI: 10.1142/9789814447300_0050 |
0.677 |
|
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