| Year |
Citation |
Score |
| 2024 |
Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations. Nature Biotechnology. PMID 39448882 DOI: 10.1038/s41587-024-02428-4 |
0.325 |
|
| 2023 |
Xiong D, Zhao J, Qiu Y, Zhou Y, Lee D, Gupta S, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. 3D structural human interactome reveals proteome-wide perturbations by disease mutations. Biorxiv : the Preprint Server For Biology. PMID 37162909 DOI: 10.1101/2023.04.24.538110 |
0.31 |
|
| 2022 |
Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, ... ... Yu H, et al. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nature Biotechnology. PMID 36217030 DOI: 10.1038/s41587-022-01474-0 |
0.328 |
|
| 2022 |
Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, ... ... Yu H, et al. A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. Research Square. PMID 35677070 DOI: 10.21203/rs.3.rs-1354127/v2 |
0.342 |
|
| 2022 |
Chen S, Liu Y, Zhang Y, Wierbowski SD, Lipkin SM, Wei X, Yu H. A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. Genome Research. 32: 135-149. PMID 34963661 DOI: 10.1101/gr.275437.121 |
0.321 |
|
| 2020 |
Chen S, Wang J, Cicek E, Roeder K, Yu H, Devlin B. De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. Molecular Autism. 11: 76. PMID 33032641 DOI: 10.1186/s13229-020-00386-7 |
0.322 |
|
| 2020 |
Li G, Pahari S, Krishna Murthy A, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-SEQ: A Sequence-based Method for Predicting Mutation Effect on Protein-protein Binding Affinity. Bioinformatics (Oxford, England). PMID 32866236 DOI: 10.1093/Bioinformatics/Btaa761 |
0.399 |
|
| 2020 |
Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, ... ... Yu H, et al. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proceedings of the National Academy of Sciences of the United States of America. PMID 32398372 DOI: 10.1073/Pnas.1918068117 |
0.442 |
|
| 2020 |
Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, ... ... Yu H, et al. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Systems. 10: 333-350.e14. PMID 32325033 DOI: 10.1016/J.Cels.2020.03.003 |
0.348 |
|
| 2020 |
Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. International Journal of Molecular Sciences. 21. PMID 32272725 DOI: 10.3390/Ijms21072563 |
0.369 |
|
| 2019 |
Yugandhar K, Wang TY, Leung AK, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H. MaXLinker: proteome-wide cross-link identifications with high specificity and sensitivity. Molecular & Cellular Proteomics : McP. PMID 31839598 DOI: 10.1074/Mcp.Tir119.001847 |
0.312 |
|
| 2019 |
Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, ... ... Yu H, et al. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nature Communications. 10: 4141. PMID 31515488 DOI: 10.1038/S41467-019-11959-3 |
0.358 |
|
| 2019 |
Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. Plos Genetics. 15: e1007860. PMID 31469829 DOI: 10.1371/Journal.Pgen.1007860 |
0.544 |
|
| 2019 |
Yugandhar K, Gupta S, Yu H. Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Computational and Structural Biotechnology Journal. 17: 805-811. PMID 31316724 DOI: 10.1016/J.Csbj.2019.05.007 |
0.455 |
|
| 2018 |
Wierbowski SD, Fragoza R, Liang S, Yu H. Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations. Current Opinion in Systems Biology. 11: 107-116. PMID 31086831 DOI: 10.1016/J.Coisb.2018.09.006 |
0.309 |
|
| 2018 |
Chen S, Fragoza R, Klei L, Liu Y, Wang J, Roeder K, Devlin B, Yu H. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Nature Genetics. PMID 29892012 DOI: 10.1038/S41588-018-0130-Z |
0.323 |
|
| 2018 |
Meyer MJ, Beltrán JF, Liang S, Fragoza R, Rumack A, Liang J, Wei X, Yu H. Interactome INSIDER: a structural interactome browser for genomic studies. Nature Methods. PMID 29355848 DOI: 10.1038/Nmeth.4540 |
0.362 |
|
| 2018 |
Gerstein M, Yu H. Editorial overview: Big data acquisition and analysis Current Opinion in Systems Biology. 11: iv. DOI: 10.1016/J.Coisb.2018.09.010 |
0.42 |
|
| 2017 |
Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, ... ... Yu H, et al. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling. Cell Systems. PMID 29128334 DOI: 10.1016/J.Cels.2017.10.010 |
0.365 |
|
| 2017 |
Chen S, Beltrán JF, Esteban-Jurado C, Franch-Expósito S, Castellví-Bel S, Lipkin S, Wei X, Yu H. GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. Nucleic Acids Research. PMID 28521008 DOI: 10.1093/Nar/Gkx398 |
0.313 |
|
| 2017 |
Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biology. 18: 10. PMID 28100260 DOI: 10.1186/S13059-016-1138-2 |
0.364 |
|
| 2016 |
Ang YS, Rivas RN, Ribeiro AJ, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TM, Fu JD, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, ... Yu H, et al. Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. Cell. 167: 1734-1749.e22. PMID 27984724 DOI: 10.1016/J.Cell.2016.11.033 |
0.32 |
|
| 2016 |
Guo Y, Alexander K, Clark AG, Grimson A, Yu H. Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. Rna (New York, N.Y.). PMID 27604961 DOI: 10.1261/Rna.048025.114 |
0.359 |
|
| 2016 |
Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, et al. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation. Molecular Biosystems. PMID 27357594 DOI: 10.1039/C6Mb00237D |
0.401 |
|
| 2016 |
Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, ... ... Yu H, et al. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Molecular Systems Biology. 12: 863. PMID 27107012 DOI: 10.15252/Msb.20156660 |
0.381 |
|
| 2016 |
Meyer MJ, Lapcevic R, Romero AE, Yoon M, Das J, Beltrán JF, Mort M, Stenson PD, Cooper DN, Paccanaro A, Yu H. Mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome. Human Mutation. PMID 26841357 DOI: 10.1002/Humu.22963 |
0.675 |
|
| 2016 |
Meyer MJ, Geske P, Yu H. BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers. Bioinformatics (Oxford, England). PMID 26803163 DOI: 10.1093/Bioinformatics/Btw043 |
0.393 |
|
| 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, ... ... Yu H, 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 |
0.573 |
|
| 2015 |
Das J, Meyer MJ, Yu H. Studying Autism in Context. Cell Systems. 1: 312-313. PMID 27136240 DOI: 10.1016/J.Cels.2015.11.004 |
0.379 |
|
| 2015 |
Das J, Gayvert KM, Bunea F, Wegkamp MH, Yu H. ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers. Bmc Genomics. 16: 263. PMID 25887568 DOI: 10.1186/S12864-015-1465-9 |
0.333 |
|
| 2015 |
Fu Y, Liu Z, Lou S, Colonna V, Bedford J, Mu X, Yip KY, Kang HM, Lappalainen T, Sboner A, Yu H, Rubin M, Tyler-Smith C, Khurana E, Gerstein M. Abstract 4854: A computational framework for prioritizing noncoding regulatory variants in cancer Cancer Research. 75: 4854-4854. DOI: 10.1158/1538-7445.Am2015-4854 |
0.417 |
|
| 2014 |
Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. Plos Genetics. 10: e1004819. PMID 25502805 DOI: 10.1371/Journal.Pgen.1004819 |
0.385 |
|
| 2014 |
Das J, Gayvert KM, Yu H. Predicting cancer prognosis using functional genomics data sets. Cancer Informatics. 13: 85-8. PMID 25392695 DOI: 10.4137/Cin.S14064 |
0.323 |
|
| 2014 |
Das J, Lee HR, Sagar A, Fragoza R, Liang J, Wei X, Wang X, Mort M, Stenson PD, Cooper DN, Yu H. Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. Human Mutation. 35: 585-93. PMID 24599843 DOI: 10.1002/Humu.22534 |
0.443 |
|
| 2014 |
Guariglia-Oropeza V, Orsi RH, Yu H, Boor KJ, Wiedmann M, Guldimann C. Regulatory network features in Listeria monocytogenes-changing the way we talk. Frontiers in Cellular and Infection Microbiology. 4: 14. PMID 24592357 DOI: 10.3389/Fcimb.2014.00014 |
0.428 |
|
| 2014 |
Das J, Fragoza R, Lee HR, Cordero NA, Guo Y, Meyer MJ, Vo TV, Wang X, Yu H. Exploring mechanisms of human disease through structurally resolved protein interactome networks. Molecular Biosystems. 10: 9-17. PMID 24096645 DOI: 10.1039/C3Mb70225A |
0.459 |
|
| 2013 |
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, ... ... Yu H, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/Science.1235587 |
0.744 |
|
| 2013 |
Guo Y, Wei X, Das J, Grimson A, Lipkin SM, Clark AG, Yu H. Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle. American Journal of Human Genetics. 93: 78-89. PMID 23791107 DOI: 10.1016/J.Ajhg.2013.05.022 |
0.345 |
|
| 2013 |
Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, ... Yu H, et al. Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Science Signaling. 6: ra38. PMID 23695164 DOI: 10.1126/Scisignal.2003350 |
0.442 |
|
| 2013 |
Meyer MJ, Das J, Wang X, Yu H. INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics (Oxford, England). 29: 1577-9. PMID 23599502 DOI: 10.1093/Bioinformatics/Btt181 |
0.422 |
|
| 2012 |
Das J, Yu H. HINT: High-quality protein interactomes and their applications in understanding human disease. Bmc Systems Biology. 6: 92. PMID 22846459 DOI: 10.1186/1752-0509-6-92 |
0.415 |
|
| 2012 |
Das J, Mohammed J, Yu H. Genome-scale analysis of interaction dynamics reveals organization of biological networks. Bioinformatics (Oxford, England). 28: 1873-8. PMID 22576179 DOI: 10.1093/Bioinformatics/Bts283 |
0.421 |
|
| 2012 |
Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods. 9: 471-2. PMID 22426491 DOI: 10.1038/Nmeth.1938 |
0.719 |
|
| 2012 |
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature Biotechnology. 30: 159-64. PMID 22252508 DOI: 10.1038/Nbt.2106 |
0.421 |
|
| 2011 |
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. Bmc Genomics. 12: S4. PMID 21810206 DOI: 10.1186/1471-2164-12-S1-S4 |
0.348 |
|
| 2011 |
Wang X, Gulbahce N, Yu H. Network-based methods for human disease gene prediction. Briefings in Functional Genomics. 10: 280-93. PMID 21764832 DOI: 10.1093/Bfgp/Elr024 |
0.378 |
|
| 2011 |
Booth JG, Eilertson KE, Olinares PD, Yu H. A bayesian mixture model for comparative spectral count data in shotgun proteomics. Molecular & Cellular Proteomics : McP. 10: M110.007203. PMID 21602509 DOI: 10.1074/Mcp.M110.007203 |
0.36 |
|
| 2011 |
Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, et al. Next-generation sequencing to generate interactome datasets. Nature Methods. 8: 478-80. PMID 21516116 DOI: 10.1038/Nmeth.1597 |
0.388 |
|
| 2011 |
Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes & Development. 25: 767-78. PMID 21460040 DOI: 10.1101/Gad.1998811 |
0.66 |
|
| 2009 |
Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, et al. Edgetic perturbation models of human inherited disorders. Molecular Systems Biology. 5: 321. PMID 19888216 DOI: 10.1038/Msb.2009.80 |
0.375 |
|
| 2009 |
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. Plos Biology. 7: e1000218. PMID 19841731 DOI: 10.1371/Journal.Pbio.1000218 |
0.623 |
|
| 2009 |
Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, ... ... Yu H, et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods. 6: 47-54. PMID 19123269 DOI: 10.1038/Nmeth.1279 |
0.482 |
|
| 2009 |
Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, et al. Literature-curated protein interaction datasets. Nature Methods. 6: 39-46. PMID 19116613 DOI: 10.1038/Nmeth.1284 |
0.431 |
|
| 2009 |
Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, ... ... Yu H, et al. An empirical framework for binary interactome mapping. Nature Methods. 6: 83-90. PMID 19060904 DOI: 10.1038/Nmeth.1280 |
0.369 |
|
| 2009 |
Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, et al. An experimentally derived confidence score for binary protein-protein interactions. Nature Methods. 6: 91-7. PMID 19060903 DOI: 10.1038/Nmeth.1281 |
0.438 |
|
| 2009 |
Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis A, Simonis N, Rual J, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, et al. Addendum: Literature-curated protein interaction datasets Nature Methods. 6: 934-935. DOI: 10.1038/Nmeth1209-934 |
0.399 |
|
| 2008 |
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, et al. High-quality binary protein interaction map of the yeast interactome network. Science (New York, N.Y.). 322: 104-10. PMID 18719252 DOI: 10.1126/Science.1158684 |
0.411 |
|
| 2008 |
Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, et al. Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Research. 18: 1294-303. PMID 18502943 DOI: 10.1101/Gr.076661.108 |
0.383 |
|
| 2007 |
Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast species. Science (New York, N.Y.). 317: 815-9. PMID 17690298 DOI: 10.1126/Science.1140748 |
0.731 |
|
| 2007 |
Yu H, Jansen R, Stolovitzky G, Gerstein M. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinformatics (Oxford, England). 23: 2163-73. PMID 17540677 DOI: 10.1093/Bioinformatics/Btm291 |
0.666 |
|
| 2007 |
Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. Plos Computational Biology. 3: e59. PMID 17447836 DOI: 10.1371/Journal.Pcbi.0030059 |
0.687 |
|
| 2007 |
Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Research. 35: e8. PMID 17158151 DOI: 10.1093/Nar/Gkl871 |
0.708 |
|
| 2007 |
Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks Bioinformatics. 23: 1048-1048. DOI: 10.1093/Bioinformatics/Btm099 |
0.488 |
|
| 2006 |
Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics (Oxford, England). 22: 2968-70. PMID 17021160 DOI: 10.1093/Bioinformatics/Btl488 |
0.655 |
|
| 2006 |
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 14724-31. PMID 17003135 DOI: 10.1073/Pnas.0508637103 |
0.581 |
|
| 2006 |
Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods in Enzymology. 411: 282-311. PMID 16939796 DOI: 10.1016/S0076-6879(06)11015-0 |
0.717 |
|
| 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 |
0.609 |
|
| 2006 |
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, PeregrÃn-Alvarez JM, Shales M, Zhang X, Davey M, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440: 637-43. PMID 16554755 DOI: 10.1038/Nature04670 |
0.739 |
|
| 2006 |
Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics (Oxford, England). 22: 823-9. PMID 16455753 DOI: 10.1093/Bioinformatics/Btl014 |
0.756 |
|
| 2006 |
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. Target hub proteins serve as master regulators of development in yeast. Genes & Development. 20: 435-48. PMID 16449570 DOI: 10.1101/Gad.1389306 |
0.716 |
|
| 2005 |
Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes & Development. 19: 2816-26. PMID 16322557 DOI: 10.1101/Gad.1362105 |
0.541 |
|
| 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 |
0.744 |
|
| 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 |
0.751 |
|
| 2004 |
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 431: 308-12. PMID 15372033 DOI: 10.1038/Nature02782 |
0.56 |
|
| 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 |
0.787 |
|
| 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 |
0.646 |
|
| 2004 |
Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends in Genetics : Tig. 20: 227-31. PMID 15145574 DOI: 10.1016/J.Tig.2004.04.008 |
0.712 |
|
| 2004 |
Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Research. 32: 328-37. PMID 14724320 DOI: 10.1093/Nar/Gkh164 |
0.698 |
|
| 2004 |
Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, ... ... Yu H, et al. A map of the interactome network of the metazoan C. elegans. Science (New York, N.Y.). 303: 540-3. PMID 14704431 DOI: 10.1126/Science.1091403 |
0.58 |
|
| 2003 |
Kluger Y, Yu H, Qian J, Gerstein M. Relationship between gene co-expression and probe localization on microarray slides. Bmc Genomics. 4: 49. PMID 14667251 DOI: 10.1186/1471-2164-4-49 |
0.468 |
|
| 2003 |
Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiology. 133: 1480-93. PMID 14605227 DOI: 10.1104/Pp.103.029439 |
0.461 |
|
| 2003 |
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (New York, N.Y.). 302: 449-53. PMID 14564010 DOI: 10.1126/Science.1087361 |
0.758 |
|
| 2003 |
Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics (Oxford, England). 19: 1917-26. PMID 14555624 DOI: 10.1093/Bioinformatics/Btg347 |
0.56 |
|
| 2003 |
Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends in Genetics : Tig. 19: 422-7. PMID 12902159 DOI: 10.1016/S0168-9525(03)00175-6 |
0.537 |
|
| 2003 |
Qian J, Kluger Y, Yu H, Gerstein M. Identification and correction of spurious spatial correlations in microarray data. Biotechniques. 35: 42-4, 46, 48. PMID 12866403 DOI: 10.2144/03351Bm03 |
0.501 |
|
| 2002 |
Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48: 682-95. PMID 12211036 DOI: 10.1002/Prot.10168 |
0.733 |
|
| 2001 |
Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M. Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions Journal of Molecular Biology. 314: 1053-1066. PMID 11743722 DOI: 10.1006/Jmbi.2000.5219 |
0.495 |
|
| 2001 |
Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M. PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Research. 29: 1750-64. PMID 11292848 DOI: 10.1093/Nar/29.8.1750 |
0.758 |
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