Haiyuan Yu, Ph.D. - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2013 Wang X, Thijssen B, Yu H. Target essentiality and centrality characterize drug side effects. Plos Computational Biology. 9: e1003119. PMID 23874169 DOI: 10.1371/journal.pcbi.1003119  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2006 Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
Show low-probability matches.