Alberto Paccanaro, Ph.D. - Publications

Computer Science Royal Holloway, University of London, Egham, England, United Kingdom 
computational biology, machine learning

38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2020 Galeano D, Li S, Gerstein M, Paccanaro A. Predicting the frequencies of drug side effects. Nature Communications. 11: 4575. PMID 32917868 DOI: 10.1038/S41467-020-18305-Y  0.6
2020 Ye C, Paccanaro A, Gerstein M, Yan KK. The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. Bmc Bioinformatics. 21: 222. PMID 32471347 DOI: 10.1186/S12859-020-03545-Y  0.6
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Paccanaro A, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.64
2017 Manfredini F, Romero AE, Pedroso I, Paccanaro A, Sumner S, Brown MJF. Neurogenomic signatures of successes and failures in life-history transitions in a key insect pollinator. Genome Biology and Evolution. PMID 29087523 DOI: 10.1093/Gbe/Evx220  0.64
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  1
2015 Caniza H, Romero AE, Paccanaro A. A network medicine approach to quantify distance between hereditary disease modules on the interactome. Scientific Reports. 5: 17658. PMID 26631976 DOI: 10.1038/Srep17658  1
2014 Smieszek SP, Yang H, Paccanaro A, Devlin PF. Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules. Journal of the Royal Society, Interface / the Royal Society. 11. PMID 25142519 DOI: 10.1098/Rsif.2014.0535  1
2014 Valentini G, Paccanaro A, Caniza H, Romero AE, Re M. An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. Artificial Intelligence in Medicine. 61: 63-78. PMID 24726035 DOI: 10.1016/J.Artmed.2014.03.003  1
2014 Caniza H, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A. GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology. Bioinformatics (Oxford, England). 30: 2235-6. PMID 24659104 DOI: 10.1093/Bioinformatics/Btu144  1
2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, ... ... Paccanaro A, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340  1
2012 Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, ... ... Paccanaro A, et al. A census of human soluble protein complexes. Cell. 150: 1068-81. PMID 22939629 DOI: 10.1016/J.Cell.2012.08.011  1
2012 Bhat P, Yang H, Bögre L, Devoto A, Paccanaro A. Computational selection of transcriptomics experiments improves Guilt-by-Association analyses. Plos One. 7: e39681. PMID 22879875 DOI: 10.1371/Journal.Pone.0039681  1
2012 Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A. GFam: a platform for automatic annotation of gene families. Nucleic Acids Research. 40: e152. PMID 22790981 DOI: 10.1093/Nar/Gks631  1
2012 Dóczi R, Okrész L, Romero AE, Paccanaro A, Bögre L. Exploring the evolutionary path of plant MAPK networks. Trends in Plant Science. 17: 518-25. PMID 22682803 DOI: 10.1016/J.Tplants.2012.05.009  1
2012 Yang H, Nepusz T, Paccanaro A. Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics (Oxford, England). 28: 1383-9. PMID 22522134 DOI: 10.1093/Bioinformatics/Bts129  1
2012 Abbruscato P, Nepusz T, Mizzi L, Del Corvo M, Morandini P, Fumasoni I, Michel C, Paccanaro A, Guiderdoni E, Schaffrath U, Morel JB, Piffanelli P, Faivre-Rampant O. OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast. Molecular Plant Pathology. 13: 828-41. PMID 22443363 DOI: 10.1111/J.1364-3703.2012.00795.X  1
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  1
2010 Nepusz T, Sasidharan R, Paccanaro A. SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. Bmc Bioinformatics. 11: 120. PMID 20214776 DOI: 10.1186/1471-2105-11-120  1
2009 Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, ... ... Paccanaro A, et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. Plos Biology. 7: e96. PMID 19402753 DOI: 10.1371/Journal.Pbio.1000096  1
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/Pnas.0808022106  1
2008 Devoto A, Paccanaro A. Signal transduction networks during stress responses in arabidopsis: High-throughput analysis and modelling Plant Cell Monographs. 10: 331-350. DOI: 10.1007/7089_2007_152  1
2007 Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Research. 17: 787-97. PMID 17567997 DOI: 10.1101/Gr.5573107  1
2006 Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M. Integration of curated databases to identify genotype-phenotype associations. Bmc Genomics. 7: 257. PMID 17038185 DOI: 10.1186/1471-2164-7-257  1
2006 Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Research. 16: 1126-35. PMID 16899653 DOI: 10.1101/Gr.5144106  1
2006 Waite RD, Paccanaro A, Papakonstantinopoulou A, Hurst JM, Saqi M, Littler E, Curtis MA. Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles. Bmc Genomics. 7: 162. PMID 16800888 DOI: 10.1186/1471-2164-7-162  1
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, ... ... Paccanaro A, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440: 637-43. PMID 16554755 DOI: 10.1038/Nature04670  1
2006 Paccanaro A, Casbon JA, Saqi MA. Spectral clustering of protein sequences. Nucleic Acids Research. 34: 1571-80. PMID 16547200 DOI: 10.1093/Nar/Gkj515  1
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  1
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  1
2003 Paccanaro A. Learning distributed representations of high-arity relational data with non-linear relational embedding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2714: 149-156.  1
2003 Chennubhotla C, Paccanaro A. Markov analysis of protein sequence similarities Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2859: 278-286.  1
2002 Paccanaro A, Hinton GE. Learning hierarchical structures with linear relational embedding Advances in Neural Information Processing Systems 1
2002 Tanello M, Paccanaro A, Griggi S, Simeone C. Value of uroflowmetry in assessing circadian changes in micturition in patients with BPH: Our experience using neural networks and probabilistic models Urodinamica. 12: 70-77.  1
2001 Paccanaro A, Hinton GE. Learning distributed representations of concepts using Linear Relational Embedding Ieee Transactions On Knowledge and Data Engineering. 13: 232-244. DOI: 10.1109/69.917563  1
2000 Paccanaro A, Hinton GE. Extracting distributed representations of concepts and relations from positive and negative propositions Proceedings of the International Joint Conference On Neural Networks. 2: 259-264.  1
1997 Mareco C, Paccanaro A. Using the tree representation of terms to recognize matching with neural networks Nonlinear Analysis, Theory, Methods and Applications. 30: 2925-2936. DOI: 10.1016/S0362-546X(97)00346-5  1
1996 Paccanaro A. Development of neural networks for accelerating automated theorem proving: Results for the group theory Journal of Computer and Systems Sciences International. 35: 695-701.  1
1995 Paccanaro A. Guiding term reduction through a neural network: Some preliminary results for the group theory Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 914: 444-449.  1
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