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Alberto Paccanaro, Ph.D. - Publications

Affiliations: 
Computer Science Royal Holloway, University of London, Egham, England, United Kingdom 
Area:
computational biology, machine learning
Website:
http://www.paccanarolab.org
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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
2024 Caniza H, Cáceres JJ, Torres M, Paccanaro A. LanDis: the disease landscape explorer. European Journal of Human Genetics : Ejhg. PMID 38200084 DOI: 10.1038/s41431-023-01511-9  0.716
2022 Galeano D, Paccanaro A. Machine learning prediction of side effects for drugs in clinical trials. Cell Reports Methods. 2: 100358. PMID 36590692 DOI: 10.1016/j.crmeth.2022.100358  0.756
2022 Sacramento CQ, Fintelman-Rodrigues N, Dias SSG, Temerozo JR, Da Silva APD, da Silva CS, Blanco C, Ferreira AC, Mattos M, Soares VC, Pereira-Dutra F, Miranda MD, Barreto-Vieira DF, da Silva MAN, Santos SS, ... ... Paccanaro A, et al. Unlike Chloroquine, Mefloquine Inhibits SARS-CoV-2 Infection in Physiologically Relevant Cells. Viruses. 14. PMID 35215969 DOI: 10.3390/v14020374  0.726
2021 de Siqueira Santos S, Torres M, Galeano D, Sánchez MDM, Cernuzzi L, Paccanaro A. Machine Learning and Network Medicine approaches for Drug Repositioning for COVID-19. Patterns (New York, N.Y.). 100396. PMID 34778851 DOI: 10.1016/j.patter.2021.100396  0.753
2021 McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, ... ... Paccanaro A, et al. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Reports. 109839. PMID 34624208 DOI: 10.1016/j.celrep.2021.109839  0.741
2021 McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, McGrath M, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, ... ... Paccanaro A, et al. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. Biorxiv : the Preprint Server For Biology. PMID 33948587 DOI: 10.1101/2021.04.23.441024  0.739
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  0.754
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  0.453
2020 Gliozzo J, Perlasca P, Mesiti M, Casiraghi E, Vallacchi V, Vergani E, Frasca M, Grossi G, Petrini A, Re M, Paccanaro A, Valentini G. Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction. Scientific Reports. 10: 3612. PMID 32107391 DOI: 10.1038/S41598-020-60235-8  0.329
2020 Dawes JC, Webster P, Iadarola B, Garcia-Diaz C, Dore M, Bolt BJ, Dewchand H, Dharmalingam G, McLatchie AP, Kaczor J, Caceres JJ, Paccanaro A, Game L, Parrinello S, Uren AG. LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites. Mobile Dna. 11: 7. PMID 32042315 DOI: 10.1186/S13100-020-0201-4  0.604
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  0.745
2019 Cáceres JJ, Paccanaro A. Disease gene prediction for molecularly uncharacterized diseases. Plos Computational Biology. 15: e1007078. PMID 31276496 DOI: 10.1371/Journal.Pcbi.1007078  0.687
2019 Webster P, Dawes JC, Dewchand H, Takacs K, Iadarola B, Bolt BJ, Caceres JJ, Kaczor J, Dharmalingam G, Dore M, Game L, Adejumo T, Elliott J, Naresh K, Karimi M, ... ... Paccanaro A, et al. Author Correction: Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates. Nature Communications. 10: 1167. PMID 30842421 DOI: 10.1038/S41467-019-09109-W  0.595
2018 Webster P, Dawes JC, Dewchand H, Takacs K, Iadarola B, Bolt BJ, Caceres JJ, Kaczor J, Dharmalingam G, Dore M, Game L, Adejumo T, Elliott J, Naresh K, Karimi M, ... ... Paccanaro A, et al. Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates. Nature Communications. 9: 2649. PMID 29985390 DOI: 10.1038/S41467-018-05069-9  0.611
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Paccanaro A, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.323
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  0.597
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  0.772
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  0.329
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  0.766
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  0.747
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  0.341
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  0.344
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  0.316
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  0.324
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  0.337
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  0.583
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  0.301
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  0.376
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  0.745
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  0.45
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  0.761
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  0.77
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  0.636
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  0.655
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  0.693
2002 Paccanaro A, Hinton GE. Learning hierarchical structures with linear relational embedding Advances in Neural Information Processing Systems.  0.463
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  0.535
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.  0.443
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