Spectral clustering of protein sequences von Paccanaro, Alberto, Casbon, James A., Saqi, Mansoor A. S.

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Learning distributed representations of concepts using linear relational embedding von Paccanaro, A., Hinton, G.E.

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Predicting interactions in protein networks by completing defective cliques von Yu, Haiyuan, Paccanaro, Alberto, Trifonov, Valery, Gerstein, Mark

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Quantifying environmental adaptation of metabolic pathways in metagenomics von Gianoulis, Tara A, Raes, Jeroen, Patel, Prianka V, Bjornson, Robert, Korbel, Jan O, Letunic, Ivica, Yamada, Takuji, Paccanaro, Alberto, Jensen, Lars J, Snyder, Michael, Bork, Peer, Gerstein, Mark B

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Assessing the limits of genomic data integration for predicting protein networks von Lu, Long J, Xia, Yu, Paccanaro, Alberto, Yu, Haiyuan, Gerstein, Mark

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Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates von Webster, P, Dawes, J, Dewchand, H, Takacs, K, Iadarola, B, Bolt, B, Caceres, J, Kaczor, J, Dharmalingham, G, Dore, M, Game, L, Adejumo, T, Elliott, J, Naresh, K, Karimi, M, Rekopoulou, K, Tan, G, Paccanaro, A, Uren, A

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Gossto: a stand-alone application and a web tool for calculating semantic similarities on the gene ontology von Caniza, H, Romero, A. E, Heron, S, Yang, H, Devoto, A, Frasca, M, Mesiti, M, Valentini, G, Paccanaro, A

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Machine Learning Prediction of Side effects for Drugs in Clinical Trials - Galeano and Paccanaro von Diego Galeano

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Machine Learning Prediction of Side effects for Drugs in Clinical Trials - Galeano and Paccanaro von Diego Galeano

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GFam: a platform for automatic annotation of gene families von Sasidharan, Rajkumar, Nepusz, Tamás, Swarbreck, David, Huala, Eva, Paccanaro, Alberto

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LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites von Dawes, J, Webster, P, Iadarola, B, Garcia-Diaz, C, Dore, M, Bolt, B, Dewchand, H, Dharmalingham, G, McClatchie, A, Kaczor, J, Caceres, J, Paccanaro, A, Game, L, Parrinello, S, Uren, A

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Learning Distributed Representations of High-Arity Relational Data with Non-linear Relational Embedding von Paccanaro, Alberto

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A large-scale evaluation of computational protein function prediction von 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, Piovesan, D, Casadio, R, Wang, Z, Cheng, J, Fang, H, Koskinen, P, Toronen, P, Nokso-Koivisto, J, Holm, L, Cozzetto, D, Bryson, K, Jones, DT, Limaye, B, Inamdar, H, Datta, A, Manjari, SK, Joshi, R, Chitale, M, Kihara, D, Lisewski, AM, Erdin, S, Venner, E, Lichtarge, O, Rentzsch, R, Yang, H, Romero, AE, Bhat, P, Paccanaro, A, Hamp, T, Kassner, R, Seemayer, S, Vicedo, E, Schaefer, C, Achten, D, Auer, F, Boehm, A, Braun, T, Hecht, M, Heron, M, Hoenigschmid, P, Hopf, TA, Kaufmann, S, Kiening, M, Krompass, D, Landerer, C, Mahlich, Y, Roos, M, Bjorne, J, Salakoski, T, Wong, A, Shatkay, H, Gatzmann, F, Sommer, I, Wass, MN, Sternberg, MJE, Skunca, N, Supek, F, Bosnjak, M, Panov, P, Dzeroski, S, Smuc, T, Kourmpetis, YAI, Van Dijk, ADJ, Ter Braak, CJF, Zhou, Y, Gong, Q, Dong, X, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Di Camillo, B, Toppo, S, Lan, L, Djuric, N, Guo, Y, Vucetic, S, Bairoch, A, Linial, M, Babbitt, PC, Brenner, SE, Orengo, C, Rost, B, Mooney, SD, Friedberg, I

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Machine Learning and Network Medicine approaches for Drug Repositioning for COVID-19. Santos et al von Suzana de Siqueira Santos

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Machine Learning and Network Medicine approaches for Drug Repositioning for COVID-19. Santos et al von Suzana de Siqueira Santos

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy von Jiang, Y, Oron, T.R, Clark, W.T, Bankapur, A.R, D'Andrea, D, Lepore, R, Funk, C.S, Kahanda, I, Verspoor, K.M, Ben-Hur, A, Koo, E, Penfold-Brown, D, Shasha, D, Youngs, N, Bonneau, R, Lin, A, Sahraeian, S.M.E, Martelli, P.L, Profiti, G, Casadio, R, Cao, R, Zhong, Z, Cheng, J, Altenhoff, A, Skunca, N, Dessimoz, C, Dogan, T, Hakala, K, Kaewphan, S, Mehryary, F, Salakoski, T, Ginter, F, Fang, H, Smithers, B, Oates, M, Gough, J, Toronen, P, Koskinen, P, Holm, L, Chen, C.T, Hsu, W.L, Bryson, K, Cozzetto, D, Minneci, F, Jones, D.T, Chapman, S, Dukka, B.K.C, Khan, I.K, Kihara, D, Ofer, D, Rappoport, N, Stern, A, Cibrian-Uhalte, E, Denny, P, Foulger, R.E, Hieta, R, Legge, D, Lovering, R.C, Magrane, M, Melidoni, A.N, Mutowo-Meullenet, P, Pichler, K, Shypitsyna, A, Li, B, Zakeri, Pooya, Elshal, Sarah, Tranchevent, Léon-Charles, Das, S, Dawson, N.L, Lee, D, Lees, J.G, Sillitoe, I, Bhat, P, Nepusz, T, Romero, A.E, Sasidharan, R, Yang, H, Paccanaro, A, Gillis, J, Sedno-Cort'es, A.E, Pavlidis, P, Feng, S, Cejuela, J.M, Goldberg, T, Hamp, T, Richter, L, Salamov, A, Gabaldon, T, Marcet-Houben, M, Supek, F, Gong, Q, Ning, W, Zhou, Y, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Toppo, S, Ferrari, C, Giollo, M

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy von Jiang, Y, Oron, TR, Clark, WT, Bankapur, AR, D'Andrea, D, Lepore, R, Funk, CS, Kahanda, I, Verspoor, KM, Ben-Hur, A, Koo, DCE, Penfold-Brown, D, Youngs, N, Bonneau, R, Lin, A, Sahraeian, SME, Martelli, PL, Profiti, G, Casadio, R, Cao, R, Zhong, Z, Cheng, J, Skunca, N, Dogan, T, Hakala, K, Mehryary, F, Ginter, F, Fang, H, Smithers, B, Gough, J, Koskinen, P, Chen, C-T, Cozzetto, D, Minneci, F, Jones, DT, Dukka, BKC, Khan, IK, Kihara, D, Ofer, D, Rappoport, N, Stern, A, Cibrian-Uhalte, E, Denny, P, Foulger, RE, Legge, D, Lovering, RC, Magrane, M, Melidoni, AN, Pichler, K, Shypitsyna, A, Li, B, ElShal, S, Dawson, NL, Sillitoe, I, Bhat, P, Nepusz, T, Paccanaro, A, Pavlidis, P, Feng, S, Cejuela, JM, Goldberg, T, Richter, L, Gabaldon, T, Supek, F, Gong, Q, Ning, W, Tian, W, Fontana, P, Toppo, S, Ferrari, C, Giollo, M, Piovesan, D, Del Pozo, A, Benso, A, Politano, G, Savino, A, Rehman, HU, Valentini, G, Bargsten, JW, Gemovic, B, Perovic, V, Almeida-e-Silva, DC, Vencio, RZN, Sharan, M, Vogel, J, Kansakar, L, Zhang, S, Vucetic, S, Wang, Z, Sternberg, MJE, Huntley, RP, Martin, MJ, O'Donovan, C, Robinson, PN, Moreau, Y, Linial, M, Orengo, CA, Rost, B, Greene, CS, Radivojac, P

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Extracting distributed representations of concepts and relations from positive and negative propositions von Paccanaro, A., Hinton, G.E.

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Markov Analysis of Protein Sequence Similarities von Chennubhotla, Chakra, Paccanaro, Alberto

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Inferring protein-protein interactions using interaction network topologies von Paccanaro, A., Trifonov, V., Haiyuan Yu, Gerstein, M.

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