Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin M. Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed M. E. Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen-Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka BKC, Ishita K. Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan G. Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, … Iddo Friedberg and Predrag Radivojac
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Genome Biology; DOI: 10.1186/s13059-016-1037-6 (2016).

Michael J. Meyer, Ryan Lapcevic, Alfonso E. Romero, Mark Yoon, Jishnu Das, Juan Felipe Beltran, Matthew Mort, Peter D. Stenson, David N. Cooper, Alberto Paccanaro,and Haiyuan Yu
mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome
Human Mutation; DOI: 10.1002/humu.22963 (2016).

H. Caniza, A. E. Romero and A. Paccanaro,
A network medicine approach to quantify distance between hereditary disease modules on the interactome
Nature Scientific Reports 5, 17658; doi: 10.1038/srep17658 (2015).
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H. Caniza, A. E. Romero, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, and A. Paccanaro,
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology
Bioinformatics, vol. 30, iss. pp. 2235-2236, 2014.
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S. P. Smieszek, H. Yang, A. Paccanaro, and P. F. Devlin,
Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules
Journal of The Royal Society Interface, vol. 11, iss. 99, 20140535, 2014
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G. Valentini, A. Paccanaro, H. Caniza, A. E. Romero, and M. Re
An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods
Artificial intelligence in medicine, vol. 61, iss. 2, pp. 63-78, 2014.
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T. Nepusz and A. Paccanaro
Structural Pattern Discovery in Protein-Protein Interaction Networks
in I. King, and K. Huang (Eds.) Springer Handbook of Bio-/Neuroinformatics, pp. 375-398, 2014.

P. Radivojac, W. T. Clark, T. R. Oron, A. M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J. M. Yunes, A. S. Talwalkar, S. Repo, M. L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Toronen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D. W. A. Buchan, K. Bryson, D. T. Jones, B. Limaye, H. Inamdar, A. Datta, S. K. Manjari, R. Joshi, M. Chitale, D. Kihara, A. M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A. E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kaszner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Boehm, T. Braun, M. Hecht, M. Heron, P. Honigschmid, T. A. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bjorne, T. Salakoski, A. Wong, H. Shatkay, F. Gatzmann, I. Sommer, M. N. Wass, M. J. E. Sternberg, N. Skunca, F. Supek, M. Bosnjak, P. Panov, S. Dzeroski, T. Smuc, Y. A. I. Kourmpetis, A. D. J. van Dijk, C. J. Braak, Y. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B. Di Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P. C. Babbitt, S. E. Brenner, C. Orengo, B. Rost, S. D. Mooney, and I. Friedberg
A large-scale evaluation of computational protein function prediction
Nature Methods, 10(3):221-7, 2013.
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P. C. Havugimana, T. G. Hart, T. Nepusz, H. Yang, A. L. Turinsky, Z. Li, P. I. Wang, D. R. Boutz, V. Fong, S. Phanse, M. Babu, S. A. Craig, P. Hu, C. Wan, J. Vlasblom, V. U. Dar, A. Bezginov, G. W. Clark, G. C. Wu, S. J. Wodak, E. R. Tillier, A. Paccanaro, E. M. Marcotte, and A. Emili
A census of human soluble protein complexes
Cell, vol. 150, iss. 5, pp. 1068-1081, 2012.
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H. Yang, T. Nepusz, and A. Paccanaro
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty
Bioinformatics, vol. 28, iss. 10, pp. 1383-1389, 2012.
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R. Sasidharan, T. Nepusz, D. Swarbreck, E. Huala, and A. Paccanaro
GFam: a platform for automatic annotation of gene families
Nucleic Acids Research, vol. 40, iss. 19, p. 152, 2012.
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T. Nepusz, H. Yu, and A. Paccanaro
Detecting overlapping protein complexes in protein-protein interaction networks
Nature Methods, vol. 9, pp. 471-472, 2012.
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P. Abbruscato, T. Nepusz, L. Mizzi, M. Del Corvo, P. Morandini, I. Fumasoni, C. Michel, A. Paccanaro, E. Guiderdoni, U. Schaffrath, J. Morel, P. Piffanelli, and O. Faivre-Rampant
OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast: OsWRKY22 role in rice resistance to blast
Molecular Plant Pathology, vol. 13, iss. 8, pp. 828-841, 2012.
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P. Bhat, H. Yang, L. Bögre, A. Devoto, and A. Paccanaro
Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses
PLoS ONE, vol. 7, iss. 8, p. 39681, 2012.
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R. Dóczi, L. Ökrész, A. E. Romero, A. Paccanaro, and L. Bögre
Exploring the evolutionary path of plant MAPK networks
Trends in Plant Science, vol. 17, iss. 9, pp. 518-525, 2012.
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T. Nepusz, R. Sasidharan, and A. Paccanaro
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
BMC Bioinformatics, vol. 11, iss. 1, p. 120, 2010.
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P. Hu, S. C. Janga, M. Babu, J. J. Díaz-Mejía, G. Butland, W. Yang, O. Pogoutse, X. Guo, S. Phanse, P. Wong, S. Chandran, C. Christopoulos, A. Nazarians-Armavil, N. K. Nasseri, G. Musso, M. Ali, N. Nazemof, V. Eroukova, A. Golshani, A. Paccanaro, J. F. Greenblatt, G. Moreno-Hagelsieb, and A. Emili
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
PLoS Biol, vol. 7, iss. 4, p. 1000096, 2009.
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T. A. Gianoulis, J. Raes, P. V. Patel, R. Bjornson, J. O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L. J. Jensen, M. Snyder, P. Bork, and M. B. Gerstein
Quantifying environmental adaptation of metabolic pathways in metagenomics
Proceedings of the National Academy of Sciences, vol. 106, iss. 5, pp. 1374-1379, 2009.
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H. Yang, P. Bhat, H. Shanahan, and A. Paccanaro
A maximal eigenvalue method for detecting process representative genes by integrating data from multiple sources
in NIPS Workshop on Learning from Multiple Sources, 2008.

A. Devoto and A. Paccanaro
Signal Transduction Networks During Stress Responses in Arabidopsis: High-Throughput Analysis and Modelling
in Plant Growth Signaling, Springer Berlin Heidelberg, 2008, pp. 331-350.

Z. D. Zhang, A. Paccanaro, Y. Fu, S. Weissman, Z. Weng, J. Chang, M. Snyder, and M. B. Gerstein
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
Genome Research, vol. 17, iss. 6, pp. 787-797, 2007.
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R. D. Waite, A. Paccanaro, A. Papakonstantinopoulou, J. M. Hurst, M. Saqi, E. Littler, and M. A. Curtis
Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
BMC Genomics, vol. 7, iss. 1, p. 162, 2006.
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A. Paccanaro, J. A. Casbon, and M. A. Saqi
Spectral clustering of protein sequences
Nucleic Acids Research, vol. 34, iss. 5, pp. 1571-1580, 2006.
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C. S. Goh, T. A. Gianoulis, Y. Liu, J. Li, A. Paccanaro, Y. A. Lussier, and M. Gerstein
Integration of curated databases to identify genotype-phenotype associations
BMC Genomics, vol. 7, p. 257, 2006.
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H. Yu, A. Paccanaro, V. Trifonov, and M. Gerstein
Predicting interactions in protein networks by completing defective cliques
Bioinformatics, vol. 22, iss. 7, pp. 823-829, 2006.
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R. Sasidharan, M. Gerstein, and A. Paccanaro
Spectral clustering of protein sequences using sequence-profile scores
in Proceedings of ICNPSC 2006 – 3rd International Conference on Neural Parallel and Scientific Computations, 2006.

N. J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A. P. Tikuisis, T. Punna, J. M. PeregrÃn-Alvarez, M. Shales, X. Zhang, M. Davey, M. D. Robinson, A. Paccanaro, J. E. Bray, A. Sheung, B. Beattie, D. P. Richards, V. Canadien, A. Lalev, F. Mena, P. Wong, A. Starostine, M. M. Canete, J. Vlasblom, S. Wu, C. Orsi, S. R. Collins, S. Chandran, R. Haw, J. J. Rilstone, K. Gandi, N. J. Thompson, G. Musso, P. St Onge, S. Ghanny, M. H. Y. Lam, G. Butland, A. M. Altaf-Ul, S. Kanaya, A. Shilatifard, E. O’Shea, J. S. Weissman, J. C. Ingles, T. R. Hughes, J. Parkinson, M. Gerstein, S. J. Wodak, A. Emili, and J. F. Greenblatt
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Nature, vol. 440, iss. 7084, pp. 637-643, 2006.
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M. Seringhaus, A. Paccanaro, A. Borneman, M. Snyder, and M. Gerstein
Predicting essential genes in fungal genomes
Genome Research, vol. 16, iss. 9, pp. 1126-1135, 2006.
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L. J. Lu, Y. Xia, A. Paccanaro, H. Yu, and M. Gerstein
Assessing the limits of genomic data integration for predicting protein networks
Genome Research, vol. 15, iss. 7, pp. 945-953, 2005.
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A. Paccanaro, V. Trifonov, Y. Haiyuan, and M. Gerstein
Inferring protein-protein interactions using interaction network topologies
in Proceedings of the International Joint Conference on Neural Networks, 2005, pp. 161-166.
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A. Paccanaro, C. Chennubhotla, J. A. Casbon, and M. A. S. Saqi
Spectral clustering of protein sequences
in Proceedings of the International Joint Conference on Neural Networks, 2003, pp. 3083-3088.
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C. Chennubhotla and A. Paccanaro
Markov analysis of protein sequence similarities
in Neural nets, 2003, vol. 2859, Springer, pp. 278-286.