Professor Alberto Paccanaro

  1. 2020
  2. Published

    Predicting the Frequencies of Drug Side effects

    Galeano, D., Li, S., Gerstein, M. & Paccanaro, A., 11 Sep 2020, In: Nature Communications. 11, p. 1-14 14 p., 4575.

    Research output: Contribution to journalArticlepeer-review

  3. Published

    The Corrected Gene Proximity map for analyzing the 3D genome organization using Hi-C data

    Ye, C., Paccanaro, A., Gerstein, M. & Yan, K-K., 29 May 2020, In: BMC Bioinformatics. 21, p. 1-18 18 p., 222.

    Research output: Contribution to journalArticlepeer-review

  4. Published

    Network modeling of patients’ biomolecular profiles for clinical phenotype/outcome prediction

    Gliozzo, J., Perlasca, P., Mesiti, M., Casiraghi, E., Vallacchi, V., Vergani, E., Frasca, M., Grossi, G., Petrini, A., Re, M., Paccanaro, A. & Valentini, G., 27 Feb 2020, In: Scientific Reports. 10, p. 1-15 15 p., 3612.

    Research output: Contribution to journalArticlepeer-review

  5. Published

    LUMI-PCR: An Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites

    Dawes, J. C., Webster, P., Iadarola, B., Garcia-Diaz, C., Dore, M., Bolt, B. J., Dewchand, H., Dharmalingam, G., McLatchie, A. P., Kaczor, J., Caceres, J. J., Paccanaro, A., Game, L., Parrinello, S. & Uren, A. G., 4 Feb 2020, In: Mobile DNA. 11, p. 1-16 16 p., 7.

    Research output: Contribution to journalArticlepeer-review

  6. 2019
  7. Published

    The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Bhat, P., Torres Bobadilla, M., Paccanaro, A., Yang, H. & Romero, A. E., 19 Nov 2019, In: Genome Biology. 20, p. 1-23 23 p., 244 (2019).

    Research output: Contribution to journalArticlepeer-review

  8. Published

    Disease gene prediction for molecularly uncharacterized diseases

    Caceres, J. & Paccanaro, A., 5 Jul 2019, In: PLoS Computational Biology. 15, 7, p. 1-14 14 p., e1007078.

    Research output: Contribution to journalArticlepeer-review

  9. Forthcoming

    Learning interpretable disease self-representations for drug repositioning

    Galeano Galeano, D., Frasca, F., Gonzalez, G., Lapanogov, I., Veselkov, K., Paccanaro, A. & Bronstein, M. M., 2019, (Accepted/In press) Conference on Neural Information Processing Systems (NeurIPS) 2019: Graph representation Learning Workshop .

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  10. 2018
  11. Published

    Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates

    Webster, P., Dawes, J., Dewchand, H., Takacs, K., Iadarola, B., Bolt, B., Caceres Silva, J., Kaczor, J., Dharmalingam, G., Dore, M., Game, L., Adejumo, T., Elliott, J., Naresh, K., Karimi, M., Rekopoulou, K., Tan, G., Paccanaro, A. & Uren, A., 9 Jul 2018, In: Nature Communications. 9, p. 1-14 14 p., 2649.

    Research output: Contribution to journalArticlepeer-review

  12. Published

    A Recommender System Approach for Predicting Drug Side Effects

    Galeano Galeano, D. & Paccanaro, A., 2018, IJCNN 2018: International Joint Conference on Neural Networks. IEEE Xplore, p. 1-7 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  13. 2017
  14. Published

    Drug cocktail selection for the treatment of chagas disease: A multi-objective approach

    Torres Bobadilla, M., Caceres Silva, J., Jimenez, R., Yubero, V., Vega, C., Rolón, M., Cernuzzi, L., Barán, B. & Paccanaro, A., 21 Dec 2017, SLIOIA - Simposio Latinoamericano de Investigación de Operaciones e Inteligencia Artificial 2017. p. 1-5 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  15. Published

    Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator

    Manfredini, F., Romero Lopez, A., Pedroso Rovira, I., Paccanaro, A., Sumner, S. & Brown, M., 1 Nov 2017, In: Genome Biology and Evolution. 9, 11, p. 3059-3072 14 p.

    Research output: Contribution to journalArticlepeer-review

  16. Published

    An Exploratory Analysis on Drug Target Locality

    Caceres Silva, J. & Paccanaro, A., Sep 2017, AGRANDA - Simposio Argentino de GRANdes DAtos 2017.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  17. Published

    Drug targets prediction using chemical similarity

    Galeano Galeano, D. & Paccanaro, A., 26 Jan 2017, XLII Conferencia Latinoamericana de Informatica (CLEI). IEEE Xplore, p. 1-7 7 p. (2016 XLII Latin American Computing Conference (CLEI)).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  18. Published

    Mining the biomedical literature to predict shared drug targets in DrugBank

    Caniza Vierci, H., Galeano Galeano, D. & Paccanaro, A., 2017, XLIII Conferencia Latinoamericana en Informática CLEI 2017. IEEE Xplore, p. 1-5 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  19. 2016
  20. Published

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    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, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 others, 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., Törönen, P., Koskinen, P., Holm, L., Chen, C-T., Hsu, W-L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Bkc, D., 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, P., ElShal, S., Tranchevent, L-C., 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., Sedeño-Cortés, 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., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., 7 Sep 2016, In: Genome Biology. 17, p. 1-19 19 p., 184.

    Research output: Contribution to journalArticlepeer-review

  21. Published

    mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

    Meyer, M. J., Lapcevic, R., Romero, A. E., Yoon, M., Das, J., Beltrán, J. F., Mort, M., Stenson, P. D., Cooper, D. N., Paccanaro, A. & Yu, H., May 2016, In: Human Mutation. 37, 5, p. 447-456 10 p.

    Research output: Contribution to journalArticlepeer-review

  22. 2015
  23. E-pub ahead of print

    A network medicine approach to quantify distance between hereditary disease modules on the interactome

    Caniza, H., Romero, A. E. & Paccanaro, A., 3 Dec 2015, (E-pub ahead of print) In: Scientific Reports. 5, p. 1-10 10 p., 17658.

    Research output: Contribution to journalArticlepeer-review

  24. 2014
  25. Published

    Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules

    Smieszek, S. P., Yang, H., Paccanaro, A. & Devlin, P. F., 6 Oct 2014, In: Journal of the Royal Society. Interface. 11, 99, p. 1-11 11 p.

    Research output: Contribution to journalArticlepeer-review

  26. Published

    GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

    Caniza, H., Romero, A. E., Heron, S., Yang, H., Devoto, A., Frasca, M., Mesiti, M., Valentini, G. & Paccanaro, A., 1 Aug 2014, In: Bioinformatics. 30, 15, p. 2235-2236 2 p.

    Research output: Contribution to journalArticlepeer-review

  27. Published

    An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods

    Valentini, G., Paccanaro, A., Caniza, H., Romero, A. E. & Re, M., Jun 2014, In: Artificial Intelligence in Medicine. 61, 2, p. 63-78 16 p.

    Research output: Contribution to journalArticlepeer-review

  28. 2013
  29. Published

    A large-scale evaluation of computational protein function prediction

    Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., Pandey, G., Yunes, J. M., Talwalkar, A. S., Repo, S., Souza, M. L., Piovesan, D., Casadio, R., Wang, Z., Cheng, J., Fang, H. & 82 others, Gough, J., Koskinen, P., Törönen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D. W. A., Bryson, K., Jones, D. T., Limaye, B., Inamdar, H., Datta, A., Manjari, S. K., Joshi, R., Chitale, M., Kihara, D., Lisewski, A. M., Erdin, S., Venner, E., Lichtarge, O., Rentzsch, R., Yang, H., Romero, A. E., 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., Hönigschmid, P., Hopf, T. A., Kaufmann, S., Kiening, M., Krompass, D., Landerer, C., Mahlich, Y., Roos, M., Björne, J., Salakoski, T., Wong, A., Shatkay, H., Gatzmann, F., Sommer, I., Wass, M. N., Sternberg, M. J. E., Škunca, N., Supek, F., Bošnjak, M., Panov, P., Džeroski, S., Šmuc, T., Kourmpetis, Y. A. I., van Dijk, A. D. J., ter Braak, C. J. F., 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, P. C., Brenner, S. E., Orengo, C., Rost, B., Mooney, S. D. & Friedberg, I., Mar 2013, In: Nature Methods. 10, 3, p. 221-7 7 p.

    Research output: Contribution to journalArticlepeer-review

  30. 2012
  31. Published

    A Census of Human Soluble Protein Complexes

    Havugimana, P. C., Hart, G. T., Nepusz, T., Yang, H., Turinsky, A. L., Li, Z., Wang, P. I., Boutz, D. R., Fong, V., Phanse, S., Babu, M., Craig, S. A., Hu, P., Wan, C., Vlasblom, J., Dar, V-N., Bezginov, A., Clark, G. W., Wu, G. C., Wodak, S. J. & 4 others, Tillier, E. R. M., Paccanaro, A., Marcotte, E. M. & Emili, A., 31 Aug 2012, In: Cell. 150, 5, p. 1068–1081

    Research output: Contribution to journalArticlepeer-review

  32. Published

    Computational selection of transcriptomics experiments improves Guilt-by-Association analyses

    Bhat, P., Yang, H., Bogre, L., Devoto, A. & Paccanaro, A., 7 Aug 2012, In: PLoS ONE. 7, 8, e39681.

    Research output: Contribution to journalArticlepeer-review

  33. Published

    Detecting overlapping protein complexes in protein-protein interaction networks

    Nepusz, T., Yu, H. & Paccanaro, A., 2012, In: Nature Methods. 9, 5, p. 471–472 2 p.

    Research output: Contribution to journalArticlepeer-review

  34. Published

    Exploring the evolutionary path of plant MAPK networks

    Dóczi, R., Okrész, L., Romero, A. E., Paccanaro, A. & Bogre, L., 2012, In: Trends in Plant Science.

    Research output: Contribution to journalArticlepeer-review

  35. Published

    GFam: a platform for automatic annotation of gene families

    Sasidharan, R., Nepusz, T., Swarbreck, D., Huala, E. & Paccanaro, A., 2012, In: Nucleic Acids Research. 40, 19, 15 p., e152.

    Research output: Contribution to journalArticlepeer-review

  36. Published

    Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty

    Yang, H., Nepusz, T. & Paccanaro, A., 2012, In: Bioinformatics. 28, 10, p. 1383-1389 7 p.

    Research output: Contribution to journalArticlepeer-review

  37. Published

    OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast

    Abbruscato, P., Nepusz, T., Mizzi, L., Del Corvo, M., Morandini, P., Fumasoni, I., Michel, C., Paccanaro, A., Guiderdoni, E., Schaffrath, U., Morel, J-B., Piffanelli, P. & Faivre-Rampant, O., 2012, In: Molecular Plant Pathology.

    Research output: Contribution to journalArticlepeer-review

  38. Forthcoming

    Structural Pattern Discovery in Protein-Protein Interaction Networks

    Nepusz, T. & Paccanaro, A., 2012, (Accepted/In press) Handbook of Bio- and Neuroinformatics. Springer

    Research output: Chapter in Book/Report/Conference proceedingChapter

  39. 2010
  40. Published

    SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

    Nepusz, T., Sasidharan, R. & Paccanaro, A., 2010, In: BMC Bioinformatics. 11, p. 120

    Research output: Contribution to journalArticlepeer-review

  41. 2009
  42. Published

    Quantifying environmental adaptation of metabolic pathways in metagenomics

    Gianoulis, T. A., Raes, J., Patel, P. V., Bjornson, R., Korbel, J. O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L. J., Snyder, M., Bork, P. & Gerstein, M. B., 3 Feb 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 5, p. 1374–1379 6 p.

    Research output: Contribution to journalArticlepeer-review

  43. Published

    Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

    Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavil, A., Nasseri, N. K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A. & 3 others, Greenblatt, J. F., Moreno-Hagelsieb, G. & Emili, A., 2009, In: PLoS Biology. 7, 4, p. e96

    Research output: Contribution to journalArticlepeer-review

  44. 2008
  45. Published
  46. Published

    Signal transduction networks during stress responses in Arabidopsis: high-throughput analysis and modelling

    Devoto, A. & Paccanaro, A., 2008, Plant Growth Signalling. Springer, p. 331-350 20 p. (Plant Cell Monogr).

    Research output: Chapter in Book/Report/Conference proceedingChapter

  47. 2007
  48. Published

    Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

    Zhang, Z. D., Paccanaro, A., Fu, Y., Weissman, S., Weng, Z., Chang, J., Snyder, M. & Gerstein, M. B., 2007, In: Genome Research. 17, 6, p. 787-97 11 p.

    Research output: Contribution to journalArticlepeer-review

  49. 2006
  50. Published

    Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

    Waite, R. D., Paccanaro, A., Papakonstantinopoulou, A., Hurst, J. M., Saqi, M., Littler, E. & Curtis, M. A., 2006, In: BMC Genomics. 7, p. 162

    Research output: Contribution to journalArticlepeer-review

  51. Published

    Integration of curated databases to identify genotype-phenotype associations

    Goh, C-S., Gianoulis, T. A., Liu, Y., Li, J., Paccanaro, A., Lussier, Y. A. & Gerstein, M., 2006, In: BMC Genomics. 7, p. 257

    Research output: Contribution to journalArticlepeer-review

  52. Published

    Predicting essential genes in fungal genomes

    Seringhaus, M., Paccanaro, A., Borneman, A., Snyder, M. & Gerstein, M., 2006, In: Genome Research. 16, 9, p. 1126-35 10 p.

    Research output: Contribution to journalArticlepeer-review

  53. Published

    Predicting interactions in protein networks by completing defective cliques

    Yu, H., Paccanaro, A., Trifonov, V. & Gerstein, M., 2006, In: Bioinformatics. 22, 7, p. 823-9 7 p.

    Research output: Contribution to journalArticlepeer-review

  54. Published

    Spectral clustering of protein sequences

    Paccanaro, A., Casbon, J. A. & Saqi, M. A. S., 2006, In: Nucleic Acids Research. 34, 5, p. 1571-80 10 p.

    Research output: Contribution to journalArticlepeer-review

  55. Published

    Spectral clustering of protein sequences using sequence-profile scores

    Sasidharan, R., Gerstein, M. B. & Paccanaro, A., 2006, Proceedings of ICNPSC – 3rd International Conference on Neural Parallel and Scientific Computations.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  56. 2005
  57. Published

    Assessing the limits of genomic data integration for predicting protein networks

    Lu, L. J., Xia, Y., Paccanaro, A., Yu, H. & Gerstein, M., 2005, In: Genome Research. 15, 7, p. 945-53 9 p.

    Research output: Contribution to journalArticlepeer-review

  58. Published

    Inferring protein-protein interactions using interaction network topologies

    Paccanaro, A., Trifonov, V., Yu, H. & Gerstein, M. B., 2005, Proceedings of the International Joint Conference on Neural Networks. p. 161 166 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  59. Published

    Spectral clustering of protein sequences

    Paccanaro, A., Trifonov, V., Yu, H. & Gerstein, M. B., 2005, International Joint Conference on Neural Networks. p. 161-166

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  60. 2003
  61. Published

    Markov analysis of protein sequence similarities

    Chennubhotla, C. & Paccanaro, A., 2003, Lecture Notes in Computer Science. Springer, Vol. 2859. p. 278-286

    Research output: Chapter in Book/Report/Conference proceedingChapter