Alberto Paccanaro - Publications by Topic:
 

 


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( Notice borrowed from  Peter Dayan, who got it from Dave Plaut ).

 

Computational Biology


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.

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.

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

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.

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.

T. Nepusz, H. Yu, and A. Paccanaro
Detecting overlapping protein complexes in protein-protein interaction networks
Nature Methods, vol. 9, pp. 471-472, 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, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A.
A census of human soluble protein complexes.
Cell, 2012 Aug 31;150(5):1068-81.

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

R. Sasidharan, T. Nepusz, D. Swarbreck, E. Huala, and A. Paccanaro
GFam: a platform for automatic annotation of gene families
Nucleic Acids Res. 2012 Jul 11. [Epub ahead of print]

P. Abbruscato, T. Nepusz, L. Mizzi, M. D. 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
Mol Plant Pathol. 2012 Oct;13(8):828-841. doi: 10.1111/j.1364-3703.2012.00795.x. Epub 2012 Mar 23.

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.

R. Dóczi, L. Ökrész, A. E. Romero, A. Paccanaro, and L. Bögre
Exploring the evolutionary path of plant MAPK networks
Trends Plant Sci. 2012 Sep;17(9):518-25. Epub 2012 Jun 8.

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.

P. Hu, S. C. Janga, M. Babu, J. J. D’iaz-Mej’ia, 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.

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.
Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9.

H. Yang, P. Bhat, H. Shanahan, A. Paccanaro
A Maximal Eigenvalue Method for Detecting Process Representative Genes by Integrating Data from Multiple Sources
NIPS 2008 -- worshop  on Learning from Multiple Sources

A. Devoto, A. Paccanaro
Signal Transduction Networks During Stress Responses in Arabidopsis: High-Throughput Analysis and Modelling
in Bögre L and Beemster G. Eds, Plant Growth Signaling, Plant Cell Monographs series, Vol. 10, Springer, 2008

Zhengdong Zhang, Alberto Paccanaro, Yutao Fu, Sherman Weissman, Zhiping Weng, Joseph Chang, Michael Snyder, Mark Gerstein
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
Genome Research, 2007,17(6):787-97

Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder and Mark Gerstein
Predicting Essential Genes in Fungal Genomes
Genome Research 2006 Sep;16(9):1126-35

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Nature 2006 Mar 30;440(7084):637-43

Paccanaro A, Casbon JA, Saqi MA.
Spectral clustering of protein sequences.
Nucleic Acids Research 2006 Mar 17;34(5):1571-80

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, 2006 Oct 12;7:257

Rajkumar Sasidharan, Mark Gerstein, Alberto Paccanaro
Spectral Clustering of Protein Sequences Using Sequence-Profile Scores
Proceeding of ICNPSC 2006 --- third International Conference on Neural Parallel and Scientific Computations

Yu H, Paccanaro A, Trifonov V, Gerstein M.
Predicting interactions in protein networks by completing defective cliques.
Bioinformatics 2006 Apr 1;22(7):823-9

Richard RD Waite, Alberto Paccanaro, Anastasia A Papakonstantinopoulou, Jacob J Hurst, Mansoor M Saqi, Eddie E Littler and Michael A Curtis
Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
BMC Genomics, 2006 Jun 26;7:162.

A. Paccanaro, V. Trifonov, H. Yu, M. Gerstein (2005).
Inferring Protein-Protein Interactions Using Interaction Network Topologies
IJCNN 2005 - International Joint Conference on Neural Networks, Montreal, Canada

L. J. Lu, Y. Xia, A. Paccanaro, H. Yu, M. Gerstein (2005).
Assessing the Limits of Genomic Data Integration for Protein-Protein Interactions
Genome Research, Jul 2005; 15: 945 - 953

A. Paccanaro, C.Chennubhotla, J. A. Casbon, M. A. S. Saqi (2003).
Spectral Clustering of Protein Sequences
IJCNN 2003 - International Joint Conference on Neural Networks, Portland, Oregon, USA

C. Chennubhotla, A. Paccanaro (2003).
Markov Analysis of Protein Sequence Similarities
Lecture Notes in Computer Science series, Vol. 2859, 278-286, Springer-Verlag.
 


Machine Learning

A. Paccanaro
Learning distributed representations of high-arity relational data with Non-Linear Relational Embedding
Lecture Notes in Computer Science series, vol. 2714,
Artificial Neural Networks and Neural Information Processing - ICANN/ICONIP 2003 , O. Kaynak, E. Alpaydin, E. Oja, L. Xu Eds., Springer-Verlag, 2003.

A. Paccanaro
Adapting Distributed Representations to incorporate new Concepts and Relations with Linear Relational Embedding
ICNPSC 2002 --- Second International Conference on Neural Parallel and Scientific Computations, M.Sambandham, ed., 7-12.

A. Paccanaro
Learning Distributed Representations of Concepts from Relational Data [pdf]
ICML 2002, Workshop on Development of Representations, E. de Jong and T. Oates, eds.

A. Paccanaro, G. E. Hinton
Learning Hierarchical Structures with Linear Relational Embedding [pdf]
NIPS 14, Advances in Neural Information Processing Systems 14, T. G. Dietterich and S. Becker and Z. Ghahramani eds., 2001

A. Paccanaro, G. E. Hinton
Learning Distributed Representations of Relational data using Linear Relational Embedding [pdf]
Proceedings of the 12-th Italian Workshop on Neural Nets, WIRN VIETRI, 2001

A. Paccanaro, G. E. Hinton
Learning Distributed Representation of Concepts using Linear Relational Embedding [pdf]
IEEE Trans. on Knowledge and Data Engineering - special issue on 'Connectionists Models for Learning in Structured Domains'
Vol. 13, N.2, March/April 2001, 232-245

A. Paccanaro, G. E. Hinton
Learning Distributed Representation of Concepts using Linear Relational Embedding
Gatsby Computational Neuroscience Unit - Technical Report 2000-002

A. Paccanaro, G. E. Hinton
Learning Distributed Representations by Mapping Concepts and Relations into a Linear Space [pdf]
ICML2000, Proceedings of the Seventeenth International Conference on Machine Learning, Langley P. (Ed.), 711-718, Stanford University, Morgan Kaufmann Publishers, San Francisco

A. Paccanaro, G. E. Hinton
Extracting Distributed Representations of Concepts and Relations from Positive and Negative Propositions [pdf]
IJCNN 2000, Proceedings of the International Joint Conference on Neural Networks

 


Neural Networks & Automated Theorem Proving

C. Mareco, A. Paccanaro
Using Neural Networks to improve the performance of Automated Theorem Provers.
in Computational Methods and Neural Networks, M.P.Bekakos, M.Sambandham Eds., 379-404, 1998, Dynamic Publishers, Inc.

C. Mareco, A. Paccanaro
Using the Tree Representation of Terms to Recognize Matching with Neural Networks
Nonlinear Analysis, vol. 30, n. 5, 2925 - 2936, 1997

A. Paccanaro
Development of Neural Networks for speeding up Automated Theorem Proving. Results for the Group Theory (in Russian)
Izvestija Rossijskoj Academii nauk. Teorija i sistemy upravlenija (Proceedings of the Russian Academy of Science), n.5, 1997
(English translation: Soviet Journal of Computer and Computer System Sciences, n.5, 1997)

A. Paccanaro
Guiding Term Reduction through a Neural Network: Some Preliminary Results for the Group Theory
RTA 95 - J. Hsiang ed., Springer-Verlag LNCS series, n. 914, 444 - 450, 1995

A. Paccanaro
Guiding Term Simplification using Neural Networks: some results for the Groups Theory
in Neural, Parallel and Scientific Computations - S.Aityan, L.Grujic et al. eds., 377 - 382
Dynamic Publishers, Inc. - 1995

C. Mareco, A. Paccanaro
Using Neural Networks for Recognizing Matching among terms
Proceedings of ICPA'95 - International Conference on Parallel Algorithms - Wuhan, China, 1995
Gordon and Breach - Computer Mathematics Series, 1995

C. Mareco, A. Paccanaro
Recognizing Matching Among Terms: A Neural Network Approach
Proceedings of the XXII Latin American Conference on Computer Science (CLEI'96), 1012 - 1020, Santafe de Bogota, Colombia

C. Mareco, A. Paccanaro
Recognizing Matching among Terms with a Neural Network: a Preliminary Study
Proc. of the XXI Latin American Conference on Computer Science (CLEI'95), 839 - 850, Canela, Brasil, 1995

A. Paccanaro, C. Willigs
Using Neural Networks for guiding Term Simplification in a Rewriting Based Automated Theorem Prover: some preliminary results
Proc. of the XX Latin American Conference on Computer Science (CLEI'94), 559 - 565, Ciudad de Mexico, Mexico, 1994

A. Paccanaro, C. Willigs
Guiding Term Simplification in a Rewriting Based Automated Theorem Prover through a Neural Network
Proc. of the XIV International Conference of the Chilean Computer Science Society, 315 - 322, Concepcion, Chile, 1994

A. Paccanaro, C. Willigs
Towards the use of Neural Networks for guiding the search of a Rewriting Based Automated Theorem Prover
Proc. of the International Congress on Technology and Applications in Computer Science, Asuncion, Paraguay, 1993
 


Term Rewriting Systems

M. Alarcon, A. Grijalba, A. Paccanaro
Res4FOL: a fast Resolution Based Automated Theorem Prover for First Order Logic
Proc. of the International Congress on Technology and Applications in Computer Science Asuncion, Paraguay, 1995

M. Kreitmair, C. Mareco, A. Paccanaro
KBTeach: a Rewriting Based Automated Theorem Prover for Didactic Purposes
Proc. of the XX Latin American Conference on Computer Science (CLEI'94), 669 - 680, Ciudad de Mexico, Mexico, 1994

G. Degli Antoni, A. Paccanaro, R.Virga
Report on KBLab: a laboratory for rewriting techniques
Proc. of GULP 92 Conference, 209-222, Pisa, Italy, 1992

G. Degli Antoni, A. Paccanaro, R. Virga
KBLab: a system for research and didactic of Rewriting Systems (in Italian)
Proc. of the 8a Conferenza Italiana di Didamatica, 225 - 234 Associazione Italiana Calcolo Automatico, Campobasso, Italy, 1992

A. Paccanaro
KBLab 1.7 - User Manual
Project Report No. 93/92, 1992 Computer Science Department - University of Milan

A. Paccanaro, A. Provetti
Revised Report on KBLab Menu
Project Report No. 18/91, 1991 Computer Science Department - University of Milan

G. Degli Antoni, A. Paccanaro
KBLab: a laboratory for experimenting rewriting techniques (in Italian)
in Bruno Fadini ed., Sistemi Informatici e Calcolo Parallelo, 339 - 344,
Franco Angeli Scientific Series, Rome, Italy, 1991
 


Term Rewriting Systems & Petri Nets

C. Jansen, A. Paccanaro
Studying the Behaviour of Place/Transition and Coloured Petri Nets - an Implementation Using LP
Technical Report 314/98, Department of Computer Science, University of Toronto, 1998

A. Paccanaro
Studying the behaviour of Petri Nets through a formalization as Term Rewriting Systems
in Computer Science 2: Research and Applications, Ed. Ricardo Baeza-Yates, 455 - 466
Plenum Publishing Corporation, 1994

A. Paccanaro
Using Modified Term Rewriting Systems for studying the behaviour of Stochastic Petri Nets
Proc. of the XIV International Conference of the Chilean Computer Science Society, 305 - 314, Concepcion, Chile, 1994

A. Paccanaro
Using rewriting techniques for studying the behaviour of Petri Nets
Proc. of the XIX Latin American Conference on Computer Science (CLEI '93), 16.57 - 16.70, Buenos Aires, Argentina, 1993
 


Miscellanea   

A. Paccanaro
Digital Processing of Signals obtained through Measurements of the Magnetic Fields induced by Cerebral Currents
Laurea Degree Thesis - University of Milan - 1990 (in Italian)

G. Crosta, A. Paccanaro
Wavelets-based matched filtering applied to Neuromagnetic Signals
Note di Software, N. 50, December 1990, 38 - 47, Milan

H. Matiauda, A.Paccanaro, H. Soley
Design and Implementation of an Interface for a function optimization tool based on Genetic Search techniques
Proc. of the XX Latin American Conference on Computer Science (CLEI'94), 947 - 956, Ciudad de Mexico, Mexico, 1994

G. Bellassai, L. Cernuzzi, A. Paccanaro
Monitoring meeting evolution in CSCW: the Conviction and Agreement coefficients
Proc. of the XV International Conference of the Chilean Computer Science Society, Arica, Chile, 1995

J. Herrero, A. Paccanaro
A Distributed Application for the Simplex Method
Proceedings of the XXII Latin American Conference on Computer Science (CLEI'96), 1069 - 1079, Santafe de Bogota, Colombia