Journals -- Book Chapters -- Book Series -- Conferences -- Workshops -- Thesis

Publications in Journals

[1] Irene Papatheodorou, Nuno A. Fonseca, Maria Keays, Y. Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Fullgrabe, Alfonso Munoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaino, Alvis Brazma, and Robert Petryszak. Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Research, -(-):-, November 2017. [ bib | DOI ]
[2] Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno A. Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, and Doreen Ware. Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Research, November 2017. [ bib | DOI ]
[3] Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A. Fonseca, Wolfgang Huber, Christian Haering, Leonid Mirny, and Francois Spitz. Two independent modes of chromosome organization are revealed by cohesin removal. Nature, 551:51-56, November 2017. [ bib | DOI ]
[4] Robert Petryszak, Nuno A. Fonseca, Anja Fullgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, and Alvis Brazma. The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data. Bioinformatics, 33(44):2218-2220, July 2017. [ bib | DOI ]
[5] Luz M Garcia-Alonso, Francesco Iorio, Angela Matchan, Nuno A. Fonseca, Patricia Jaaks, Gareth Peat, Miguel Pignatelli, Fiammetta Falcone, Cyril H. Benes, Ian Dunham, Graham R Bignell, Simon McDade, Mathew J. Garnett, and Julio Saez-Rodriguez. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Research, 2017. [ bib | DOI | arXiv ]
[6] Marcela K. Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen Parkinson, Antonio Fabregat, Sheldon McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, and Doreen Ware. Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research, 44:1133-1140, 2016. [ bib | DOI ]
[7] Robert Petryszak, Maria Keays, Y Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Fullgrabe, Alfonso Mu noz-Pomer Fuentes, Simon Jupp, Satu Koskinen, et al. Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Research, 44:746-752, 2016. [ bib | DOI ]
[8] Adam Frankish, Barbara Uszczynska, Graham RS Ritchie, Jose M Gonzalez, Dmitri Pervouchine, Robert Petryszak, Jonathan M Mudge, Nuno A. Fonseca, Alvis Brazma, Roderic Guigo, et al. Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC genomics, 16(Suppl 8):S2, June 2015. [ bib | DOI ]
[9] Bruno Aguiar, Jorge Vieira, Ana E. Cunha, Nuno A. Fonseca, Amy Iezzoni, Steve van Nocker, and Cristina P. Vieira. Convergent Evolution at the Gametophytic Self-Incompatibility System in Malus and Prunus. PLoS ONE, 10(5):e0126138, 05 2015. [ bib | DOI ]
[10] Pedro Ferreira, Nuno A. Fonseca, Ines Dutra, Ryan Woods, and Elizabeth Burnside. Predicting Malignancy from Mammography Findings and Image-Guided Core Biopsies. International Journal of Data Mining and Bioinformatics, 11(3):257-277, 2015. [ bib ]
[11] Nuno A. Fonseca, John Marioni, and Alvis Brazma. RNA-Seq Gene Profiling - A Systematic Empirical Comparison. PLoS ONE, 9(9):e107026, September 2014. [ bib | DOI ]
[12] Bianca M. Schmitt, Konrad L.M. Rudolph, Panagiota Karagianni, Nuno A. Fonseca, Robert J. White, Iannis Talianidis, Duncan T. Odom, John C. Marioni, and Claudia Kutter. High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface. Genome Research, August 2014. [ bib | DOI ]
[13] Veli Vural Uslu, Massimo Petretich, Sandra Ruf, Katja Langenfeld, Nuno A. Fonseca, John C. Marioni, and Francois Spitz. Long-range enhancers regulating Myc expression are required for normal facial morphogenesis. Nature Genetics, 46:753-758, May 2014. [ bib | DOI ]
[14] YY Lin, Nuno A. Fonseca, SR Maruyama, M Fernandez-Fuente, A Brazma, J Marioni, F Muntoni, and SC Brown. P59 Transcriptome analysis in a mouse model of FKRP-deficient muscular dystrophy. Neuromuscular Disorders, 24:S22-S23, 2014. [ bib | DOI ]
[15] Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C. Marioni, James Malone, Karine Megy, Gabriella Rustici, Amy Y. Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, and Alvis Brazma. Expression atlas update - a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments. Nucleic Acids Research, December 2013. [ bib | DOI ]
[16] Tiago Loureiro, Rui Camacho, Jorge Vieira, and Nuno A. Fonseca. Improving the performance of transposable elements detection tools. Journal of integrative bioinformatics, 10(3):231, November 2013. [ bib | DOI ]
[17] Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanc Birol, S'ebastien Boisvert, Jarrod A. Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T. Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, El'enie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B. Hiatt, Isaac Y. Ho, Jason Howard, Martin Hunt, Shaun D. Jackman, David B Jaffe, Erich Jarvis, Huaiyang Jiang, and et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(10), July 2013. [ bib | DOI ]
[18] Ana Rita Araujo, Micael Reis, Helder Rocha, Bruno Aguiar, Ramiro Morales-Hojas, Sandra Ribeiro, Nuno A. Fonseca, Daniel Reboiro-Jato, Miguel Reboiro Jato, Florentino Fdez-Riverola, Cristina P. Vieira, and Jorge Vieira. The Drosophila melanogaster methuselah gene: a novel gene with ancient functions. PLoS ONE, 8(5):e63747, May 2013. [ bib | DOI ]
[19] Bruno Aguiar, Jorge Vieira, Ana E Cunha, Nuno A. Fonseca, David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Olivier Rasp'e, and Cristina P Vieira. Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S- pollen genes support the 'non-self recognition by multiple factors' model. Journal of Experimental Botany, April 2013. [ bib | DOI ]
[20] Nuno A. Fonseca, Ramiro Morales-Hojas, Micael Reis, Helder Rocha, Cristina P. Vieira, Viola Nolte, Christian Schl"otterer, and Jorge Vieira. D. americana as a model species for comparative studies on the molecular basis of phenotypic variation. Genome Biology and Evolution, 5(4):661-679, March 2013. [ bib | DOI ]
[21] Nuno A. Fonseca, Johan Rung, Alvis Brazma, and John Marioni. Tools for mapping high-throughput sequencing data. Bioinformatics, 28(24):3169-3177, December 2012. [ bib | DOI ]
[22] David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Nuno A. Fonseca, and Jorge Vieira. ADOPS - Automatic Detection of Positively Selected Sites. Journal of Integrative Bioinformatics, 9(3):200, July 2012. [ bib ]
[23] Nuno A. Fonseca, Cristina P. Vieira, Christian Schl"otterer, and Jorge Vieira. The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions. Fly, 6(2):1-4, April 2012. [ bib | DOI ]
[24] Rui Camacho, Rita Ferreira, Natacha Rosa, Vania Guimaraes, Nuno A. Fonseca, Vitor Santos Costa, Miguel Sousa, and Alexandre Magalhaes. Predicting the secondary structure of proteins using Machine Learning algorithms. International Journal of Data Mining and Bioinformatics, 6(6):571-584, 2012. [ bib | DOI ]
[25] Dent Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo, Daniel Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha, Zemin Ning, Matthias Haimel, Jared T. Simpson, emphNuno A. Fonseca, Ynanc Birol, T. Roderick Docking, Isaac Y. Ho, Daniel S. Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C. Schatz, David R. Kelley, Adam M. Phillippy, Sergey Koren, Shiaw-Pyng Yang, Wei Wu, Wen-Chi Chou, Anuj Srivastava, Timothy I. Shaw, J. Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T. Dimon, Victor Solovyev, Igor Seledtsov, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan MacLean, Fangfang Xia, Ruibang Luo, Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J. Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, Richard Durbin, Shaun D Jackman, Jarrod A. Chapman, Xiaoqiu Huang, Joseph L. DeRisi, Mario Caccamo, David B. Jaffe, Richard E. Green, David Haussler, Ian Korf, and Benedict Paten. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21:2224-2241, December 2011. [ bib | http ]
[26] Rui Camacho, Max Pereira, Vitor Santos Costa, Nuno A. Fonseca, Carlos Adriano, Carlos J.V. Simoes, and Rui M. M. Brito. A relational learning approach to structure-activity relationships in drug design toxicity studies. Journal of Integrative Bioinformatics, 8(3):182-, September 2011. [ bib | DOI ]
[27] Miguel M. de Sousa, Cristian R. Munteanu, Alejandro Pazos, Nuno A. Fonseca, Rui Camacho, and Alexandre Lopes Magalhaes. Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins. Journal of Theoretical Biology, 271(1), February 2011. [ bib | DOI ]
[28] Lu'isa Pereira, Farida Alshamali, Rune Andreassen, Ruth Ballard, Wasun Chantratita, Nam Soo Cho, Clotilde Coudray, Jean-Michel Dugoujon, Marta Espinoza, Fabricio Gonz'alez-Andrade, Sibte Hadi, Uta-Dorothee Immel, Nina Jeran, Dubravka Havas, Catalin Marian, Antonio Gonzalez-Martin, Gerd Mertens, Walther Parson, Carlos Perone, Lourdes Prieto, Haruo Takeshita, H'ector Rangel Villalobos, Zhaoshu Zeng, Lev Zhivotovsky, Rui Camacho, and Nuno A. Fonseca. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile. International Journal of Legal Medicine, 125:629-636, June 2010. [ bib | DOI ]
[29] Jorge Vieira, Pedro Ferreira, Bruno Aguiar, Nuno A. Fonseca, and Cristina P. Vieira. Evolutionary patterns at the RNase based gametophytic self -incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus). BMC Evolutionary Biology, 10(200), June 2010. [ bib | DOI ]
[30] Joana S. Santos, Nuno A. Fonseca, Cristina Vieira, Jorge Vieira, and Fernando Casares. Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish. Developmental Dynamics, 239(3):1010-1018, March 2010. [ bib | DOI ]
[31] Jorge Vieira, Nuno A. Fonseca, and Cristina Vieira. RNase based gametophytic self-incompatibility evolution: questioning the hypothesis of multiple independent recruitments of the S-pollen gene. Journal of Molecular Evolution, 69(1):32-41, July 2009. [ bib | DOI ]
[32] Nuno A. Fonseca, Cristina Vieira, and Jorge Vieira. Gene classification based on amino acid motifs and residues: The DLX (emphdistal-less) test case. PLoS ONE, 4(6):e5748, June 2009. [ bib | http ]
[33] Nuno A. Fonseca, Ashwin Srinivasan, Fernando Silva, and Rui Camacho. Parallel ILP for Distributed-Memory Architectures. Machine Learning, 74(3):257-279, March 2009. [ bib | DOI ]
[34] Nuno A. Fonseca, Vitor Santos Costa, Ricardo Rocha, Rui Camacho, and Fernando Silva. Improving the Efficiency of ILP Systems. Software - Practice and Experience, 39(2):189-219, February 2009. [ bib | DOI ]
[35] Jorge Vieira, Nuno A. Fonseca, and Cristina P. Vieira. An S-RNase-Based Gametophytic Self-Incompatibility System Evolved Only Once in Eudicots. Journal of Molecular Evolution, 67(2):179-190, August 2008. [ bib | http ]
[36] Nuno A. Fonseca, Cristina P. Vieira, Peter W. Holland, and Jorge Vieira. Protein evolution of ANTP and PRD homeobox genes. BMC Evolutionary Biology, 8(200), July 2008. [ bib | DOI ]
[37] Jorge Vieira, Nuno A. Fonseca, Raquel A.M. Santos, Tsuyoshi Habu, Ryutaro Tao, and Cristina P. Vieira. The number, age, sharing and relatedness of S-locus specificities in Prunus. Genetics Research, 90(01):17-26, February 2008. [ bib | DOI ]
[38] Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, and Vitor Santos Costa. Compile the hypothesis space: do it once, use it often. Fundamenta Informaticae, Special Issue on Multi-Relational Data Mining(89):45-67, 2008. [ bib | http ]
[39] Nuno A. Fonseca, Rui Camacho, and Alexandre Magalhaes. A study on amino acid pairing at the N- and C-termini of helical segments in proteins. PROTEINS: Structure, Function, and Bioinformatics, 70(1):188-196, January 2008. [ bib | DOI ]

Publications in Books

[1] Rui Camacho, Jorge G Barbosa, Altino Sampaio, Joao Ladeiras, Nuno A Fonseca, and Vitor S Costa. chapter Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems, pages 339-363. Springer International Publishing, 2016. [ bib ]
[2] Stasinos Konstantopoulos, Rui Camacho, Nuno A. Fonseca, and Vitor Santos Costa. chapter Induction as a Search Procedure, pages 158-205. IGI Global, 2008. [ bib | http ]
[3] Nuno A. Fonseca, Ines Dutra, and Vitor Santos Costa. chapter VisAll: A new tool to visualise parallel execution of Logic Programs, pages 1-20. Nova Science, 1999. Extended and revised version of the paper in the proceedings of JICLPS98. [ bib ]

Publications in Book Series

[1] Bruno Cavadas, Joana Ferreira, Rui Camacho, emphNuno A. Fonseca, and Luisa Pereira. QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq. In 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, volume 616, pages 173-179. Springer-Verlag, 2017. [ bib | DOI ]
[2] Rui Camacho, Ruy Ramos, and Nuno A. Fonseca. AND Parallelism for ILP: The APIS System. In Gerson Zaverucha, Vitor Santos Costa, and Aline Paes, editors, Inductive Logic Programming, volume 8812 of Lecture Notes in Computer Science, pages 93-106. Springer-Verlag, September 2014. [ bib | DOI ]
[3] Tiago Loureiro, Rui Camacho, Jorge Vieira, and Nuno A. Fonseca. Boosting the detection of transposable elements using machine learning. In 7th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB'13), volume 222 of Advances in Intelligent Systems and Computing, pages 85-91. Springer-Verlag, 2013. [ bib | DOI ]
[4] David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Nuno A. Fonseca, and Jorge Vieira. On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. In Miguel P. Rocha, Nicholas Luscombe, Florentino Fdez-Riverola, and Juan M. Corchado Rodr'iguez, editors, 6th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB'12), volume 154 of Advances in Intelligent and Soft Computing, pages 225-229. Springer-Verlag, 2012. [ bib ]
[5] Nuno A. Fonseca, Vitor Santos Costa, and Rui Camacho. Conceptual Clustering of Multi-Relational Data. In Proceedings of the 2011 International Conference on Inductive Logic Programming (ILP 2011), volume 7207 of Lecture Notes in Artificial Intelligence, pages 145-159. Springer-Verlag, 2012. [ bib ]
[6] Nuno A. Fonseca, Max Pereira, Vitor Santos Costa, and Rui Camacho. Interactive Discriminative Mining of Chemical Fragments. In Proceedings of the 2010 International Conference on Inductive Logic Programming (ILP 2010), number 6489 in Lecture Notes in Artificial Intelligence, pages 59-66. Springer-Verlag, 2011. [ bib ]
[7] Rui Camacho, Max Pereira, Vitor Santos Costa, Nuno A. Fonseca, Carlos J. V. Simoes, and Rui M. M. Brito. Assessing the effect of 2D fingerprint filtering on ILP-based structure-activity relationships toxicity studies in drug design. In Miguel P. Rocha, Juan M. Corchado, Florentino Fdez-Riverola, and Alfonso Valencia, editors, 5th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB'11), volume 93 of Advances in Intelligent and Soft Computing, pages 355-363. Springer-Verlag, 2011. [ bib ]
[8] Rui Camacho, Rita Ferreira, Natacha Rosa, Vania Guimaraes, Nuno A. Fonseca, Vitor Santos Costa, Miguel Sousa, and Alexandre Magalhaes. Predicting the Start of Protein α-Helices Using Machine Learning Algorithms. In Advances in Bioinformatics, 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB'10), volume 74 of Advances in Intelligent and Soft Computing, pages 33-41. Springer-Verlag, June 2010. [ bib ]
[9] Max Pereira, Vitor Santos Costa, Rui Camacho, Nuno A. Fonseca, Carlos Simoes, and Rui Brito. Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases. In Advances in Bioinformatics and Computational Biology - Proceedings of the 4th Brazilian Symposium on Bioinformatics (BSB 2009), volume 5676 of Lecture Notes in Computer Science, pages 121-132. Springer-Verlag, July 2009. [ bib | DOI | http ]
[10] Nuno A. Fonseca, Vitor Santos Costa, Rui Camacho, Cristina Vieira, and Jorge Vieira. Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach. In IWANN (2), volume 5518 of Lecture Notes in Computer Science, pages 1001-1004. Springer-Verlag, June 2009. [ bib | http ]
[11] Max Pereira, Vitor Santos Costa, Rui Camacho, and Nuno A. Fonseca. Visually Guiding and Controlling the search while Mining Chemical Structures. In IWANN (2), volume 5518 of Lecture Notes in Computer Science, pages 1043-1046. Springer-Verlag, June 2009. [ bib | http ]
[12] Pedro Pereira, Fernando Silva, and Nuno A. Fonseca. BIORED - A Genetic Algorithm for Pattern Detection in Biosequences. In Proceedings of 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), volume 49 of Advances in Soft. Computing Series, pages 156-165. Springer-Verlag, 2009. [ bib | http ]
[13] Nuno A. Fonseca, Rui Camacho, Vitor Santos Costa, and Ricardo Rocha. k-RNN: k-Relational Nearest Neighbour Algorithm. In Proceedings of 2008 ACM Symposium on Applied Computing (SAC 2008), pages 184-198. ACM Press, March 2008. [ bib ]
[14] Rui Camacho, Nuno A. Fonseca, Vitor Santos Costa, and R. Rocha. ILP :- Just Trie It. In H. Blockeel et al., editor, Proceedings of the 2007 International Conference on Inductive Logic Programming (ILP 2007), number 4894 in Lecture Notes in Artificial Intelligence, pages 78-87. Springer-Verlag, 2008. Revised version of the paper appearing in the Work-in-progress proceedings. [ bib | DOI ]
[15] M. Ferreira, Nuno A. Fonseca, R. Rocha, and T. Soares. Efficient and Scalable Induction of Logic Programs using a Deductive Database System. In Stephen Muggleton and Ramon Otero, editors, Proceedings of the 16th International Conference on Inductive Logic Programming (ILP'2006) Revised Selected Papers, number 4455 in Lecture Notes in Artificial Intelligence, pages 184-198, Santiago de Compostela, Spain, 2007. Springer-Verlag. Extended and revised version of the short paper. [ bib ]
[16] Nuno A. Fonseca, Fernando Silva, and Rui Camacho. April - An Inductive Logic Programming System. In Fisher M, VanDerHoek W, Konev B, and Lisitsa A, editors, Proceedings of the 10th European Conference on Logics in Artificial Intelligence (JELIA06), volume 4160 of Lecture Notes in Artificial Intelligence, pages 481-484, Liverpool, September 2006. Springer-Verlag. [ bib | .pdf ]
[17] Ricardo Rocha, Nuno A. Fonseca, and Vitor Santos Costa. On Applying Tabling to Inductive Logic Programming. In Proceedings of the 16th European Conference on Machine Learning, ECML-05, volume 3720 of Lecture Notes in Artificial Intelligence, pages 707-714. Springer-Verlag, October 2005. [ bib ]
[18] Nuno A. Fonseca, Fernando Silva, and Rui Camacho. Strategies to Parallelize ILP Systems. In Stefan Kramer and Bernhard Pfahringer, editors, Proceedings of the 15th International Conference on Inductive Logic Programming (ILP 2005), volume 3625 of Lecture Notes in Artificial Intelligence, pages 136-153, Bonn, Germany, August 2005. Springer-Verlag. (Best Student Paper). [ bib | .pdf ]
[19] Nuno A. Fonseca, Vitor Santos Costa, Rui Camacho, and Fernando Silva. On avoiding redundancy in Inductive Logic Programming. In Rui Camacho, Ross D. King, and Ashwin Srinivasan, editors, Proceedings of the 14th International Conference on Inductive Logic Programming (ILP 2004), volume 3194 of Lecture Notes in Artificial Intelligence, pages 132-146, Porto, Portugal, September 2004. Springer-Verlag. [ bib ]
[20] Nuno A. Fonseca, Vitor Santos Costa, Fernando Silva, and Rui Camacho. Experimental Evaluation of a Caching Technique for ILP. In Fernando Moura Pires and Salvador Abreu, editors, EPIA 03 - 11th Portuguese Conference on Artificial Intelligence, volume 2902 of Lecture Notes in Artificial Intelligence, pages 151-155, Beja, Portugal, December 2003. Springer-Verlag. Resumed version of the technical report DCC-2003-03. [ bib ]
[21] Nuno A. Fonseca, Ricardo Rocha, Rui Camacho, and Fernando Silva. Efficient Data Structures for Inductive Logic Programming. In T. Horv'ath and A. Yamamoto, editors, Proceedings of the 13th International Conference on Inductive Logic Programming (ILP 2003), volume 2835 of Lecture Notes in Artificial Intelligence, pages 130-145, Szeged, Hungary, September 2003. Springer-Verlag. [ bib ]
[22] N. Fonseca, V. Santos Costa, and I. de Castro Dutra. VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs. In Joxan Jaffar, editor, Proceedings of the 1998 Joint International Conference and Symposium on Logic Programming (JICSLP-98), pages 100-114, Cambridge, June 1998. MIT Press. [ bib ]

Publications in Conferences

[1] Pedro Ferreira, Nuno A. Fonseca, Ines Dutra, Ryan Woods, and Elizabeth Burnside. Predicting Malignancy from Mammography Findings and Surgical Biopsies. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM11), pages 339-344. IEEE Computer Society, 2011. [ bib ]
[2] Pedro Ferreira, Ines C. Dutra, Nuno A. Fonseca, Ryan Woods, and Elizabeth Burnside. Studying the Relevance of Breast Imaging Features. In HEALTHINF 2011 - Proceedings of the International Conference on Health Informatics. SciTePress, 2011. [ bib ]
[3] Nuno A. Fonseca, Vitor Santos Costa, and Rui Camacho. Conceptual clustering of multi-relational data. In Inductive Logic Programming, 21th International Conference, ILP 2011, Short papers, London, UK, 31 July-3 August, 2011, 2011. [ bib | .pdf ]
[4] Nuno A. Fonseca and Ines Dutra. UbiDis: a Flexible and General top-level Middleware to Manage Applications in Grids and Clusters. In Proceedings of the 3rd Iberian GRID Infraestructure Conference (IBERGRID 2009), pages 247-255, May 2009. [ bib ]
[5] Vitor Santos Costa, Nuno A. Fonseca, and Rui Camacho. LogCHEM: Interactive Discriminative Mining of Chemical Structure. In Proceedings of 2008 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), pages 421-426, Philadelphia, USA, November 2008. IEEE Computer Society. [ bib ]
[6] M. Ferreira, R. Rocha, T. Soares, and Nuno A. Fonseca. Efficient and Scalable Induction of Logic Programs using a Deductive Database System. In Stephen Muggleton and Ramon Otero, editors, 16th International Conference on Inductive Logic Programming (ILP 2006) - Short Papers, pages 74-76, Santiago de Compostela, Spain, August 2006. University of Corunna. [ bib ]
[7] Alexandre Magalhaes and Nuno A. Fonseca. On Predicting Protein Secondary Structure from their Aminoacid Sequences using Inductive Logic Programming. In EPIA 05 - 12th Portuguese Conference on Artificial Intelligence, Workshop on Computational Methods in Bioinformatics. IEEE Computer Society, December 2005. [ bib ]
[8] Nuno A. Fonseca, Fernando Silva, Vitor Santos Costa, and Rui Camacho. A pipelined data-parallel algorithm for ILP. In Proceedings of 2005 IEEE International Conference on Cluster Computing, pages 253-262, Boston, Massachusetts, USA, September 2005. IEEE Computer Society. [ bib | DOI | .pdf ]

Publications in Workshops

[1] Nuno A. Fonseca, Ricardo Rocha, Rui Camacho, and Vitor Santos Costa. ILP: Compute Once, Reuse Often. In Donato Malerba, Annalisa Appice, and Michelangelo Ceci, editors, Proceedings of the 6th Workshop on Multi-Relational Data Mining (MRDM 2007), pages 34-45, Warsaw, Poland, September 2007. [ bib ]
[2] T. Soares, M. Ferreira, R. Rocha, and Nuno A. Fonseca. On Applying Deductive Databases to Inductive Logic Programming: a Performance Study. In E. Pontelli and Hai-Feng Guo, editors, Proceedings of the Colloquium on Implementation of Constraint and LOgic Programming Systems, CICLOPS'2006, pages 80-94, Seattle, Washington, USA, August 2006. [ bib ]
[3] Nuno A. Fonseca, Rui Camacho, and Fernando Silva. A parallel ILP algorithm that incorporates incremental batch learning. In Proceedings of the Workshop on Parallel and Distributed Computing for Machine Learning, co-located with ECML/PKDD'2003, pages 23-34, Dubrovnik, Croatia, September 2003. [ bib ]
[4] Nuno A. Fonseca, Vitor Santos Costa, and Ines de Castro Dutra. VisAll: A New Tool to Visualise the Parallel Execution of Logic Programs. In Proceedings of the Workshop on Parallelism and Implementation Technology for (Constraint) Logic Programming Languages, 1997. Also as Technical Report DCC-97-17, DCC-FC LIACC, Universidade do Porto, December, 1997. [ bib ]

Thesis

[1] Nuno A. Fonseca. Parallelism in Inductive Logic Programming Systems. PhD thesis, University of Porto, 2006. [ bib | .pdf ]