VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs. - Nuno A. Fonseca; Vítor Santos Costa; Inês de Castro Dutra (IJCSLP, 1998)

Experimental Evaluation of a Caching Technique for ILP. - Nuno A. Fonseca; Vítor Santos Costa; Fernando M. A. Silva; Rui Camacho (EPIA, 2003)

Efficient Data Structures for Inductive Logic Programming. - Nuno A. Fonseca; Ricardo Rocha 001; Rui Camacho; Fernando M. A. Silva (ILP, 2003)

On Avoiding Redundancy in Inductive Logic Programming. - Nuno A. Fonseca; Vítor Santos Costa; Fernando M. A. Silva; Rui Camacho (ILP, 2004)

A pipelined data-parallel algorithm for ILP. - Nuno A. Fonseca; Fernando M. A. Silva; Vítor Santos Costa; Rui Camacho (CLUSTER, 2005)

On Applying Tabling to Inductive Logic Programming. - Ricardo Rocha 001; Nuno A. Fonseca; Vítor Santos Costa (ECML, 2005)

Strategies to Parallelize ILP Systems. - Nuno A. Fonseca; Fernando M. A. Silva; Rui Camacho (ILP, 2005)

Efficient and Scalable Induction of Logic Programs Using a Deductive Database System. - Michel Ferreira; Nuno A. Fonseca; Ricardo Rocha 001; Tiago Soares (ILP, 2006)

April - An Inductive Logic Programming System. - Nuno A. Fonseca; Fernando M. A. Silva; Rui Camacho (JELIA, 2006)

ILP : - Just Trie It. - Rui Camacho; Nuno A. Fonseca; Ricardo Rocha 001; Vítor Santos Costa (ILP, 2007)

LogCHEM: Interactive Discriminative Mining of Chemical Structure. - Vítor Santos Costa; Nuno A. Fonseca; Rui Camacho (BIBM, 2008)

BIORED - A Genetic Algorithm for Pattern Detection in Biosequences. - Pedro Pereira Rodrigues; Fernando M. A. Silva; Nuno A. Fonseca (IWPACBB, 2008)

k-RNN: k-relational nearest neighbour algorithm. - Nuno A. Fonseca; Vítor Santos Costa; Rui Camacho (SAC, 2008)

Compile the Hypothesis Space: Do it Once, Use it Often. - Nuno A. Fonseca; Rui Camacho; Ricardo Rocha 001; Vítor Santos Costa (Fundam. Informaticae, 2008)

Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach. - Nuno A. Fonseca; Vítor Santos Costa; Rui Camacho; Cristina P. Vieira; Jorge Vieira (IWANN (2), 2009)

Visually Guiding and Controlling the Search While Mining Chemical Structures. - Max Pereira; Vítor Santos Costa; Rui Camacho; Nuno A. Fonseca (IWANN (2), 2009)

Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases. - Max Pereira; Vítor Santos Costa; Rui Camacho; Nuno A. Fonseca; Carlos J. V. Simões; Rui M. M. Brito (BSB, 2009)

Parallel ILP for distributed-memory architectures. - Nuno A. Fonseca; Ashwin Srinivasan 001; Fernando M. A. Silva; Rui Camacho (Mach. Learn., 2009)

Improving the efficiency of inductive logic programming systems. - Nuno A. Fonseca; Vítor Santos Costa; Ricardo Rocha 001; Rui Camacho; Fernando M. A. Silva (Softw. Pract. Exp., 2009)

Interactive Discriminative Mining of Chemical Fragments. - Nuno A. Fonseca; Max Pereira; Vítor Santos Costa; Rui Camacho (ILP, 2010)

Predicting the Start of Protein alpha-Helices Using Machine Learning Algorithms. - Rui Camacho; Rita Ferreira; Natacha Rosa; Vânia Guimarães; Nuno A. Fonseca; Vítor Santos Costa; Miguel de Sousa; Alexandre Magalhães (IWPACBB, 2010)

Predicting Malignancy from Mammography Findings and Surgical Biopsies. - Pedro Ferreira 002; Nuno A. Fonseca; Inês de Castro Dutra; Ryan W. Woods; Elizabeth S. Burnside (BIBM, 2011)

Studying the Relevance of Breast Imaging Features. - Pedro Ferreira 002; Inês de Castro Dutra; Nuno A. Fonseca; Ryan W. Woods; Elizabeth S. Burnside (HEALTHINF, 2011)

Conceptual Clustering of Multi-Relational Data. - Nuno A. Fonseca; Vítor Santos Costa; Rui Camacho (ILP, 2011)

Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design. - Rui Camacho; Max Pereira; Vítor Santos Costa; Nuno A. Fonseca; Carlos J. V. Simões; Rui M. M. Brito (PACBB, 2011)

A Relational Learning Approach to Structure-Activity Relationships in Drug Design Toxicity Studies. - Rui Camacho; Max Pereira; Vítor Santos Costa; Nuno A. Fonseca; Carlos Adriano Gonçalves; Carlos J. V. Simões; Rui M. M. Brito (J. Integr. Bioinform., 2011)

On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. - David Reboiro-Jato; Miguel Reboiro-Jato; Florentino Fdez-Riverola; Nuno A. Fonseca; Jorge Vieira (PACBB, 2012)

Tools for mapping high-throughput sequencing data. - Nuno A. Fonseca; Johan Rung; Alvis Brazma; John C. Marioni (Bioinform., 2012)

Predicting the secondary structure of proteins using machine learning algorithms. - Rui Camacho; Rita Ferreira; Natacha Rosa; Vânia Guimarães; Nuno A. Fonseca; Vítor Santos Costa; Miguel de Sousa; Alexandre Magalhães (Int. J. Data Min. Bioinform., 2012)

ADOPS - Automatic Detection Of Positively Selected Sites. - David Reboiro-Jato; Miguel Reboiro-Jato; Florentino Fdez-Riverola; Cristina P. Vieira; Nuno A. Fonseca; Jorge Vieira (J. Integr. Bioinform., 2012)

AND Parallelism for ILP: The APIS System. - Rui Camacho; Ruy Ramos; Nuno A. Fonseca (ILP, 2013)

Boosting the Detection of Transposable Elements Using Machine Learning. - Tiago Loureiro; Rui Camacho; Jorge Vieira; Nuno A. Fonseca (PACBB, 2013)

Improving the performance of Transposable Elements detection tools. - Tiago Loureiro; Rui Camacho; Jorge Vieira; Nuno A. Fonseca (J. Integr. Bioinform., 2013)

Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. - Robert Petryszak; Tony Burdett; Benedetto Fiorelli; Nuno A. Fonseca; Mar Gonzalez-Porta; Emma Hastings; Wolfgang Huber; Simon Jupp; Maria Keays; Nataliya Kryvych; Julie A. McMurry; John C. Marioni; et al. (Nucleic Acids Res., 2014)

Predicting malignancy from mammography findings and image-guided core biopsies. - Pedro Ferreira 002; Nuno A. Fonseca; Inês de Castro Dutra; Ryan W. Woods; Elizabeth S. Burnside (Int. J. Data Min. Bioinform., 2015)

Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. - Robert Petryszak; Maria Keays; Y. Amy Tang; Nuno A. Fonseca; Elisabet Barrera; Tony Burdett; Anja Füllgrabe; Alfonso Muñoz-Pomer Fuentes; Simon Jupp; Satu Koskinen; Oliver Mannion; Laura Huerta; et al. (Nucleic Acids Res., 2016)

Gramene 2016: comparative plant genomics and pathway resources. - Marcela K. Tello-Ruiz; Joshua C. Stein; Sharon Wei; Justin Preece; Andrew Olson; Sushma Naithani; Vindhya Amarasinghe; Palitha Dharmawardhana; Yinping Jiao; Joseph Mulvaney; Sunita Kumari; Kapeel Chougule; et al. (Nucleic Acids Res., 2016)

Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems. - Rui Camacho; Jorge G. Barbosa; Altino M. Sampaio; João Ladeiras; Nuno A. Fonseca; Vítor Santos Costa (Resource Management for Big Data Platforms, 2016)

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq. - Bruno Cavadas; Joana Ferreira 001; Rui Camacho; Nuno A. Fonseca; Luísa Pereira (PACBB, 2017)

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data. - Robert Petryszak; Nuno A. Fonseca; Anja Füllgrabe; Laura Huerta; Maria Keays; Y. Amy Tang; Alvis Brazma (Bioinform., 2017)

Expression Atlas: gene and protein expression across multiple studies and organisms. - Irene Papatheodorou; Nuno A. Fonseca; Maria Keays; Y. Amy Tang; Elisabet Barrera; Wojciech Bazant; Melissa L. Burke; Anja Füllgrabe; Alfonso Muñoz-Pomer Fuentes; Nancy George; Laura Huerta; Satu Koskinen; et al. (Nucleic Acids Res., 2018)

Gramene 2018: unifying comparative genomics and pathway resources for plant research. - 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 117; et al. (Nucleic Acids Res., 2018)

ArrayExpress update - from bulk to single-cell expression data. - Awais Athar; Anja Füllgrabe; Nancy George; Haider Iqbal; Laura Huerta; Ahmed Ali 009; Catherine Snow; Nuno A. Fonseca; Robert Petryszak; Irene Papatheodorou; Ugis Sarkans; Alvis Brazma (Nucleic Acids Res., 2019)

Expression Atlas update: from tissues to single cells. - Irene Papatheodorou; Pablo A. Moreno; Jonathan R. Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A. Fonseca; Anja Füllgrabe; Matthew Green 005; Ni Huang; Laura Huerta; Haider Iqbal; et al. (Nucleic Acids Res., 2020)

Genomic basis for RNA alterations in cancer. - Claudia Calabrese; Natalie R. Davidson; Deniz Demircioglu; Nuno A. Fonseca; Yao He; André Kahles; Kjong-Van Lehmann; Fenglin Liu; Yuichi Shiraishi; Cameron M. Soulette; Lara Urban; Liliana Greger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

A Study on Burrows-Wheeler Aligner's Performance Optimization for Ancient DNA Mapping. - Cindy Sarmento; Sílvia Guimarães; Gülsah Merve Kilinç; Anders Götherström; Ana Elisabete Pires; Catarina Ginja; Nuno A. Fonseca (PACBB, 2021)