Nuno A. Fonseca

According to our database, Nuno A. Fonseca authored at least 47 papers between 1998 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

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

Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021

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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 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, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina K. Yung, Shida Zhu, Philip Awadalla, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Samirkumar B. Amin, Aurélien Chateigner, Isidro Cortés-Ciriano, Brian Craft, Milana Frenkel-Morgenstern, Mary Goldman, Ekta Khurana, Fabien C. Lamaze, Chang Li, Xiaobo Li, Xinyue Li, Xingmin Liu, Morten Muhlig Nielsen, Akinyemi I. Ojesina, Peter J. Park, Jakob Skou Pedersen, Bin Tean Teh, Jian Wang, Heng Xiong, Sergei Yakneen, Chen Ye, Xiuqing Zhang, Liangtao Zheng, Jingchun Zhu, Chad Creighton, Jonathan Göke, Roland F. Schwarz, Oliver Stegle, Zemin Zhang, Alvis Brazma, Gunnar Rätsch, Angela N. Brooks

Nat., 2020

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, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp, John C. Marioni, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma

Nucleic Acids Res., 2020

2019

ArrayExpress update - from bulk to single-cell expression data.

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma

Nucleic Acids Res., 2019

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, 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 Muñoz-Pomer Fuentes, Y. 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, Doreen Ware

Nucleic Acids Res., 2018

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, Suhaib Mohammed, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaíno, Alvis Brazma, Robert Petryszak

Nucleic Acids Res., 2018

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

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq.

Bruno Cavadas, Joana Ferreira, Rui Camacho, Nuno A. Fonseca, Luísa Pereira

Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

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

Proceedings of the Resource Management for Big Data Platforms, 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, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen E. Parkinson, Antonio Fabregat, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware

Nucleic Acids Res., 2016

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, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James C. Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, Alvis Brazma

Nucleic Acids Res., 2016

2015

Predicting malignancy from mammography findings and image-guided core biopsies.

Pedro Ferreira, Nuno A. Fonseca, Inês de Castro Dutra, Ryan W. Woods, Elizabeth S. Burnside

Int. J. Data Min. Bioinform., 2015

2014

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, James Malone, Karine Megy, Gabriella Rustici, Y. Amy Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, Alvis Brazma

Nucleic Acids Res., 2014

2013

Improving the performance of Transposable Elements detection tools.

Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A. Fonseca

J. Integr. Bioinform., 2013

Boosting the Detection of Transposable Elements Using Machine Learning.

Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A. Fonseca

Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

AND Parallelism for ILP: The APIS System.

Rui Camacho, Ruy Ramos, Nuno A. Fonseca

Proceedings of the Inductive Logic Programming - 23rd International Conference, 2013

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

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

Tools for mapping high-throughput sequencing data.

Nuno A. Fonseca, Johan Rung, Alvis Brazma, John C. Marioni

Bioinform., 2012

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

Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

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

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

Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

Conceptual Clustering of Multi-Relational Data.

Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho

Proceedings of the Inductive Logic Programming - 21st International Conference, 2011

Studying the Relevance of Breast Imaging Features.

Pedro Ferreira, Inês de Castro Dutra, Nuno A. Fonseca, Ryan W. Woods, Elizabeth S. Burnside

Proceedings of the HEALTHINF 2011, 2011

Predicting Malignancy from Mammography Findings and Surgical Biopsies.

Pedro Ferreira, Nuno A. Fonseca, Inês de Castro Dutra, Ryan W. Woods, Elizabeth S. Burnside

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010

Predicting the Start of Protein <i>alpha</i>-Helices Using Machine Learning Algorithms.

Rui Camacho, Rita Ferreira, Natacha Rosa, Vânia Guimarães, Nuno A. Fonseca, Vítor Santos Costa, Miguel de Sousa, Alexandre Magalhães

Proceedings of the Advances in Bioinformatics, 2010

Interactive Discriminative Mining of Chemical Fragments.

Nuno A. Fonseca, Max Pereira, Vítor Santos Costa, Rui Camacho

Proceedings of the Inductive Logic Programming - 20th International Conference, 2010

2009

Improving the efficiency of inductive logic programming systems.

Nuno A. Fonseca, Vítor Santos Costa, Ricardo Rocha, Rui Camacho, Fernando M. A. Silva

Softw. Pract. Exp., 2009

Parallel ILP for distributed-memory architectures.

Nuno A. Fonseca, Ashwin Srinivasan, Fernando M. A. Silva, Rui Camacho

Mach. Learn., 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

Proceedings of the Advances in Bioinformatics and Computational Biology, 2009

Visually Guiding and Controlling the Search While Mining Chemical Structures.

Max Pereira, Vítor Santos Costa, Rui Camacho, Nuno A. Fonseca

Proceedings of the Distributed Computing, 2009

Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach.

Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho, Cristina P. Vieira, Jorge Vieira

Proceedings of the Distributed Computing, 2009

2008

Compile the Hypothesis Space: Do it Once, Use it Often.

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, Vítor Santos Costa

Fundam. Informaticae, 2008

k-RNN: k-relational nearest neighbour algorithm.

Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho

Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008

BIORED - A Genetic Algorithm for Pattern Detection in Biosequences.

Pedro Pereira Rodrigues, Fernando M. A. Silva, Nuno A. Fonseca

Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008

LogCHEM: Interactive Discriminative Mining of Chemical Structure.

Vítor Santos Costa, Nuno A. Fonseca, Rui Camacho

Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

2007

ILP : - Just Trie It.

Rui Camacho, Nuno A. Fonseca, Ricardo Rocha, Vítor Santos Costa

Proceedings of the Inductive Logic Programming, 17th International Conference, 2007

2006

April - An Inductive Logic Programming System.

Nuno A. Fonseca, Fernando M. A. Silva, Rui Camacho

Proceedings of the Logics in Artificial Intelligence, 10th European Conference, 2006

Efficient and Scalable Induction of Logic Programs Using a Deductive Database System.

Michel Ferreira, Nuno A. Fonseca, Ricardo Rocha, Tiago Soares

Proceedings of the Inductive Logic Programming, 16th International Conference, 2006

2005

Strategies to Parallelize ILP Systems.

Nuno A. Fonseca, Fernando M. A. Silva, Rui Camacho

Proceedings of the Inductive Logic Programming, 15th International Conference, 2005

On Applying Tabling to Inductive Logic Programming.

Ricardo Rocha, Nuno A. Fonseca, Vítor Santos Costa

Proceedings of the Machine Learning: ECML 2005, 2005

A pipelined data-parallel algorithm for ILP.

Nuno A. Fonseca, Fernando M. A. Silva, Vítor Santos Costa, Rui Camacho

Proceedings of the 2005 IEEE International Conference on Cluster Computing (CLUSTER 2005), September 26, 2005

2004

On Avoiding Redundancy in Inductive Logic Programming.

Nuno A. Fonseca, Vítor Santos Costa, Fernando M. A. Silva, Rui Camacho

Proceedings of the Inductive Logic Programming, 14th International Conference, 2004

2003

Efficient Data Structures for Inductive Logic Programming.

Nuno A. Fonseca, Ricardo Rocha, Rui Camacho, Fernando M. A. Silva

Proceedings of the Inductive Logic Programming: 13th International Conference, 2003

Experimental Evaluation of a Caching Technique for ILP.

Nuno A. Fonseca, Vítor Santos Costa, Fernando M. A. Silva, Rui Camacho

Proceedings of the Progress in Artificial Intelligence, 2003

1998

VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs.

Nuno A. Fonseca, Vítor Santos Costa, Inês de Castro Dutra

Proceedings of the 1998 Joint International Conference and Symposium on Logic Programming, 1998