Nuno A. Fonseca

Publication Activity (10 Years)

Years Active: 1998-2021
Publications (10 Years): 11

Top Topics

Machine Learning

Differential Expression

Top Venues

Nucleic Acids Res.

Int. J. Data Min. Bioinform.

Publications

Cindy Sarmento, Sílvia Guimarães, Gülsah Merve Kilinç, Anders Götherström, Ana Elisabete Pires, Catarina Ginja, Nuno A. Fonseca
A Study on Burrows-Wheeler Aligner's Performance Optimization for Ancient DNA Mapping. PACBB (2021)
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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
Irene Papatheodorou, Pablo 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
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
Genomic basis for RNA alterations in cancer. Nat. 578 (7793) (2020)
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
ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 47 (Database-Issue) (2019)
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
Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46 (Database-Issue) (2018)
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
Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46 (Database-Issue) (2018)
Bruno Cavadas, Joana Ferreira, Rui Camacho, Nuno A. Fonseca, Luísa Pereira
QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq. PACBB (2017)
Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brazma
The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data. Bioinform. 33 (14) (2017)
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
Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44 (Database-Issue) (2016)
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
Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Pedro Ferreira, Nuno A. Fonseca, Inês de Castro Dutra, Ryan W. Woods, Elizabeth S. Burnside
Predicting malignancy from mammography findings and image-guided core biopsies. Int. J. Data Min. Bioinform. 11 (3) (2015)
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
Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 42 (Database-Issue) (2014)
Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A. Fonseca
Boosting the Detection of Transposable Elements Using Machine Learning. PACBB (2013)
Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A. Fonseca
Improving the performance of Transposable Elements detection tools. J. Integr. Bioinform. 10 (3) (2013)
Rui Camacho, Ruy Ramos, Nuno A. Fonseca
AND Parallelism for ILP: The APIS System. ILP (2013)
David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Cristina P. Vieira, Nuno A. Fonseca, Jorge Vieira
ADOPS - Automatic Detection Of Positively Selected Sites. J. Integr. Bioinform. 9 (3) (2012)
Rui Camacho, Rita Ferreira, Natacha Rosa, Vânia Guimarães, Nuno A. Fonseca, Vítor Santos Costa, Miguel de Sousa, Alexandre Magalhães
Predicting the secondary structure of proteins using machine learning algorithms. Int. J. Data Min. Bioinform. 6 (6) (2012)
Nuno A. Fonseca, Johan Rung, Alvis Brazma, John C. Marioni
Tools for mapping high-throughput sequencing data. Bioinform. 28 (24) (2012)
David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Nuno A. Fonseca, Jorge Vieira
On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. PACBB (2012)
Pedro Ferreira, Nuno A. Fonseca, Inês de Castro Dutra, Ryan W. Woods, Elizabeth S. Burnside
Predicting Malignancy from Mammography Findings and Surgical Biopsies. BIBM (2011)
Rui Camacho, Max Pereira, Vítor Santos Costa, Nuno A. Fonseca, Carlos J. V. Simões, Rui M. M. Brito
Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design. PACBB (2011)
Pedro Ferreira, Inês de Castro Dutra, Nuno A. Fonseca, Ryan W. Woods, Elizabeth S. Burnside
Studying the Relevance of Breast Imaging Features. HEALTHINF (2011)
Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho
Conceptual Clustering of Multi-Relational Data. ILP (2011)
Rui Camacho, Max Pereira, Vítor Santos Costa, Nuno A. Fonseca, Carlos Adriano Gonçalves, Carlos J. V. Simões, Rui M. M. Brito
A Relational Learning Approach to Structure-Activity Relationships in Drug Design Toxicity Studies. J. Integr. Bioinform. 8 (3) (2011)
Nuno A. Fonseca, Max Pereira, Vítor Santos Costa, Rui Camacho
Interactive Discriminative Mining of Chemical Fragments. ILP (2010)
Rui Camacho, Rita Ferreira, Natacha Rosa, Vânia Guimarães, Nuno A. Fonseca, Vítor Santos Costa, Miguel de Sousa, Alexandre Magalhães
-Helices Using Machine Learning Algorithms. IWPACBB (2010)
Nuno A. Fonseca, Ashwin Srinivasan, Fernando M. A. Silva, Rui Camacho
Parallel ILP for distributed-memory architectures. Mach. Learn. 74 (3) (2009)
Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho, Cristina P. Vieira, Jorge Vieira
Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach. IWANN (2) (2009)
Max Pereira, Vítor Santos Costa, Rui Camacho, Nuno A. Fonseca, Carlos J. V. Simões, Rui M. M. Brito
Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases. BSB (2009)
Nuno A. Fonseca, Vítor Santos Costa, Ricardo Rocha, Rui Camacho, Fernando M. A. Silva
Improving the efficiency of inductive logic programming systems. Softw. Pract. Exp. 39 (2) (2009)
Max Pereira, Vítor Santos Costa, Rui Camacho, Nuno A. Fonseca
Visually Guiding and Controlling the Search While Mining Chemical Structures. IWANN (2) (2009)
Pedro Pereira Rodrigues, Fernando M. A. Silva, Nuno A. Fonseca
BIORED - A Genetic Algorithm for Pattern Detection in Biosequences. IWPACBB (2008)
Vítor Santos Costa, Nuno A. Fonseca, Rui Camacho
LogCHEM: Interactive Discriminative Mining of Chemical Structure. BIBM (2008)
Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, Vítor Santos Costa
Compile the Hypothesis Space: Do it Once, Use it Often. Fundam. Informaticae 89 (1) (2008)
Nuno A. Fonseca, Vítor Santos Costa, Rui Camacho
k-RNN: k-relational nearest neighbour algorithm. SAC (2008)
Rui Camacho, Nuno A. Fonseca, Ricardo Rocha, Vítor Santos Costa
ILP : - Just Trie It. ILP (2007)
Michel Ferreira, Nuno A. Fonseca, Ricardo Rocha, Tiago Soares
Efficient and Scalable Induction of Logic Programs Using a Deductive Database System. ILP (2006)
Nuno A. Fonseca, Fernando M. A. Silva, Rui Camacho
April - An Inductive Logic Programming System. JELIA (2006)
Nuno A. Fonseca, Fernando M. A. Silva, Vítor Santos Costa, Rui Camacho
A pipelined data-parallel algorithm for ILP. CLUSTER (2005)
Ricardo Rocha, Nuno A. Fonseca, Vítor Santos Costa
On Applying Tabling to Inductive Logic Programming. ECML (2005)
Nuno A. Fonseca, Fernando M. A. Silva, Rui Camacho
Strategies to Parallelize ILP Systems. ILP (2005)
Nuno A. Fonseca, Vítor Santos Costa, Fernando M. A. Silva, Rui Camacho
On Avoiding Redundancy in Inductive Logic Programming. ILP (2004)
Nuno A. Fonseca, Ricardo Rocha, Rui Camacho, Fernando M. A. Silva
Efficient Data Structures for Inductive Logic Programming. ILP (2003)
Nuno A. Fonseca, Vítor Santos Costa, Fernando M. A. Silva, Rui Camacho
Experimental Evaluation of a Caching Technique for ILP. EPIA (2003)
Nuno A. Fonseca, Vítor Santos Costa, Inês de Castro Dutra
VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs. IJCSLP (1998)