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Nuno A. Fonseca
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- affiliation: University of Porto, Portugal
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2020 – today
- 2021
- [c27]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: 105-114 - 2020
- [j19]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
:
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48(Database-Issue): D77-D83 (2020) - [j18]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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j17]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): 129-136 (2020)
2010 – 2019
- 2019
- [j16]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): D711-D715 (2019) - 2018
- [j15]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): D1181-D1189 (2018) - [j14]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): D246-D251 (2018) - 2017
- [j13]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): 2218-2220 (2017) - [c26]Bruno Cavadas
, Joana Ferreira
, Rui Camacho
, Nuno A. Fonseca
, Luísa Pereira
:
QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq. PACBB 2017: 173-179 - 2016
- [j12]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): 746-752 (2016) - [j11]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): 1133-1140 (2016) - [p1]Rui Camacho
, Jorge G. Barbosa
, Altino M. Sampaio
, João Ladeiras, Nuno A. Fonseca
, Vítor Santos Costa
:
Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems. Resource Management for Big Data Platforms 2016: 339-363 - 2015
- [j10]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): 257-276 (2015) - 2014
- [j9]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): 926-932 (2014) - 2013
- [j8]Tiago Loureiro, Rui Camacho
, Jorge Vieira
, Nuno A. Fonseca
:
Improving the performance of Transposable Elements detection tools. J. Integr. Bioinform. 10(3) (2013) - [c25]Rui Camacho
, Ruy Ramos, Nuno A. Fonseca
:
AND Parallelism for ILP: The APIS System. ILP 2013: 93-106 - [c24]Tiago Loureiro, Rui Camacho
, Jorge Vieira
, Nuno A. Fonseca
:
Boosting the Detection of Transposable Elements Using Machine Learning. PACBB 2013: 85-91 - 2012
- [j7]Nuno A. Fonseca
, Johan Rung
, Alvis Brazma
, John C. Marioni
:
Tools for mapping high-throughput sequencing data. Bioinform. 28(24): 3169-3177 (2012) - [j6]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): 571-584 (2012) - [j5]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) - [c23]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: 225-229 - 2011
- [j4]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) - [c22]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: 339-344 - [c21]Pedro Ferreira, Inês de Castro Dutra, Nuno A. Fonseca, Ryan W. Woods, Elizabeth S. Burnside:
Studying the Relevance of Breast Imaging Features. HEALTHINF 2011: 337-342 - [c20]Nuno A. Fonseca
, Vítor Santos Costa
, Rui Camacho
:
Conceptual Clustering of Multi-Relational Data. ILP 2011: 145-159 - [c19]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: 355-363 - 2010
- [c18]Nuno A. Fonseca
, Max Pereira, Vítor Santos Costa
, Rui Camacho
:
Interactive Discriminative Mining of Chemical Fragments. ILP 2010: 59-66 - [c17]Rui Camacho
, Rita Ferreira, Natacha Rosa
, Vânia Guimarães
, Nuno A. Fonseca
, Vítor Santos Costa
, Miguel de Sousa, Alexandre Magalhães
:
Predicting the Start of Protein alpha-Helices Using Machine Learning Algorithms. IWPACBB 2010: 33-41
2000 – 2009
- 2009
- [j3]Nuno A. Fonseca
, Ashwin Srinivasan, Fernando M. A. Silva
, Rui Camacho
:
Parallel ILP for distributed-memory architectures. Mach. Learn. 74(3): 257-279 (2009) - [j2]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): 189-219 (2009) - [c16]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: 1001-1004 - [c15]Max Pereira, Vítor Santos Costa
, Rui Camacho
, Nuno A. Fonseca
:
Visually Guiding and Controlling the Search While Mining Chemical Structures. IWANN (2) 2009: 1043-1046 - [c14]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: 121-132 - 2008
- [j1]Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, Vítor Santos Costa:
Compile the Hypothesis Space: Do it Once, Use it Often. Fundam. Informaticae 89(1): 45-67 (2008) - [c13]Vítor Santos Costa
, Nuno A. Fonseca
, Rui Camacho
:
LogCHEM: Interactive Discriminative Mining of Chemical Structure. BIBM 2008: 421-426 - [c12]Pedro Pereira Rodrigues, Fernando M. A. Silva
, Nuno A. Fonseca
:
BIORED - A Genetic Algorithm for Pattern Detection in Biosequences. IWPACBB 2008: 156-165 - [c11]Nuno A. Fonseca
, Vítor Santos Costa
, Rui Camacho
:
k-RNN: k-relational nearest neighbour algorithm. SAC 2008: 944-948 - 2007
- [c10]Rui Camacho
, Nuno A. Fonseca
, Ricardo Rocha
, Vítor Santos Costa
:
ILP : - Just Trie It. ILP 2007: 78-87 - 2006
- [c9]Michel Ferreira, Nuno A. Fonseca
, Ricardo Rocha
, Tiago Soares:
Efficient and Scalable Induction of Logic Programs Using a Deductive Database System. ILP 2006: 184-198 - [c8]Nuno A. Fonseca
, Fernando M. A. Silva
, Rui Camacho
:
April - An Inductive Logic Programming System. JELIA 2006: 481-484 - 2005
- [c7]Nuno A. Fonseca
, Fernando M. A. Silva
, Vítor Santos Costa
, Rui Camacho
:
A pipelined data-parallel algorithm for ILP. CLUSTER 2005: 1-10 - [c6]Ricardo Rocha
, Nuno A. Fonseca
, Vítor Santos Costa
:
On Applying Tabling to Inductive Logic Programming. ECML 2005: 707-714 - [c5]Nuno A. Fonseca
, Fernando M. A. Silva
, Rui Camacho
:
Strategies to Parallelize ILP Systems. ILP 2005: 136-153 - 2004
- [c4]Nuno A. Fonseca
, Vítor Santos Costa
, Fernando M. A. Silva
, Rui Camacho
:
On Avoiding Redundancy in Inductive Logic Programming. ILP 2004: 132-146 - 2003
- [c3]Nuno A. Fonseca
, Vítor Santos Costa
, Fernando M. A. Silva
, Rui Camacho
:
Experimental Evaluation of a Caching Technique for ILP. EPIA 2003: 151-155 - [c2]Nuno A. Fonseca
, Ricardo Rocha
, Rui Camacho
, Fernando M. A. Silva
:
Efficient Data Structures for Inductive Logic Programming. ILP 2003: 130-145
1990 – 1999
- 1998
- [c1]Nuno A. Fonseca, Vítor Santos Costa, Inês de Castro Dutra:
VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs. IJCSLP 1998: 100-114
Coauthor Index
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