???global.info.a_carregar???
Nuno Fonseca is a bioinformatics scientist and Head of IT and Bioinformatics at BIOPOLIS/CIBIO. He brings a diverse background in computer science, artificial intelligence, and bioinformatics, with experience in both academia and industry. Earned a first degree in Computer Science, an M.Sc. in Artificial Intelligence and Computation, and a PhD in exploiting parallelism in multi-relational learning at the University of Porto. Held positions as a lecturer and researcher in academia, and as a senior programmer, system administrator, and department manager in industry. More precisely, as: a Postdoctoral fellow at the Molecular Evolution group in the Institute for Molecular and Cell Biology (Portugal); a Senior research scientist at INESC-TEC (Portugal); a research scientist at EMBL-EBI (jointly in John Marioni and Alvis Brazma groups); a Project Leader for high-throughput sequencing data analysis and management in the Expression Atlas team at EMBL-EBI; the ERA Chair in Environmental Metagenomics at CIBIO/InBIO (2018); and Bioinformatics scientist and Head of IT and Bioinformatics at BIOPOLIS/CIBIO (since 2023). Co-authored three book chapters and more than seventy papers in internationally peer-reviewed book series or journals (including Nature, Nature Genetics, Genome Research, Cell, and Nucleic Acids Research). More information is available in ResearchGate (https://www.researchgate.net/profile/Nuno_Fonseca3), and Google Scholar (https://scholar.google.com/citations?user=y3vZ6R4AAAAJ).
Read full resume ↓
Identification

Personal identification

Full name
Nuno Alberto Paulino da Fonseca

Citation names

  • Fonseca, Nuno A

Author identifiers

Ciência ID
5612-C65F-D4DA
ORCID iD
0000-0003-4832-578X
Google Scholar ID
y3vZ6R4AAAAJ

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2006/06/01
Concluded
 Empreendedorismo/Entrepreneurship (Outros)
Universidade do Porto Porto Business School, Portugal
 18
2006
Concluded
 Ciências de Computadores (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
"Parallelism in Inductive Logic Programming" (THESIS/DISSERTATION)
 maximum
2001/10/26
Concluded
 RedHat Certified Engineer (Outros)
Major in Computer Science
RedHat Europe, United Kingdom
2001/05/25
Concluded
 Formação Pedagógica Inicial de Formadores/Initial Pedagogic Training (Outros)
Instituto de Informática do Porto, Portugal
2001/01/31
Concluded
 Inteligência Artificial e Computação (Mestrado)
Universidade do Porto Faculdade de Engenharia, Portugal
"Optimizing the Communications between Applications and Databases" (THESIS/DISSERTATION)
 Very Good
1998/07/01
Concluded
 Ciência de Computadores (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
 14
Outputs

Publications

Book chapter
  1. Rui Camacho; Jorge G. Barbosa; Altino Sampaio; João Ladeiras; Nuno A. Fonseca; Vítor S. Costa. "Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems". In Resource Management for Big Data Platforms. 2016.
    10.1007/978-3-319-44881-7_16
  2. Konstantopoulos, S; Camacho, R; Fonseca, NA; Costa, VS. "Induction as a search procedure". 2008.
    10.4018/978-1-59904-705-8.ch007
  3. Fonseca, Nuno; Vitor Santos Costa; Ines Dutra. "VisAll: A new tool to visualise parallel execution of Logic Programs". In Parallelism and Implementation of Logic and Constraint Logic Programming, 1-20. Nova Science, 1999.
    Published • 10.7551/mitpress/4316.003.0019
Conference paper
  1. Sarmento, C; Guimaraes, S; Kilinc, GM; Gotherstrom, A; Pires, AE; Ginja, C; Fonseca, NA. "A Study on Burrows-Wheeler Aligner's Performance Optimization for Ancient DNA Mapping". 2022.
    10.1007/978-3-030-86258-9_11
  2. Cavadas, B; Ferreira, J; Camacho, R; Fonseca, NA; Pereira, L. "QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq". 2017.
    10.1007/978-3-319-60816-7_21
  3. Camacho, R; Ramos, R; Fonseca, NA. "AND Parallelism for ILP: The APIS System". 2014.
    10.1007/978-3-662-44923-3_7
  4. Camacho, R; Ferreira, R; Rosa, N; Guimaraes, V; Fonseca, NA; Costa, VS; de Sousa, M; Magalhaes, A. "Predicting the Start of Protein alpha-Helices Using Machine Learning Algorithms". 2010.
    10.1007/978-3-642-13214-8_5
  5. Fonseca, NA; Dutra, I. "UbiDis: a Flexible and General top-level Middleware to Manage Applications in Grids and Clusters". 2009.
  6. Costa, V.S.; Fonseca, N.A.; Camacho, R.. "LogCHEM: Interactive discriminative mining of chemical structure". 2008.
    10.1109/BIBM.2008.45
  7. Fonseca, Nuno; Ricardo Rocha; Rui Camacho; Vitor Santos Costa. "ILP: Compute Once, Reuse Often". Paper presented in 6th Workshop on Multi-Relational Data Mining (MRDM 2007), 2007.
    Published
  8. T. Soares; M. Ferreira; R. Rocha; Fonseca, Nuno. "On Applying Deductive Databases to Inductive Logic Programming: a Performance Study". Paper presented in Colloquium on Implementation of Constraint and LOgic Programming Systems, CICLOPS’2006, 2006.
    Published
  9. Magalhaes, A; Fonseca, NA. "On predicting protein secondary structure from their aminoacid sequences using Inductive Logic Programming". 2005.
    10.1109/epia.2005.341281
  10. Fonseca, N.A.; Silva, F.; Costa, V.S.; Camacho, R.. "A pipelined data-parallel algorithm for ILP". Paper presented in IEEE International Conference on Cluster Computing, 2005.
    Published • 10.1109/CLUSTR.2005.347059
  11. Fonseca, Nuno; Rui Camacho; Fernando Silva. "A parallel ILP algorithm that incorporates incremental batch learning". Paper presented in Workshop on Parallel and Distributed Com- puting for Machine Learning, 2003.
    Published
  12. Fonseca, N; Costa, VS; Dutra, ID. "VisAll: A universal tool to visualise the parallel execution of logic programs". 1998.
Journal article
  1. Joana G Guedes; Rogério Ribeiro; Inês Carqueijeiro; Ana Luísa Guimarães; Cláudia Bispo; John Archer; Herlander Azevedo; et al. "The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism". Journal of Experimental Botany (2024): https://doi.org/10.1093/jxb/erad374.
    10.1093/jxb/erad374
  2. Yiqun Zhang; Fengju Chen; Nuno A. Fonseca; Yao He; Masashi Fujita; Hidewaki Nakagawa; Zemin Zhang; et al. "Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations". Nature Communications (2022): https://doi.org/10.1038/s41467-022-32333-w.
    10.1038/s41467-022-32333-w
  3. Bastian Egeter; Joana Veríssimo; Manuel Lopes-Lima; Cátia Chaves; Joana Pinto; Nicoletta Riccardi; Pedro Beja; Nuno A. Fonseca. "Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison". Molecular Ecology Resources 22 6 (2022): 2232-2247. https://doi.org/10.1111/1755-0998.13610.
    10.1111/1755-0998.13610
  4. Manik Garg; Dominique-Laurent Couturier; Jérémie Nsengimana; Nuno A. Fonseca; Matthew Wongchenko; Yibing Yan; Martin Lauss; et al. "Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes". Nature Communications (2022): https://doi.org/10.1038/s41467-022-30365-w.
    10.1038/s41467-022-30365-w
  5. Manik Garg; Dominique-Laurent Couturier; Jérémie Nsengimana; Nuno A. Fonseca; Matthew Wongchenko; Yibing Yan; Martin Lauss; et al. "Tumour gene expression signature in primary melanoma predicts long-term outcomes". Nature Communications 12 1 (2021): https://doi.org/10.1038/s41467-021-21207-2.
    10.1038/s41467-021-21207-2
  6. Daniel Oliveira; Cátia Chaves; Joana Pinto; Joana Paupério; Nuno Fonseca; Pedro Beja; Sónia Ferreira. "DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida)". ZooKeys (2021): https://doi.org/10.3897/zookeys.1054.64608.
    10.3897/zookeys.1054.64608
  7. Camila Fernandes; Leonor Martins; Miguel Teixeira; Jochen Blom; Joël F. Pothier; Nuno A. Fonseca; Fernando Tavares. "Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree". Microorganisms 9 3 (2021): 624-624. https://doi.org/10.3390/microorganisms9030624.
    10.3390/microorganisms9030624
  8. Miguel Teixeira; Camila Fernandes; Cátia Chaves; Joana Pinto; Fernando Tavares; Nuno A. Fonseca; Steven R. Gill. "Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree". Microbiology Resource Announcements 10 10 (2021): https://doi.org/10.1128/MRA.00085-21.
    10.1128/MRA.00085-21
  9. Filipa MS Martins; Nuno A Fonseca; Bastian Egeter; Joana Pinto; Tiago Assunção; Cátia Chaves; Pedro Sousa; Joaquim Jesus; Pedro Beja. "Evaluating the impact of sampling strategies and bioinformatics on ethanol-based DNA metabarcoding". ARPHA Conference Abstracts (2021): https://doi.org/10.3897/aca.4.e64708.
    10.3897/aca.4.e64708
  10. Bastian Egeter; Joana Veríssimo; Manuel Lopes-Lima; catia chaves; Joana Pinto; Nicoletta Riccardi; Pedro Beja; Nuno A. Fonseca. "Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing". ARPHA Conference Abstracts (2021): https://doi.org/10.3897/aca.4.e65036.
    10.3897/aca.4.e65036
  11. Bruno Cavadas; Marina Leite; Nicole Pedro; Ana C. Magalhães; Joana Melo; Marcelo Correia; Valdemar Máximo; et al. "Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution". Microorganisms 9 2 (2021): 240-240. https://doi.org/10.3390/microorganisms9020240.
    10.3390/microorganisms9020240
  12. Yiqun Zhang; Fengju Chen; Nuno A. Fonseca; Yao He; Masashi Fujita; Hidewaki Nakagawa; Zemin Zhang; Alvis Brazma; Chad J. Creighton. "High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations". Nature Communications (2020): https://doi.org/10.1038/s41467-019-13885-w.
    10.1038/s41467-019-13885-w
  13. Bidesh Mahata; Jhuma Pramanik; Louise van der Weyden; Krzysztof Polanski; Gozde Kar; Angela Riedel; Xi Chen; et al. "Tumors induce de novo steroid biosynthesis in T cells to evade immunity". Nature Communications 11 1 (2020): https://doi.org/10.1038/s41467-020-17339-6.
    10.1038/s41467-020-17339-6
  14. Mary J. Goldman; Junjun Zhang; Nuno A. Fonseca; Isidro Cortés-Ciriano; Qian Xiang; Brian Craft; Elena Piñeiro-Yáñez; et al. "A user guide for the online exploration and visualization of PCAWG data". Nature Communications 11 1 (2020): https://doi.org/10.1038/s41467-020-16785-6.
    10.1038/s41467-020-16785-6
  15. Miguel Teixeira; Leonor Martins; Camila Fernandes; Cátia Chaves; Joana Pinto; Fernando Tavares; Nuno A. Fonseca; et al. "Complete Genome Sequences of Walnut-Associated Xanthomonas euroxanthea Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly". Microbiology Resource Announcements (2020): https://doi.org/10.1128/MRA.00902-20.
    10.1128/MRA.00902-20
  16. Bailey MH; Meyerson WU; Dursi LJ; Wang LB; Dong G; Liang WW; Weerasinghe A; et al. "Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.". Nature communications (2020): http://europepmc.org/abstract/med/32958763.
    10.1038/s41467-020-18151-y
  17. Bruno Cavadas; Rui Camacho; Joana C. Ferreira; Rui M. Ferreira; Ceu Figueiredo; Alvis Brazma; Nuno A. Fonseca; Luísa Pereira. "Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci". Microorganisms 8 8 (2020): 1196-1196. https://doi.org/10.3390/microorganisms8081196.
    10.3390/microorganisms8081196
  18. Sonia Ferreira; José Manuel Tierno de Figueroa; Filipa Martins; Joana Verissimo; Lorenzo Quaglietta; José Manuel Grosso-Silva; Pedro Lopes; et al. "The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera". Biodiversity Data Journal (2020): https://doi.org/10.3897/BDJ.8.e55137.
    10.3897/BDJ.8.e55137
  19. Estévez O; Anibarro L; Garet E; Pallares Á; Barcia L; Calviño L; Maueia C; et al. "An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile.". Frontiers in immunology (2020): http://europepmc.org/abstract/med/32760401.
    10.3389/fimmu.2020.01470
  20. Sonia Ferreira; Rui Andrade; Ana Gonçalves; Pedro Sousa; Joana Paupério; Nuno Fonseca; Pedro Beja. "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01". Biodiversity Data Journal (2020): http://dx.doi.org/10.3897/bdj.8.e49985.
    10.3897/bdj.8.e49985
  21. Fonseca, Nuno A. "Pan-cancer analysis of whole genomes". Nature (2020): http://dx.doi.org/10.1038/s41586-020-1969-6.
    10.1038/s41586-020-1969-6
  22. Calabrese, C; Davidson, NR; Demircioglu, D; Fonseca, NA; He, Y; Kahles, A; Lehmann, KV; et al. "Genomic basis for RNA alterations in cancer". Nat. (2020):
    10.1038/s41586-020-1970-0
  23. Rheinbay, E; Nielsen, MM; Abascal, F; Wala, J; Shapira, O; Tiao, G; Hornshøj, H; et al. "Analyses of non-coding somatic drivers in 2,658 cancer whole genomes". Nat. (2020):
    10.1038/s41586-020-1965-x
  24. Reyna, M.A.; Haan, D.; Paczkowska, M.; Verbeke, L.P.C.; Vazquez, M.; Kahraman, A.; Pulido-Tamayo, S.; et al. "Pathway and network analysis of more than 2500 whole cancer genomes". Nature Communications 11 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079060258&partnerID=MN8TOARS.
    10.1038/s41467-020-14367-0
  25. Yakneen, S.; Waszak, S.M.; Aminou, B.; Bartolome, J.; Boroevich, K.A.; Boyce, R.; Brooks, A.N.; et al. "Butler enables rapid cloud-based analysis of thousands of human genomes". Nature Biotechnology (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079041410&partnerID=MN8TOARS.
    10.1038/s41587-019-0360-3
  26. Carlevaro-Fita, J.; Lanzós, A.; Feuerbach, L.; Hong, C.; Mas-Ponte, D.; Pedersen, J.S.; Abascal, F.; et al. "Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis". Communications Biology 3 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079071080&partnerID=MN8TOARS.
    10.1038/s42003-019-0741-7
  27. Paczkowska, M.; Barenboim, J.; Sintupisut, N.; Fox, N.S.; Zhu, H.; Abd-Rabbo, D.; Mee, M.W.; et al. "Integrative pathway enrichment analysis of multivariate omics data". Nature Communications 11 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079073313&partnerID=MN8TOARS.
    10.1038/s41467-019-13983-9
  28. Shuai, S.; Abascal, F.; Amin, S.B.; Bader, G.D.; Bandopadhayay, P.; Barenboim, J.; Beroukhim, R.; et al. "Combined burden and functional impact tests for cancer driver discovery using DriverPower". Nature Communications 11 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079072523&partnerID=MN8TOARS.
    10.1038/s41467-019-13929-1
  29. Yakneen, S.; Waszak, S.M.; Aminou, B.; Bartolome, J.; Boroevich, K.A.; Boyce, R.; Brooks, A.N.; et al. "Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes (Nature Biotechnology, (2020), 10.1038/s41587-019-0360-3)". Nature Biotechnology (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85079721096&partnerID=MN8TOARS.
    10.1038/s41587-020-0448-9
  30. Irene Papatheodorou; Pablo Moreno; Jonathan Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A Fonseca; et al. "Expression Atlas update: from tissues to single cells". Nucleic Acids Research (2019): https://doi.org/10.1093/nar/gkz947.
    10.1093/nar/gkz947
  31. Demircioglu, D; Cukuroglu, E; Kindermans, M; Nandi, T; Calabrese, C; Fonseca, NA; Kahles, A; et al. "A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters". CELL (2019):
    10.1016/j.cell.2019.08.018
  32. Athar, A; Fullgrabe, A; George, N; Iqbal, H; Huerta, L; Ali, A; Snow, C; et al. "ArrayExpress update - from bulk to single-cell expression data". NUCLEIC ACIDS RESEARCH (2019):
    10.1093/nar/gky964
  33. Maria I. Pratas; Bruno Aguiar; Jorge Vieira; Vanessa Nunes; Vanessa Teixeira; Nuno A. Fonseca; Amy Iezzoni; Steve van Nocker; Cristina P. Vieira. "Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system". Scientific Reports 8 1 (2018): https://doi.org/10.1038/s41598-018-19820-1.
    10.1038/s41598-018-19820-1
  34. Irene Papatheodorou; Nuno A Fonseca; Maria Keays; Y Amy Tang; Elisabet Barrera; Wojciech Bazant; Melissa Burke; et al. "Expression Atlas: gene and protein expression across multiple studies and organisms". Nucleic Acids Research (2018): https://doi.org/10.1093/nar/gkx1158.
    10.1093/nar/gkx1158
  35. Garcia-Alonso, L.; Iorio, F.; Matchan, A.; Fonseca, N.; Jaaks, P.; Peat, G.; Pignatelli, M.; et al. "Transcription factor activities enhance markers of drug sensitivity in cancer". Cancer Research 78 3 (2018): 769-780. http://www.scopus.com/inward/record.url?eid=2-s2.0-85041469991&partnerID=MN8TOARS.
    10.1158/0008-5472.CAN-17-1679
  36. Tello-Ruiz, Marcela K; Naithani, Sushma; Stein, Joshua C; Gupta, Parul; Campbell, Michael; Olson, Andrew; Wei, Sharon; et al. "Gramene 2018: unifying comparative genomics and pathway resources for plant research". Nucleic Acids Research 46 D1 (2017): D1181-D1189. http://dx.doi.org/10.1093/nar/gkx1111.
    Published • 10.1093/nar/gkx1111
  37. Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; et al. "Two independent modes of chromatin organization revealed by cohesin removal". Nature 551 7678 (2017): 51-56. http://dx.doi.org/10.1038/nature24281.
    Published • 10.1038/nature24281
  38. Petryszak, Robert; Fonseca, Nuno A; Füllgrabe, Anja; Huerta, Laura; Keays, Maria; Tang, Y Amy; Brazma, Alvis. "The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data". Bioinformatics 33 14 (2017): 2218-2220. http://dx.doi.org/10.1093/bioinformatics/btx143.
    Open access • Published • 10.1093/bioinformatics/btx143
  39. Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; et al. "Gramene 2016: comparative plant genomics and pathway resources". Nucleic Acids Research 44 D1 (2015): D1133-D1140. http://dx.doi.org/10.1093/nar/gkv1179.
    Published • 10.1093/nar/gkv1179
  40. Petryszak, Robert; Keays, Maria; Tang, Y. Amy; Fonseca, Nuno A.; Barrera, Elisabet; Burdett, Tony; Füllgrabe, Anja; et al. "Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants". Nucleic Acids Research 44 D1 (2015): D746-D752. http://dx.doi.org/10.1093/nar/gkv1045.
    Open access • 10.1093/nar/gkv1045
  41. Aguiar, Bruno; Vieira, Jorge; Cunha, Ana E.; Fonseca, Nuno A.; Iezzoni, Amy; van Nocker, Steve; Vieira, Cristina P.. "Convergent Evolution at the Gametophytic Self-Incompatibility System in Malus and Prunus". PLOS ONE 10 5 (2015): e0126138. http://dx.doi.org/10.1371/journal.pone.0126138.
    Published • 10.1371/journal.pone.0126138
  42. Frankish, A; Uszczynska, B; Ritchie, GRS; Gonzalez, JM; Pervouchine, D; Petryszak, R; Mudge, JM; et al. "Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction". BMC GENOMICS (2015): http://europepmc.org/abstract/med/26110515.
    10.1186/1471-2164-16-s8-s2
  43. Ferreira, Pedro; Fonseca, Nuno A.; Dutra, Inês; Woods, Ryan; Burnside, Elizabeth. "Predicting malignancy from mammography findings and image-guided core biopsies". International Journal of Data Mining and Bioinformatics 11 3 (2015): 257. http://dx.doi.org/10.1504/ijdmb.2015.067319.
    Published • 10.1504/ijdmb.2015.067319
  44. Fonseca, Nuno A.; Marioni, John; Brazma, Alvis. "RNA-Seq Gene Profiling - A Systematic Empirical Comparison". PLoS ONE 9 9 (2014): e107026. http://dx.doi.org/10.1371/journal.pone.0107026.
    Open access • Published • 10.1371/journal.pone.0107026
  45. Schmitt, Bianca M.; Rudolph, Konrad L.M.; Karagianni, Panagiota; Fonseca, Nuno A.; White, Robert J.; Talianidis, Iannis; Odom, Duncan T.; Marioni, John C.; Kutter, Claudia. "High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface". Genome Research 24 11 (2014): 1797-1807. http://dx.doi.org/10.1101/gr.176784.114.
    Published • 10.1101/gr.176784.114
  46. Uslu, Veli Vural; Petretich, Massimo; Ruf, Sandra; Langenfeld, Katja; Fonseca, Nuno A; Marioni, John C; Spitz, François. "Long-range enhancers regulating Myc expression are required for normal facial morphogenesis". Nature Genetics 46 7 (2014): 753-758. http://dx.doi.org/10.1038/ng.2971.
    Published • 10.1038/ng.2971
  47. Petryszak, Robert; Burdett, Tony; Fiorelli, Benedetto; Fonseca, Nuno A.; Gonzalez-Porta, Mar; Hastings, Emma; Huber, Wolfgang; et al. "Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments". Nucleic Acids Research 42 D1 (2013): D926-D932. http://dx.doi.org/10.1093/nar/gkt1270.
    Published • 10.1093/nar/gkt1270
  48. Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; et al. "Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species". GigaScience 2 1 (2013): http://dx.doi.org/10.1186/2047-217x-2-10.
    10.1186/2047-217x-2-10
  49. Araújo, Ana Rita; Reis, Micael; Rocha, Helder; Aguiar, Bruno; Morales-Hojas, Ramiro; Macedo-Ribeiro, Sandra; Fonseca, Nuno A.; et al. "The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions". PLoS ONE 8 5 (2013): e63747. http://dx.doi.org/10.1371/journal.pone.0063747.
    Published • 10.1371/journal.pone.0063747
  50. Aguiar, Bruno; Vieira, Jorge; Cunha, Ana E.; Fonseca, Nuno A.; Reboiro-Jato, David; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino; Raspé, Olivier; Vieira, Cristina P.. "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 64 8 (2013): 2423-2434. http://dx.doi.org/10.1093/jxb/ert098.
    Published • 10.1093/jxb/ert098
  51. Fonseca, Nuno A.; Morales-Hojas, Ramiro; Reis, Micael; Rocha, Helder; Vieira, Cristina P.; Nolte, Viola; Schlötterer, Christian; Vieira, Jorge. "Drosophila americana as a Model Species for Comparative Studies on the Molecular Basis of Phenotypic Variation". Genome Biology and Evolution 5 4 (2013): 661-679. http://dx.doi.org/10.1093/gbe/evt037.
    Published • 10.1093/gbe/evt037
  52. Loureiro, T.; Camacho, R.; Vieira, J.; Fonseca, N.A.. "Boosting the Detection of Transposable Elements Using Machine Learning". Advances in Intelligent Systems and Computing 222 (2013): 85-91. http://www.scopus.com/inward/record.url?eid=2-s2.0-84880361824&partnerID=MN8TOARS.
    10.1007/978-3-319-00578-2_12
  53. Loureiro T; Camacho R; Vieira J; Fonseca NA. "Improving the performance of Transposable Elements detection tools.". Journal of Integrative Bioinformatics 10 3 (2013): 231. http://europepmc.org/abstract/med/24231145.
    Published • 10.1515/jib-2013-231
  54. Fonseca, Nuno A.; Rung, Johan; Brazma, Alvis; Marioni, John C.. "Tools for mapping high-throughput sequencing data". Bioinformatics 28 24 (2012): 3169-3177. http://dx.doi.org/10.1093/bioinformatics/bts605.
    Open access • Published • 10.1093/bioinformatics/bts605
  55. Fonseca, Nuno A.; Vieira, Cristina P.; Schlötterer, Christian; Vieira, Jorge. "The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions". Fly 6 2 (2012): 71-74. http://dx.doi.org/10.4161/fly.19423.
    Published • 10.4161/fly.19423
  56. Fonseca, N.A.; Santos Costa, V.; Camacho, R.. "Conceptual clustering of multi-relational data". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7207 LNAI (2012): 145-159. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864862749&partnerID=MN8TOARS.
    10.1007/978-3-642-31951-8_16
  57. Reboiro-Jato, D.; Reboiro-Jato, M.; Fdez-Riverola, F.; Fonseca, N.A.; Vieira, J.. "On the development of a pipeline for the automatic detection of positively selected sites". Advances in Intelligent and Soft Computing 154 AISC (2012): 225-229. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861205541&partnerID=MN8TOARS.
    10.1007/978-3-642-28839-5_26
  58. Camacho R; Ferreira R; Rosa N; Guimarães V; Fonseca NA; Costa VS; de Sousa M; et al. "Predicting the secondary structure of proteins using machine learning algorithms.". International Journal of Data Mining and Bioinformatics 6 6 (2012): 571-584. http://europepmc.org/abstract/med/23356008.
    10.1504/ijdmb.2012.050265
  59. Reboiro-Jato D; Reboiro-Jato M; Fdez-Riverola F; Vieira CP; Fonseca NA; Vieira J. "ADOPS--Automatic Detection Of Positively Selected Sites.". Journal of Integrative Bioinformatics 9 3 (2012): 200. http://europepmc.org/abstract/med/22829571.
    Published • 10.1515/jib-2012-200
  60. Ferreira P; Fonseca NA; Dutra I; Woods R; Burnside E; Ferreira, P.; Fonseca, N.A.; et al. "Predicting Malignancy from Mammography Findings and Surgical Biopsies.". (2011): 339-344. http://europepmc.org/abstract/med/24363962.
    10.1109/BIBM.2011.71
  61. Earl, D.; Bradnam, K.; St. John, J.; Darling, A.; Lin, D.; Fass, J.; Yu, H. O. K.; et al. "Assemblathon 1: A competitive assessment of de novo short read assembly methods". Genome Research 21 12 (2011): 2224-2241. http://dx.doi.org/10.1101/gr.126599.111.
    Open access • Published • 10.1101/gr.126599.111
  62. de Sousa, Miguel M.; Munteanu, Cristian R.; Pazos, Alejandro; Fonseca, Nuno A.; Camacho, Rui; Magalhães, A.L.. "Amino acid pair- and triplet-wise groupings in the interior of a-helical segments in proteins". Journal of Theoretical Biology 271 1 (2011): 136-144. http://dx.doi.org/10.1016/j.jtbi.2010.11.028.
    Published • 10.1016/j.jtbi.2010.11.028
  63. Camacho, R.; Pereira, M.; Costa, V.S.; Fonseca, N.A.; Simões, C.J.V.; Brito, R.M.M.. "Assessing the effect of 2D fingerprint filtering on ilp-based structure-activity relationships toxicity studies in drug design". Advances in Intelligent and Soft Computing 93 (2011): 355-363. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052957010&partnerID=MN8TOARS.
    10.1007/978-3-642-19914-1_46
  64. Fonseca, N.A.; Pereira, M.; Santos Costa, V.; Camacho, R.. "Interactive discriminative mining of chemical fragments". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6489 LNAI (2011): 59-66. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959311760&partnerID=MN8TOARS.
    10.1007/978-3-642-21295-6_10
  65. Ferreira, P.; Dutra, I.; Fonseca, N.A.; Woods, R.; Burnside, E.. "Studying the relevance of breast imaging features". HEALTHINF 2011 - Proceedings of the International Conference on Health Informatics (2011): 337-342. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960190863&partnerID=MN8TOARS.
  66. Camacho R; Pereira M; Costa VS; Fonseca NA; Adriano C; Simões CJ; Brito RM. "A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.". Journal of Integrative Bioinformatics 8 3 (2011): 182. http://europepmc.org/abstract/med/21926445.
    Published • 10.2390/biecoll-jib-2011-182
  67. Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; et al. "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 5 (2010): 629-636. http://dx.doi.org/10.1007/s00414-010-0472-2.
    Published • 10.1007/s00414-010-0472-2
  68. Santos, Joana S.; Fonseca, Nuno A.; Vieira, Cristina P.; Vieira, Jorge; Casares, Fernando. "Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression oftshz2andtshz3bin the zebrafish". Developmental Dynamics 239 3 (2010): 1010-1018. http://dx.doi.org/10.1002/dvdy.22228.
    Published • 10.1002/dvdy.22228
  69. Vieira, Jorge; Ferreira, Pedro G; Aguiar, Bruno; Fonseca, Nuno A; Vieira, Cristina P. "Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)". BMC Evolutionary Biology 10 1 (2010): 200. http://dx.doi.org/10.1186/1471-2148-10-200.
    Published • 10.1186/1471-2148-10-200
  70. Vieira, Jorge; Fonseca, Nuno A.; Vieira, Cristina P.. "RNase-Based Gametophytic Self-Incompatibility Evolution: Questioning the Hypothesis of Multiple Independent Recruitments of the S-Pollen Gene". Journal of Molecular Evolution 69 1 (2009): 32-41. http://dx.doi.org/10.1007/s00239-009-9249-y.
    Published • 10.1007/s00239-009-9249-y
  71. Fonseca, Nuno A.; Vieira, Cristina P.; Vieira, Jorge. "Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case". PLoS ONE 4 6 (2009): e5748. http://dx.doi.org/10.1371/journal.pone.0005748.
    Published • 10.1371/journal.pone.0005748
  72. Pereira, M.; Costa, V.S.; Camacho, R.; Fonseca, N.A.; Simões, C.; Brito, R.M.M.. "Comparative study of classification algorithms using molecular descriptors in toxicological databases". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5676 LNBI (2009): 121-132. http://www.scopus.com/inward/record.url?eid=2-s2.0-69949180023&partnerID=MN8TOARS.
    10.1007/978-3-642-03223-3_11
  73. Fonseca, N.A.; Costa, V.S.; Camacho, R.; Vieira, C.; Vieira, J.. "Partitional clustering of protein sequences - An inductive logic programming approach". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5518 LNCS PART 2 (2009): 1001-1004. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952573704&partnerID=MN8TOARS.
    10.1007/978-3-642-02481-8_152
  74. Pereira, M.; Costa, V.S.; Camacho, R.; Fonseca, N.A.. "Visually guiding and controlling the search while mining chemical structures". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5518 LNCS PART 2 (2009): 1043-1046. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952579858&partnerID=MN8TOARS.
    10.1007/978-3-642-02481-8_158
  75. Pereira, P.; Silva, F.; Fonseca, N.A.. "BIORED - A genetic algorithm for pattern detection in biosequences". Advances in Soft Computing 49 (2009): 156-165. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149105770&partnerID=MN8TOARS.
    10.1007/978-3-540-85861-4_19
  76. Fonseca, N.A.; Costa, V.S.; Rocha, R.; Camacho, R.; Silva, F.. "Improving the efficiency of inductive logic programming systems". Software - Practice and Experience 39 2 (2009): 189-219. http://www.scopus.com/inward/record.url?eid=2-s2.0-60349091006&partnerID=MN8TOARS.
    10.1002/spe.896
  77. Fonseca, N.A.; Srinivasan, A.; Silva, F.; Camacho, R.. "Parallel ILP for distributed-memory architectures". Machine Learning 74 3 (2009): 257-279. http://www.scopus.com/inward/record.url?eid=2-s2.0-60349126987&partnerID=MN8TOARS.
    10.1007/s10994-008-5094-2
  78. Vieira, Jorge; Fonseca, Nuno A.; Vieira, Cristina P.. "An S-RNase-Based Gametophytic Self-Incompatibility System Evolved Only Once in Eudicots". Journal of Molecular Evolution 67 2 (2008): 179-190. http://dx.doi.org/10.1007/s00239-008-9137-x.
    Published • 10.1007/s00239-008-9137-x
  79. VIEIRA, JORGE; FONSECA, NUNO A.; SANTOS, RAQUEL A. M.; HABU, TSUYOSHI; TAO, RYUTARO; VIEIRA, CRISTINA P.. "The number, age, sharing and relatedness of S-locus specificities in Prunus". Genetics Research 90 1 (2008): 17-26. http://dx.doi.org/10.1017/s0016672307009044.
    Published • 10.1017/s0016672307009044
  80. Fonseca, N.A.; Camacho, R.; Rocha, R.; Costa, V.S.. "Compile the hypothesis space: Do it once, use it often". Fundamenta Informaticae 89 1 (2008): 45-67. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149520441&partnerID=MN8TOARS.
  81. Fonseca, N.A.; Costa, V.S.; Rocha, R.; Camacho, R.. "K-RNN: K-relational nearest neighbour algorithm". Proceedings of the ACM Symposium on Applied Computing (2008): 944-948. http://www.scopus.com/inward/record.url?eid=2-s2.0-56849110162&partnerID=MN8TOARS.
    10.1145/1363686.1363901
  82. Camacho, R.; Fonseca, N.A.; Rocha, R.; Costa, V.S.. "ILP :- Just trie it". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4894 LNAI (2008): 78-87. http://www.scopus.com/inward/record.url?eid=2-s2.0-40249098653&partnerID=MN8TOARS.
    10.1007/978-3-540-78469-2_11
  83. Fonseca, Nuno A; Vieira, Cristina P; Holland, Peter WH; Vieira, Jorge. "Protein evolution of ANTP and PRD homeobox genes". BMC Evolutionary Biology 8 1 (2008): 200. http://dx.doi.org/10.1186/1471-2148-8-200.
    Published • 10.1186/1471-2148-8-200
  84. Fonseca, Nuno A.; Camacho, Rui; Magalhães, A. L.. "Amino acid pairing at the N- and C-termini of helical segments in proteins". Proteins: Structure, Function, and Bioinformatics 70 1 (2007): 188-196. http://dx.doi.org/10.1002/prot.21525.
    Published • 10.1002/prot.21525
  85. Ferreira, M.; Fonseca, N.A.; Rocha, R.; Soares, T.. "Efficient and scalable induction of logic programs using a deductive database system". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4455 LNAI (2007): 184-198. http://www.scopus.com/inward/record.url?eid=2-s2.0-38149043443&partnerID=MN8TOARS.
    10.1007/978-3-540-73847-3_22
  86. Fonseca, N.A.; Silva, F.; Camacho, R.. "April - An inductive logic programming system". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4160 LNAI (2006): 481-484. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750047866&partnerID=MN8TOARS.
    10.1007/11853886_42
  87. Rocha, R.; Fonseca, N.; Costa, V.S.. "On applying tabling to inductive logic programming". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3720 LNAI (2005): 707-714. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646427718&partnerID=MN8TOARS.
    10.1007/11564096_72
  88. Fonseca, N.A.; Silva, F.; Camacho, R.. "Strategies to parallelize ILP systems". Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science) 3625 (2005): 136-153. http://www.scopus.com/inward/record.url?eid=2-s2.0-26944463458&partnerID=MN8TOARS.
    10.1007/11536314_9
  89. Fonseca, N.; Costa, V.S.; Silva, F.; Camacho, R.. "On avoiding redundancy in inductive logic programming". Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science) 3194 (2004): 132-146. http://www.scopus.com/inward/record.url?eid=2-s2.0-22944447732&partnerID=MN8TOARS.
    10.1007/978-3-540-30109-7_13
  90. Fonseca, N.; Costa, V.S.; Silva, F.; Camacho, R.. "Experimental evaluation of a caching technique for ILP". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2902 (2003): 151-155. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347586870&partnerID=MN8TOARS.
    10.1007/978-3-540-24580-3_22
  91. Fonseca, N.; Rocha, R.; Camacho, R.; Silva, F.. "Efficient data structures for inductive logic programming". Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science) 2835 (2003): 130-145. http://www.scopus.com/inward/record.url?eid=2-s2.0-9444241022&partnerID=MN8TOARS.
    10.1007/978-3-540-39917-9_10
Preprint
  1. Joana G. Guedes; Rogério Ribeiro; Inês Carqueijeiro; Ana Luísa Guimarães; Cláudia Bispo; John Archer; Herlander Azevedo; Nuno A. Fonseca; Mariana Sottomayor. "Idioblasts accumulating anticancer alkaloids inCatharanthus roseusleaves are a unique cell type". 2023. https://doi.org/10.1101/2023.02.24.529939.
    10.1101/2023.02.24.529939
  2. Cabezas, M. Pilar; Fonseca, Nuno A.; Muñoz-Mérida, Antonio. "MIMt – A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification". 2023. http://dx.doi.org/10.1101/2023.12.15.571851.
    10.1101/2023.12.15.571851
Report
  1. Faculdade de Ciências. 2018. Deliverable 4.3 (D4.3): Protocol for field collection and preservation of eDNA samples, EnvMetaGen project (Grant Agreement No 668981). https://hdl.handle.net/10216/119637.
    10.5281/zenodo.2598129
  2. Faculdade de Ciências. 2018. Deliverable 4.4 (D4.4): Protocol for next-gen analysis of eDNA samples, EnMetaGen project (Grant Agreement No 668981). https://hdl.handle.net/10216/119568.
    10.5281/zenodo.2586885

Other

Other output
  1. Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing. 2020. Bastian Egeter; Joana Veríssimo; Manuel Lopes-Lima; Cátia Chaves; Joana Pinto; Nicoletta Riccardi; Pedro Beja; Nuno A. Fonseca. https://doi.org/10.1101/2020.06.09.142521.
    10.1101/2020.06.09.142521
  2. Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study. 2020. Garg M; Couturier D; Nsengimana J; Fonseca NA; Wongchenko M; Yan Y; Lauss M; et al. http://europepmc.org/abstract/PPR/PPR114406.
    10.1101/2020.02.24.961771
  3. Tumors induce de novo steroid biosynthesis in T cells to evade immunity. 2018. Mahata B; Pramanik J; van der Weyden L; Kar G; Riedel A; Fonseca NA; Kundu K; et al. http://europepmc.org/abstract/PPR/PPR62289.
    10.1101/471359
  4. Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes. 2017. Rheinbay E; Nielsen MM; Abascal F; Tiao G; Hornshøj H; Hess JM; Pedersen RI; et al. http://europepmc.org/abstract/PPR/PPR20994.
    10.1101/237313
  5. Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. 2017. C Calabrese; K Lehmann; L Urban; F Liu; S Erkek; NA Fonseca; A Kahles; et al. https://doi.org/10.1101/225441.
    10.1101/225441
  6. Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments. 2017. Yung CK; O’Connor BD; Yakneen S; Zhang J; Ellrott K; Kleinheinz K; Miyoshi N; et al. http://europepmc.org/abstract/PPR/PPR7071.
    10.1101/161638
  7. Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer. 2017. Nuno A. Fonseca; Yao He; Liliana Greger; Alvis Brazma; Zemin Zhang. https://doi.org/10.1101/148684.
    10.1101/148684
  8. Two independent modes of chromosome organization are revealed by cohesin removal. 2016. Schwarzer W; Abdennur N; Goloborodko A; Pekowska A; Fudenberg G; Loe-Mie Y; Fonseca NA; et al. http://europepmc.org/abstract/PPR/PPR20667.
    10.1101/094185
  9. A pipelined data-parallel algorithm for ILP. 2005. Nuno A. Fonseca; Fernando Silva; Vitor Santos Costa; Rui Camacho. https://doi.org/10.1109%2Fclustr.2005.347059.
    10.1109/clustr.2005.347059