Nuno D. Mendes
Index - Publications - Software - Documents

Publications

Journal or Conference articles
Book Chapters
  • N. D. Mendes (2013), miRNA gene prediction. Encyclopedia of Systems Biology, Editors: W. Dubitzy, O. Wolkenhauer, K.-H. Cho and H. Yokota. Springer-Verlag. (3 pages)

Extended Abstracts and Posters
  • P. Varela, N. D. Mendes, P. T. Monteiro, A. Fauré, C. Chaouiya (2013), Epilog: a software for the logical modelling of epithelial patterning. Bioinformatics Open Days, Braga, Portugal.

  • J. Oliveira, N. D. Mendes, V. Carocha, J. A. Paiva, A. T. Freitas (2014), Identification of miRNAs and analysis of their expression in Eucalyptus globulus. Work selected for oral presentation at Bioinformatics Open Days, Braga, Portugal.

  • V. Carocha, C. S. Graça N. D. Mendes, J. Oliveira, A. J. Amaral, L. Neves, C. Araújo, S. Araújo, S. Pera, P. M. Fevereiro, J. Grima-Pettenati, A. T. Freitas, J. A. Paiva (2012). The microEGO project: unravelling the post-transcriptional regulation mechanisms on Eucalyptus wood formation. Plant and Animal Genome XXI Conference, San Diego, CA, USA.

  • V. Carocha, C. Graca, J. Amado, N. Mendes, A. Amaral, H. San-Clemente, P. Fonseca, I. Trindade, S. Araújo, H. Wang, N. Borralho, T. Quilhió, J. Rodrigues, P. Fevereiro, L. Neves, C. Araújo, A. Freitas, J. Grima-Pettenati, J. Paiva (2011), Identification of miRNAs in E. globulus xylem tissues formed upon gravitropic stimulation, 26th New Phytologist Symposium, Nancy, France

  • N. D. Mendes, A. T. Freitas, A. T. Vasconcelos and M.-F. Sagot (2010), CRAVELA: a framework to identify and evaluate miRNA regulatory modules, Poster selected for oral presentation at RECOMB'2010, Lisbon, Portugal

  • M. C. Teixeira, P. Monteiro, S. Tenreiro, N. P. Mira, A. B. Lourenco, A. M. Carvalho, N. Mendes, S. d'Orey, H. Pais, A. T. Freitas, A. L. Oliveira and Isabel Sá-Correia (2007), Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Extended abstract in 3rd Conference on Physiology of Yeasts and Filamentous Fungi, S245: 52, Helsinki, Finland

  • P. Monteiro, N. Mendes, M. C. Teixeira, S. d'Orey, S. Tenreiro, N. P. Mira, H. Pais, A. P. Francisco, A. M. Carvalho, A. B. Lourenco, I. Sá-Correia, A. L. Oliveira and A. T. Freitas (2007), Analysis of new and known DNA-binding site motifs in Saccharomyces cerevisiae using the YEASTRACT-DISCOVERER tools, Poster and Extended abstract in Congresso Nacional MICROBIOTEC'07, Lisbon, Portugal

  • M. C. Teixeira, P. Monteiro, S. Tenreiro, N. Mira, A. M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A. T. Freitas, A. L. Oliveira and I. Sá-Correia (2006), Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Poster at the Yeast Genetics and Molecular Biology Meeting, Book of Abstracts 529A, Princeton, USA

  • M. C. Teixeira, P. Monteiro, S. Tenreiro, N. P. Mira, A. M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A. T. Freitas, A. L. Oliveira and I. Sá-Correia (2006), Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Poster at the 2nd FEMS Congress of European Microbiologists, Book of Abstracts W12.4-P.COM.3, Madrid, Spain

Theses
Technical Reports
  • Nuno D. Mendes and David V. Nunes, IUPAC Code Generation, Graduation thesis, IST, Universidade Técnica de Lisboa, 2004.
    Supervised by Ana T. Freitas and Arlindo L. Oliveira.
    Get a preprint: [pdf] (in portuguese)

Other Communications
  • Nuno D. Mendes. Identification and quantification of reachable attractors over asynchornous dynamics, EAO Seminar, Nov 2013, Oeiras, Portugal.

  • Nuno D. Mendes. CRAVELA: Navigating the genome in search of miRNAs, DataStorm Seminar, Jul 2013, Porto Salvo, Portugal.

  • Nuno D. Mendes. Composition and abstraction of logical regulatory modules: applications to multicellular systems, EAO Seminar, Jan 2012, Oeiras, Portugal.

  • Nuno D. Mendes. Dynamic modelling of large regulatory networks, PDBC Meeting, Dec 2011, Oeiras, Portugal.

  • Nuno D. Mendes. Towards a framework for the identification of miRNA regulatory modules, Bioinformatics Seminar, Mar 2010, Freiburg, Germany.

  • Nuno D. Mendes. A framework for the identification of miRNA regulatory modules: sieving pre-miRNA candidates, First Regional Workship on Small RNA Biology, Nov 2009, Montevideo, Uruguay.

  • Nuno D. Mendes. Efficient algorithms for the identification of miRNA motifs, B2FI Seminar, Dec 2008, Lyon, France.