Nuno D. Mendes, Pedro T. Monteiro, Jorge Carneiro, Elisabeth Remy, Claudine Chaouiya. Quantification of reachable attractors in asynchronous discrete dynamics. arXiv Preprint, 2014.
Nuno D. Mendes, Pedro T. Monteiro, Cátia Vaz, Inês Chaves. Towards a Plant Experimental Assay Ontology. DILS, 2014.
Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Grégory Batt, Claudine Chaouiya. Composition and abstraction of logical regulatory modules: application to multicellular systems. Bioinformatics, 2013.
Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen. Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinformatics, 2012.
Nuno D. Mendes, Ana T. Freitas, Ana T. Vasconcelos, Marie-France Sagot. Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi. BMC Genomics, 2010.
Nuno D. Mendes, Ana T. Freitas, Marie-France Sagot. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Research, 2009.
Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas. YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research, 2007.
Nuno D. Mendes, Ana C. Casimiro, Pedro M. Santos, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas. MUSA: a parameter free algorithm for the identification of biologically significant motifs. Bioinformatics, 2006
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)
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 (2013), 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
Nuno D. Mendes, Efficient algorithms for the identifications of miRNA motifs in DNA sequences, PhD thesis, IST/UTL and UCBL, 2011. Supervised by Ana T. Freitas and Marie-France Sagot. Get a preprint: [pdf.gz]
Nuno D. Mendes, Inference of Complex Motifs using Biclustering Techniques, Master's thesis, IST, Universidade Técnica de Lisboa, 2005. Supervised by Ana T. Freitas and Arlindo L. Oliveira. Get a preprint: [ps] [pdf]
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)
Nuno D. Mendes. Identification and quantification of reachable attractors over asynchronous 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.