Research archive

These are the publications of my academic career in computational biology, from 2004 to 2018 — doctoral and postdoctoral years in Lisbon and Lyon that ended when I moved into industry full-time. The list is kept complete, as a record for citation; it is not current work. These papers reflect the knowledge of their time; where a field has moved on, a brief note says so.

Journal papers

Estimating attractor reachability in asynchronous logical models

Nuno D. Mendes, Rui Henriques, Elisabeth Remy, Jorge Carneiro, Pedro T. Monteiro, Claudine Chaouiya

Frontiers in Physiology · 2018 · Publisher
Composition and abstraction of logical regulatory modules: application to multicellular systems

Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Grégory Batt, Claudine Chaouiya

Bioinformatics · 2013 · Publisher
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen

Bioinformatics · 2012 · Publisher
Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno D. Mendes, Ana T. Freitas, Ana T. Vasconcelos, Marie-France Sagot

BMC Genomics · 2010 · Publisher
Current tools for the identification of miRNA genes and their targets

Nuno D. Mendes, Ana T. Freitas, Marie-France Sagot

Nucleic Acids Research · 2009 · Publisher
Then & now — miRNA

Context, from the vantage point of today: this work dates from a period when miRNA catalogues were expanding rapidly and target identification was largely computational prediction. Since then the field has been recognised at the highest level — the 2024 Nobel Prize in Physiology or Medicine went to Victor Ambros and Gary Ruvkun for the discovery of microRNA — and it has also corrected itself: large-scale reannotation (miRBase high-confidence sets, MirGeneDB) pruned many early catalogue entries as fragments or false positives; AGO CLIP-seq experiments shifted target identification from pure prediction toward measured binding; isomiRs and non-canonical biogenesis complicated the one-sequence–one-miRNA picture; and circulating miRNAs were explored as biomarkers, with mixed reproducibility. These papers are the state of the art of their moment, not a summary of current miRNA biology.
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

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

Nucleic Acids Research · 2007 · Publisher
MUSA: a parameter free algorithm for the identification of biologically significant motifs

Nuno D. Mendes, Ana C. Casimiro, Pedro M. Santos, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas

Bioinformatics · 2006

Book chapter

miRNA gene prediction

N. D. Mendes

Encyclopedia of Systems Biology (Springer-Verlag), eds. W. Dubitzky, O. Wolkenhauer, K.-H. Cho, H. Yokota · 2013 · Publisher

Conference

Towards a Plant Experimental Assay Ontology

Nuno D. Mendes, Pedro T. Monteiro, Cátia Vaz, Inês Chaves

DILS — Data Integration in the Life Sciences · 2014 · Publisher

Abstracts & posters

Epilog: a software for the logical modelling of epithelial patterning

P. Varela, N. D. Mendes, P. T. Monteiro, A. Fauré, C. Chaouiya

Bioinformatics Open Days, Braga, Portugal · 2013
Identification of miRNAs and analysis of their expression in Eucalyptus globulus

J. Oliveira, N. D. Mendes, V. Carocha, J. A. Paiva, A. T. Freitas

Bioinformatics Open Days, Braga, Portugal · 2013
The microEGO project: unravelling the post-transcriptional regulation mechanisms on Eucalyptus wood formation

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

Plant and Animal Genome XXI Conference, San Diego, CA, USA · 2012
Identification of miRNAs in E. globulus xylem tissues formed upon gravitropic stimulation

V. Carocha, C. Graca, J. Amado, N. Mendes, A. Amaral, H. San-Clemente, P. Fonseca, I. Trindade, S. Araújo, H. Wang, N. Borralho, T. Quilhó, J. Rodrigues, P. Fevereiro, L. Neves, C. Araújo, A. Freitas, J. Grima-Pettenati, J. Paiva

26th New Phytologist Symposium, Nancy, France · 2011
CRAVELA: a framework to identify and evaluate miRNA regulatory modules

N. D. Mendes, A. T. Freitas, A. T. Vasconcelos, M.-F. Sagot

RECOMB 2010, Lisbon, Portugal · 2010
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database

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, Isabel Sá-Correia

3rd Conference on Physiology of Yeasts and Filamentous Fungi, Helsinki, Finland · 2007
Analysis of new and known DNA-binding site motifs in Saccharomyces cerevisiae using the YEASTRACT-DISCOVERER tools

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, A. T. Freitas

Congresso Nacional MICROBIOTEC'07, Lisbon, Portugal · 2007
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database

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, I. Sá-Correia

Yeast Genetics and Molecular Biology Meeting, Princeton, USA · 2006
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database

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, I. Sá-Correia

2nd FEMS Congress of European Microbiologists, Madrid, Spain · 2006

Theses

Efficient algorithms for the identifications of miRNA motifs in DNA sequences

Nuno D. Mendes

PhD thesis, IST/UTL and Université Claude Bernard Lyon 1 · 2011 · PDF
Inference of Complex Motifs using Biclustering Techniques

Nuno D. Mendes

Master's thesis, IST, Universidade Técnica de Lisboa · 2005 · PDF

Technical reports

IUPAC Code Generation

Nuno D. Mendes, David V. Nunes

Graduation thesis (TFC), IST, Universidade Técnica de Lisboa · 2004 · PDF

Talks

Identification and quantification of reachable attractors over asynchronous dynamics

Nuno D. Mendes

EAO Seminar, Oeiras, Portugal · 2013
CRAVELA: Navigating the genome in search of miRNAs

Nuno D. Mendes

DataStorm Seminar, Porto Salvo, Portugal · 2013
Composition and abstraction of logical regulatory modules: applications to multicellular systems

Nuno D. Mendes

EAO Seminar, Oeiras, Portugal · 2012
Dynamic modelling of large regulatory networks

Nuno D. Mendes

PDBC Meeting, Oeiras, Portugal · 2011
Towards a framework for the identification of miRNA regulatory modules

Nuno D. Mendes

Bioinformatics Seminar, Freiburg, Germany · 2010
A framework for the identification of miRNA regulatory modules: sieving pre-miRNA candidates

Nuno D. Mendes

First Regional Workshop on Small RNA Biology, Montevideo, Uruguay · 2009
Efficient algorithms for the identification of miRNA motifs

Nuno D. Mendes

B2FI Seminar, Lyon, France · 2008