Publications

Pais et al. (2021) “Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: clues on host adaptation and probiotic activity based on promoter sequence variability”, Genomics 

Pais, Vagueiro et al. (2020) “A new regulator in the crossroads of oxidative stress resistance and virulence in Candida glabrata: the transcription factor CgTog1”, Virulence, https://doi.org/10.1080/21505594.2020.1839231

Viana et al. (2020) “Genome-scale metabolic model of the human pathogen Candida albicans: a platform for drug target prediction”, Journal of Fungi, https://doi.org/10.3390/jof6030171

Pais et al. (2020) “Candida glabrata transcription factor Rpn4 mediates fluconazole resistance through regulation of ergosterol biosynthesis and plasma membrane permeability”, Antimicrobial Agents and Chemotherapy, https://doi.org/10.1128/AAC.00554-20 

Monteiro et al. (2020) “YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts”, Nucleic Acids Research https://doi.org/10.1093/nar/gkz859

Correia et al. (2020) "Isolation, identification and biotechnological applications of a novel, robust, free-living Chlorococcum(Oophila) amblystomatis strain isolated from a local pond", Appl. Sci. https://doi.org/10.3390/app10093040 

Egger et al. (2020) "Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America", ZooKeys https://doi.org/10.3897/zookeys.968.52986 

Carlier et al. (2020) "Prokaryotic diversity in stream sediments affected by acid mine drainage" Extremophiles https://doi.org/10.1007/s00792-020-01196-8

Sousa et al. (2020) "The chloroplast land plant phylogeny: analyses employing better-fitting tree-and site-heterogeneous composition models" Frontiers in plant science https://doi.org/10.3389/fpls.2020.01062

Sousa et al. (2020) "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models" PeerJ https://doi.org/10.7717/peerj.8995   

Williams et al. (2020) "Phylogenomics provides robust support for a two-domains tree of life" Nature ecology & evolution https://doi.org/10.1038/s41559-019-1040-x 

Louro et al. (2019) "A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)" GigaScience https://doi.org/10.1093/gigascience/giz059

Ettamimi et al. (2019) "A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal" Extremophiles https://doi.org/10.1007/s00792-019-01136-1 

Monteiro et al. (2019) “YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts”, Nucleic Acids Research https://doi.org/10.1093/nar/gkz859

Selby et al. (2019) "BrAPI—an application programming interface for plant breeding applications", Bioinformatics https://doi.org/10.1093/bioinformatics/btz190

Vázquez et al. (2019) "DBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus", Interdisciplinary Sciences: Computational Life Sciences https://doi.org/10.1007/s12539-019-00320-3

Vázquez et al. (2019) "EvoPPI 1.0: a Web Platform for Within- and Between-Species Multiple Interactome Comparisons and Application to Nine PolyQ Proteins Determining Neurodegenerative Diseases", Interdisciplinary Sciences: Computational Life Sciences https://doi.org/10.1007/s12539-019-00317-y

Antunes et al. (2018) "Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stress mediated by ZbHaa1", Scientific Reports, 8: 14122 https://doi.org/10.1038/s41598-018-32266-9

Costa et al. (2018) "PHENO - the BrAPI endpoint provided by the Portuguese node of ELIXIR" https://brapi.biodata.pt

López-Fernández et al. (2018) "A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees", 12th International Conference on Practical Applications of Computational Biology & Bioinformatics. Toledo, Spain https://doi.org/10.1007/978-3-319-98702-6_11

López-Fernández et al. (2018) "Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences", https://doi.org/10.1007/s12539-018-0312-5

Ouma-Mugabe et al. (2018) "Characterising partnership for research and innovation in Sub-Saharan Africa: Lessons from the case of the Africa-EU ProIntensAfrica Initiative", South African Journal of International Affairs-SAJIA, 25:531-545 https://doi.org/10.1080/10220461.2018.1551152

Pommier et al. (2018) "Plant Phenotype Experiment Ontology (PPEO)" http://purl.org/ppeo

Ramos et al. (2018) "The draft genome sequence of cork oak", Sci Data 5:180069 https://doi.org/10.1038/sdata.2018.69 

Teixeira et al. (2018) “YEASTRACT, an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae", Nucleic Acids Research, 46: D348-D353 https://doi.org/10.1093/nar/gkx842 

Vázquez et al. (2018) "EvoPPI: a Web Application to Compare Protein-Protein Interactions (PPIs) From Different Databases and Species", 12th International Conference on Practical Applications of Computational Biology & Bioinformatics. Toledo, Spain https://doi.org/10.1007/978-3-319-98702-6_18

Vázquez et al. (2018) "Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects", Interdisciplinary Sciences: Computational Life Sciences https://doi.org/10.1007/s12539-018-0282-7

Chaves et al. (2017) "miRPursuit - sRNA-workflow analysis using NGS Data to non-model plants", FEBS Letters https://doi.org/10.1002/1873-3468.12746

Michotey and Chaves (2017) "Woody Plant Ontology (WPO) Crop Ontology" http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology

Monteiro et al. (2017) “The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts", Nucleic Acids Research, 45: D597-D603 https://doi.org/10.1093/nar/gkw817 

Vázquez et al. (2017) "Automated Collection and Sharing of Adaptive Amino Acid Changes Data", 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. Porto, Portugal https://doi.org/10.1007/978-3-319-60816-7_3