Publications

Harrow et al. (2021). ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future. The EMBO Journal40(6), e107409. https://doi.org/10.15252/embj.2020107409

Oliveira et al. (2021). A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLoS computational biology, 17(3), e1008704. https://doi.org/10.1371/journal.pcbi.1008704

Martin et al. (2021). Demonstrating public value to funders and other stakeholders—the journey of ELIXIR, a virtual and distributed research infrastructure for life science data. Annals of Public and Cooperative Economics. https://doi.org/10.1111/apce.12328

Ezeokoli et al. (2021). Assessing the Impact of Rice Cultivation and Off-Season Period on Dynamics of Soil Enzyme Activities and Bacterial Communities in Two Agro-Ecological Regions of Mozambique. Agronomy, 11(4), 694.  https://doi.org/10.3390/agronomy11069404

Keller et al. (2021). Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. Microbiome, 9 (1), 1-21. https://doi.org/10.1186/s40168-021-01031-y

Pommier et al. (2021) ELIXIR Plant sciences 2020-2023 Roadmap [version 1; not peer reviewed]. F1000Research 2021,  10(ELIXIR):145 (document). https://doi.org/10.7490/f1000research.1118482.1 

López et al. (2021) Inferences on Mycobacterium Leprae Host Immune Response Escape and Antibiotic Resistance Using Genomic Data and GenomeFastScreen. In: Panuccio G., Rocha M., Fdez-Riverola F., Mohamad M., Casado-Vara R. (eds) Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020). PACBB 2020. Advances in Intelligent Systems and Computing, vol 1240. Springer, Cham https://doi.org/10.1007/978-3-030-54568-0_5

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. https://doi.org/10.1016/j.ygeno.2020.11.034

Arias et al. (2020). CorkOakDB—The Cork Oak Genome Database Portal. Database2020.https://doi.org/10.1093/database/baaa114

Papoutsoglou et al.  (2020). Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist227(1), 260-273.

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 

Cardoso et al. (2019). WebSpecmine: a website for metabolomics data analysis and mining. Metabolites9(10), 237. https://doi.org/10.3390/metabo9100237

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 

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

Palma et al. (2019). Physiological genomics of the highly weak-acid-tolerant food spoilage yeasts of Zygosaccharomyces bailii sensu lato. Yeasts in Biotechnology and Human Health, 85-109. https://doi.org/10.1007/978-3-030-13035-0_4

Godinho et al. (2019). Physiological Genomics of Multistress Resistance in the Yeast Cell Model and Factory: Focus on MDR/MXR Transporters. Yeasts in Biotechnology and Human Health, 1-35. https://doi.org/10.1007/978-3-030-13035-0_1

Yeasts in Biotechnology and Human Health (Sá-Correia I, Ed.), Springer International Publishing, 2019 https://www.springer.com/gp/book/9783030130343

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. (2019). Applying FAIR principles to plant phenotypic data management in GnpIS. Plant Phenomics2019 https://doi.org/10.34133/2019/1671403

Ramos et al. (2018). The draft genome sequence of cork oak. Scientific data5(1), 1-12. 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). mi RP ursuit—a pipeline for automated analyses of small RNA s in model and nonmodel plants. FEBS letters591(15), 2261-2268. 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