Publications

 

Monteiro PT, Oliveira J, Pais P, Antunes M, Palma M, Cavalheiro M, Galocha M, Godinho CP, Martins LC, Bourbon N, Mota MN, Ribeiro RA, Viana R, Sá-Correia I, Teixeira MC (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 P, Abbeloos R, Backlund JE, Salido MB, Bauchet G, Benites-Alfaro OE, Birkett C, Calaminos VC, Carceller P, Cornut G, Costa BV, Edwards JD, Finkers R, Gao SY, Ghaffar M, Glaser P, Guignon V, Hok P, Kilian A, König P, Lagare JEB, Lange M, Laporte MA, Larmande P, LeBauer DS, Lyon DA, Marshall DS, Matthews D, Milne I, Mistry N, Morales N, Mueller LA, Neveu P, Papoutsoglou E, Pearce B, Perez-Masias I, Pommier C, Ramírez-González RH, Rathore A, Raquel AM, Raubach S, Rife T, Robbins K, Rouard M, Sarma C, Scholz U, Sempéré G, Shaw PD, Simon R, Soldevilla N, Stephen G, Sun Q, Trovar C, Uszynski G, Verouden M on behalf of the BrAPI consortium (2019) "BrAPI—an application programming interface for plant breeding applications", Bioinformatics https://doi.org/10.1093/bioinformatics/btz190

Vázquez N, López-Fernández H, Vieira CP, Fdez-Riverola F, Vieira J, Reboiro-Jato M (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 N, Rocha S, López-Fernández H, Torres A, Camacho R, Fdez-Riverola F, Vieira J, Vieira C, Reboiro-Jato M (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 M, Palma M, Sá-Correia I (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 BV, Faria D, Chaves I, Miguel CM (2018) "PHENO - the BrAPI endpoint provided by the Portuguese node of ELIXIR" https://brapi.biodata.pt

López-Fernández H, Duque P, Henriques S, Vázquez N, Fdez-Riverola F, Vieira CP, Reboiro-Jato M, Vieira J (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 H, Duque P, Henriques S, Vázquez N, Fdez-Riverola F, Vieira CP, Reboiro-Jato M, Vieira J (2018) "Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences", https://doi.org/10.1007/s12539-018-0312-5

Ouma-Mugabe J, Chaminuka P, Melo AP (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 C, Cwiek H, Faria D, Papoutsoglou E, Costa B, Laporte M-A, Chaves I, Neveu P, Cornut G, Ruiz M (2018) "Plant Phenotype Experiment Ontology (PPEO)" http://purl.org/ppeo

Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, Guimarães J, Mendonça D, Nóbrega F, Rodrigues L, Saibo N, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S (2018) "The draft genome sequence of cork oak", Sci Data 5:180069 https://doi.org/10.1038/sdata.2018.69 

Teixeira MC, Monteiro PT, Palma M, Catarina C, Godinho CP, Pais P, Cavalheiro M, Antunes M, Lemos A, Pedreira T, Sá-Correia I (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 N, Rocha S, López-Fernández H, Torres A, Camacho R, Fdez-Riverola F, Vieira J, Vieira CP, Reboiro-Jato M (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 N, Vieira CP, Amorin BSR, Torres A, López-Fernández H, Fdez-Riverola F, Sousa JLR, Reboiro-Jato M, Vieira J (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 I, Costa B, Rodrigues A, Bohn A, Miguel CM (2017) "miRPursuit - sRNA-workflow analysis using NGS Data to non-model plants", FEBS Letters https://doi.org/10.1002/1873-3468.12746

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

Monteiro PT, Pais P, Costa C, Manna S, Sá-Correia I, Teixeira MC (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 N, Vieira CP, Amorin BSR, Torres A, López-Fernández H, Fdez-Riverola F, Sousa JLR, Reboiro-Jato M, Vieira J (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