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Other IDs

ISNI: 0000000493547573
Loop profile: 1656099
Scopus Author ID: 55246121700

Keywords

Bioinformatics, Web Services, Machine Learning, Sequence Analysis

Countries

United Kingdom

Activities

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Employment (4)

European Bioinformatics Institute: Cambridge, GB

2022-09-01 to present | Bioinformatics Project Lead (ITS Operations - Sarah Butcher)
Employment
Source: Self-asserted source
Fabio Madeira

European Bioinformatics Institute: Cambridge, GB

2020-03-01 to 2022-08-31 | Technical Project Lead (Web Production - Rodrigo Lopez)
Employment
Source: Self-asserted source
Fabio Madeira

European Bioinformatics Institute: Cambridge, GB

2018-01-08 to 2020-02-29 | Software Engineer (Web Production - Rodrigo Lopez)
Employment
Source: Self-asserted source
Fabio Madeira

University of Dundee: Dundee, GB

2016-09-01 to 2018-01-05 | Postdoctoral Research Assistant in Bioinformatics (School of Life Sciences, Division of Computational Biology, Geoff Barton's Group)
Employment
Source: Self-asserted source
Fabio Madeira

Education and qualifications (5)

Scrum.org: Massachusetts, US

2020-02-07 to present | Professional Scrum Master™ I (PSM I)
Qualification
Source: Self-asserted source
Fabio Madeira

APMG International: Wycombe, GB

2019-11-22 to present | FitSM® Foundation
Qualification
Source: Self-asserted source
Fabio Madeira

University of Dundee: Dundee, GB

2012-09-03 to 2016-09-03 | Ph.D. in Computational Biology (School of Life Sciences, Division of Computational Biology, Geoff Barton's Group)
Education
Source: Self-asserted source
Fabio Madeira

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia: Caparica, Setúbal, PT

2008-09-01 to 2010-09-01 | MSc in Molecular Genetics and Biomedicine (Life Sciences)
Education
Source: Self-asserted source
Fabio Madeira

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia: Caparica, Setúbal, PT

2004-09-01 to 2008-09-01 | BSc in Biochemistry (ECTN Chemistry Eurobachelor Degree) (Chemistry)
Education
Source: Self-asserted source
Fabio Madeira

Professional activities (1)

International Society for Computational Biology: Bethesda, Maryland, US

2015-03-10 to 2023-07-12 | Academic/Professional
Membership
Source: Self-asserted source
Fabio Madeira

Funding (2)

Wellcome 4-Year PhD Programme in Integrated Molecular, Cellular and Translational Biology

Source: Self-asserted source
Fabio Madeira

Functional and structural studies of human phenylalanine hydroxylase

2009-08 to 2010-08 | Award
SANTANDER-NOVA (Lisboa, PT)
Source: Self-asserted source
Fabio Madeira

Works (31)

Taxonomy Resolver: A Python package for building and filtering taxonomy trees

Journal of Open Source Software
2025-02-21 | Journal article
DOI: 10.21105/joss.07604
Contributors: Fábio Madeira; Nandana Madhusoodanan; Joonheung Lee; Alberto Eusebi; Ania Niewielska; Sarah Butcher
Source: check_circle
Crossref

The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024

Nucleic Acids Research
2024-07-05 | Journal article
DOI: 10.1093/nar/gkae241
Contributors: Fábio Madeira; Nandana Madhusoodanan; Joonheung Lee; Alberto Eusebi; Ania Niewielska; Adrian R N Tivey; Rodrigo Lopez; Sarah Butcher
Source: check_circle
Crossref

Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

Current Protocols
2024-06 | Journal article
DOI: 10.1002/cpz1.1065
Contributors: Fábio Madeira; Nandana Madhusoodanan; Joonheung Lee; Alberto Eusebi; Ania Niewielska; Adrian R. N. Tivey; Stuart Meacham; Rodrigo Lopez; Sarah Butcher
Source: check_circle
Crossref

A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites

Communications Biology
2024-04-11 | Journal article
DOI: 10.1038/s42003-024-06117-5
Contributors: Stuart A. MacGowan; Fábio Madeira; Thiago Britto-Borges; Geoffrey J. Barton
Source: check_circle
Crossref

A unified approach to evolutionary conservation and population constraint in protein domains highlights structural features and pathogenic sites

2023-07-14 | Preprint
DOI: 10.21203/rs.3.rs-3160340/v1
Contributors: Stuart A. MacGowan; Fábio Madeira; Thiago Britto-Borges; Geoffrey J. Barton
Source: check_circle
Crossref

UniProt and mass spectrometry-based proteomics - a 2-way working relationship.

Molecular & cellular proteomics : MCP
2023-06 | Journal article
DOI: 10.1016/j.mcpro.2023.100591
PMID: 37301379
Contributors: Bowler-Barnett EH; Fan J; Luo J; Magrane M; Martin MJ; Orchard S; UniProt Consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central

UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping.

Current protocols
2023-03 | Journal article
DOI: 10.1002/cpz1.697
PMID: 36943033
Contributors: Zaru R; Orchard S; UniProt Consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central

Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Bioinformatics (Oxford, England)
2023-01 | Journal article
DOI: 10.1093/bioinformatics/btac793
PMID: 36484697
PMC: PMC9825770
Contributors: Coudert E; Gehant S; de Castro E; Pozzato M; Baratin D; Neto T; Sigrist CJA; Redaschi N; Bridge A; UniProt Consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central

UniProt: the Universal Protein Knowledgebase in 2023.

Nucleic acids research
2022-11 | Journal article
DOI: 10.1093/nar/gkac1052
PMID: 36408920
Contributors: UniProt Consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central

Search and sequence analysis tools services from EMBL-EBI in 2022

Nucleic Acids Research
2022-07-05 | Journal article
DOI: 10.1093/nar/gkac240
Contributors: Fábio Madeira; Matt Pearce; Adrian R N Tivey; Prasad Basutkar; Joon Lee; Ossama Edbali; Nandana Madhusoodanan; Anton Kolesnikov; Rodrigo Lopez
Source: check_circle
Crossref

A crowdsourcing open platform for literature curation in UniProt

PLoS Biology
2021 | Journal article
DOI: 10.1371/JOURNAL.PBIO.3001468
EID:

2-s2.0-85121919287

Part of ISSN: 15457885 15449173
Contributors: Wang, Y.; Wang, Q.; Huang, H.; Huang, W.; Chen, Y.; McGarvey, P.B.; Wu, C.H.; Arighi, C.N.; Bateman, A.; Martin, M.-J. et al.
Source: Self-asserted source
Fabio Madeira via Scopus - Elsevier

The European Nucleotide Archive in 2021.

Nucleic acids research
2021-11 | Journal article
DOI: 10.1093/nar/gkab1051
PMID: 34850158
Contributors: Cummins C; Ahamed A; Aslam R; Burgin J; Devraj R; Edbali O; Gupta D; Harrison PW; Haseeb M; Holt S et al.
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central

R2DT is a framework for predicting and visualising RNA secondary structure using templates

Nature Communications
2021-06-09 | Journal article
DOI: 10.1038/s41467-021-23555-5
Contributors: Blake A. Sweeney; David Hoksza; Eric P. Nawrocki; Carlos Eduardo Ribas; Fábio Madeira; Jamie J. Cannone; Robin Gutell; Aparna Maddala; Caeden D. Meade; Loren Dean Williams et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

UniProt: the universal protein knowledgebase in 2021.

Nucleic acids research
2020-11 | Journal article
DOI: 10.1093/nar/gkaa1100
PMID: 33237286
Contributors: UniProt Consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central
grade
Preferred source (of 2)‎

The Dundee Resource for Sequence Analysis and Structure Prediction.

Protein science : a publication of the Protein Society
2019-11 | Journal article
DOI: 10.1002/pro.3783
PMID: 31710725
Contributors: MacGowan SA; Madeira F; Britto-Borges T; Warowny M; Drozdetskiy A; Procter JB; Barton GJ
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central
grade
Preferred source (of 3)‎

PDBe-KB: a community-driven resource for structural and functional annotations.

Nucleic acids research
2019-10 | Journal article
DOI: 10.1093/nar/gkz853
PMID: 31584092
Contributors: PDBe-KB consortium
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central
grade
Preferred source (of 2)‎

The EMBL-EBI search and sequence analysis tools APIs in 2019.

Nucleic acids research
2019-04 | Journal article
DOI: 10.1093/nar/gkz268
PMID: 30976793
Contributors: Madeira F; Park YM; Lee J; Buso N; Gur T; Madhusoodanan N; Basutkar P; Tivey ARN; Potter SC; Finn RD et al.
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central
grade
Preferred source (of 2)‎

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.

Current protocols in bioinformatics
2019-04 | Journal article
DOI: 10.1002/cpbi.74
PMID: 31039604
Contributors: Madeira F; Madhusoodanan N; Lee J; Tivey ARN; Lopez R
Source: Self-asserted source
Fabio Madeira via Europe PubMed Central
grade
Preferred source (of 2)‎

Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]

2019-03-20 | Journal article
DOI: 10.12688/f1000research.15140.2
Part of ISSN: 2046-1402
Contributors: Bjorn Gruening; Olivier Sallou; Pablo Moreno; Felipe da Veiga Leprevost; Hervé Ménager; Dan Søndergaard; Hannes Röst; Timo Sachsenberg; Brian O'Connor; Fábio Madeira et al.
Source: check_circle
F1000
grade
Preferred source (of 6)‎

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Nucleic Acids Research
2018-11-06 | Journal article
DOI: 10.1093/nar/gky1100
Part of ISSN: 0305-1048
Contributors: Alex L Mitchell; Teresa K Attwood; Patricia C Babbitt; Matthias Blum; Peer Bork; Alan Bridge; Shoshana D Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew I Fraser et al.
Source: Self-asserted source
Fabio Madeira via Crossref Metadata Search
grade
Preferred source (of 2)‎

UniProt: a worldwide hub of protein knowledge

Nucleic Acids Research
2018-11-05 | Journal article
DOI: 10.1093/nar/gky1049
Part of ISSN: 0305-1048
Contributors: The UniProt Consortium; Alex Bateman; Maria-Jesus Martin; Sandra Orchard; Michele Magrane; Emanuele Alpi; Benoit Bely; Mark Bingley; Ramona Britto; Borisas Bursteinas et al.
Source: Self-asserted source
Fabio Madeira via Crossref Metadata Search

JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure

Bioinformatics
2018-01 | Journal article
DOI: 10.1093/bioinformatics/bty045
Part of ISSN: 1367-4803
Contributors: Peter V Troshin; James B Procter; Alexander Sherstnev; Daniel L Barton; Fábio Madeira; Geoffrey J Barton
Source: Self-asserted source
Fabio Madeira via Crossref Metadata Search
grade
Preferred source (of 2)‎

Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

2017-04 | Preprint
DOI: 10.1101/127050
Source: Self-asserted source
Fabio Madeira
grade
Preferred source (of 4)‎

Analysis of Variation in Protein Domain Families and Interfaces

2016 | Dissertation or Thesis
ETHOS: uk.bl.ethos.818447
Source: Self-asserted source
Fabio Madeira

14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides

Bioinformatics
2015-03-03 | Journal article
DOI: 10.1093/bioinformatics/btv133
Contributors: Fábio Madeira; Michele Tinti; Gavuthami Murugesan; Emily Berrett; Margaret Stafford; Rachel Toth; Christian Cole; Carol MacKintosh; Geoffrey J. Barton
Source: Self-asserted source
Fabio Madeira via Crossref Metadata Search
grade
Preferred source (of 2)‎

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

Database
2014-02-05 | Journal article
DOI: 10.1093/database/bat085
Contributors: M. Tinti; F. Madeira; G. Murugesan; G. Hoxhaj; R. Toth; C. MacKintosh
Source: Self-asserted source
Fabio Madeira via Crossref Metadata Search
grade
Preferred source (of 2)‎

Improving Protein Docking with Constraint Programming and Coevolution Data

2014-02-03 | Preprint
DOI: 10.1101/002329
Source: Self-asserted source
Fabio Madeira
grade
Preferred source (of 2)‎

Constraining Protein Docking with Coevolution Data for Medical Research

Artificial Intelligence in Medicine
2013 | Conference paper
DOI: 10.1007/978-3-642-38326-7_17
Source: Self-asserted source
Fabio Madeira
grade
Preferred source (of 3)‎

Pycoevol: A Python workflow to study protein-protein coevolution

BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
2012 | Conference paper
EID:

2-s2.0-84861977038
Contributors: Madeira, F.; Krippahl, L.
Source: Self-asserted source
Fabio Madeira via Scopus - Elsevier

Improving Multiple Sequence Alignments with Constraint Programming and Local Search

WCB'11 - Prooceedings of the Workshop on Constraint Based Methods for Bioinformatics, Perugia, Italy, September 12th, 2011. http://www.dmi.unipg.it/WCB11/wcb11proc.pdf
2011 | Conference paper
Source: Self-asserted source
Fabio Madeira

Estudos estruturais e funcionais da fenilalanina hidroxilase humana

2010 | Dissertation or Thesis
HANDLE: 10362/5805
Source: Self-asserted source
Fabio Madeira

Peer review (4 reviews for 4 publications/grants)

Review activity for Applied sciences. (1)
Review activity for Digital. (1)
Review activity for Electronics. (1)
Review activity for PLoS computational biology. (1)
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