Fábio Madeira

+44 7450 223192

14 Gowrie Street
DD2 1ES Dundee
United Kingdom


Github / Twitter


Postdoctoral Research Assistant in Computational Biology

University of Dundee
United Kingdom

Various projects which rely heavily on software development and data analysis with Python and R.

PhD student in Computational Biology

University of Dundee
United Kingdom

The project focused on software development, statistical data analysis, web development and development/benchmarking of machine learning classifiers.

Research in Bioinformatics and Artificial Intelligence

New University of Lisbon

The project involved software development and development/benchmarking of constraint programming algorithms.



Scientific Posters

Fábio Madeira and Geoffrey J. Barton. 2015. Protein interactions and genetic variation. ISMB/ECCB 2015 (23rd Annual International Conference on Intelligent Systems for Molecular Biology - 14th European Conference on Computational Biology) Dublin, Jul 10-14th. Selected for Oral Poster Presentation and Travel Fellowship.
Paulo Roque Lino, Fábio Madeira, Isabel Tavares de Almeida and Paula Leandro. 2010. Alternative Answers to Everlasting Problems: Protein Engineering Towards New Approaches for Phenylketonuria Treatment. SPDM Annual Symposium Albufeira, Portugal, November 4-5th.

Research Projects

PhD research project

Geoff Barton's Group
Dundee, United Kingdom

Investigating the consequences of genetic variation on protein-protein and protein-ligand interactions.

Wellcome Trust PhD Programme - 3rd rotation

Ron Hay's Group
Dundee, United Kingdom

Deciphering the substrate specificity of ubiquitin conjugating enzymes.

Wellcome Trust PhD Programme - 2nd rotation

Geoff Barton's Group
Dundee, United Kingdom

Development of classification methods to predict new 14-3-3-binding proteins and phosphopeptides.

Wellcome Trust PhD Programme - 1st rotation

Carol MacKintosh's Group
Dundee, United Kingdom

Mapping the 14-3-3-binding 2R-ohnologue protein families of the human kinome.

Studentship in Bioinformatics

Ludwig Krippahl's Group
Lisbon, Portugal

CREMA: Constrained Refining of Multiple Alignments to identify correlations between mutations.

Studentship in Cell Biology

Júlia Costa's Group
Oeiras, Portugal

Glycosylation and Lewis X motif in neuronal tissue.

Studentship in Structural Biology

Maria João Romão's Group
Lisbon, Portugal

Production of a stable form of human phenylalanine hydroxylase: towards the 3D structure determination.
Co-supervised by Prof. Ana Paula Leandro

Workshops Attended

PDBe API Workshop

European Bioinformatics Institute
Cambridge, United Kingdom

Programmatic Access to the Molecular Structure Information at EMBL-EBI Hinxton, November 20-21st.


Papers et al.

Founder @papersetal
Dundee, United Kingdom

A startup providing new clever ways of managing and consuming research literature.

Biotechnology YES

Entrepreneur and R&D officer @ IntelliGene
Glasgow, United Kingdom

Participated with a team project "IntelliGene: Empower your future" in the Biotechnology Young Entrepreneurs Scheme Competition.

Coding Projects


Dundee, United Kingdom

A webserver to predict 14-3-3-binding sites in proteins. Built with Flask.


Source code
Lisbon, Portugal

Python routines to study correlated mutations and work with multiple sequence alignments.


Source code
Lisboa, Portugal

A Python workflow to study protein-protein coevolution and interaction.


Python, data analysis, machine learning & web development

Adopter of Test-driven and Agile development practices.
Software development: OOP Python 2/3 (Numpy, Unittest, pyMock, ...), Version control (Git/Github) and Continuous Integration (Travis-CI & Coveralls)
Web development: Python (Flask, webapp2, requests, GAE, ...), HTML/CSS (Bootstrap, Skeleton, ...), Javascript (jQuery, AngularJS, ...) and Ruby (Jekyll)
Data Analysis and visualisation: Python (pandas, matplotlib, ...) and R (ggplot2, ROCR, ...)
Machine learning: Python (scikit-learn and PyML) and R (RSNNS)
Database management: Relational (MySQL and SQLite3) and non-relational (MongoDB)
Other coding and scripting: Bash, Perl and C

Interests & Hobbies