About [ Contact, Education/positions, Publications ] ● Research [ Current and past research, R/Bioconductor ]

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Positions

October 2013 (current) Senior Research Associate. Computational Proteomics Unit (CPU).

October 2012 (current) Affiliated teaching staff at the Cambridge Computational Biology Institute (CCBI), University of Cambridge.

January 2010 (current) Visiting scientist at the European Bioinformatics Institute (EBI).

January 2010 - September 2013 Post-doctoral Research Associate at the Cambridge Centre For Proteomics (CCP).

July 2006 - December 2009 Bioinformatician at DNAVision. My involvement as bioinformatician and project manager at DNAVision has led me to deal with various types of microarrays and projects, ranging from small scale projects to European research projects and large projects with pharmaceutical companies. These included expression profiling, SNP chips as well as general purpose bioinformatical expertise. Project management consisted in the scientific and technical overview of the project, from sample quality control and process to data analysis. The data analyses consisted essentially in (i) quality control, identification of differentially expressed probes and subsequent GO and pathway inference and (ii) analysis and comparison of genotypes or copy number variation between samples or other custom analyses. I also participated in several in-house projects (such as design of custom chips) and the evaluation of new technologies (high throughput sequencing). See also past research.

October 2005 - March 2006 Research contract at the Free University of Brussels (ULB). See past research for details.

Professional memberships

The Bioconductor project, providing widespread access to a broad range of powerful statistical and graphical methods for the analysis of high-throughput data.

The Foundation for Open Access Statistics, promoting free software, open access publishing, and reproducible research in statistics.

Honours

Software Sustainability Institute Fellow 2014.

Paul Brien prize for the best Master thesis in Zoology, 1999-2000. Thesis title: Etude phylogéographique des sous-espèces de Gonioctena variabilis Ol. (Coleoptera; Chrysomelidae) au moyen de caractères morphologiques et moléculaires.

Teaching

The pdf and source of the slides and lecture notes are available in the TeachingMaterial repository.

Introduction to Integrative Omics The nature of proteomics data - caveats and integration, 4 - 5 March 2015, EMBL-EBI, UK.

An introduction to R/Bioconductor for computational proteomics Atelier PROSPECTOM - Grenoble, France, 19 November 2014.

R programming boot camp, 7 - 8 January 2014, Centre for Mathematical Sciences, University of Cambridge (Course repository).

Building an R package (invited course), 4 September 2013, Royal Statistical Society International Conference, Newcastle UK (slides, review).

Integrating R and C using Rcpp (invited course), 21 May 2013, Postgraduate Statistics Centre, Lancaster Univsersity, UK (slides).

Organelle Proteomics Data Analysis Workshop Mon 12 - Tue 13 November 2012, Cambridge, UK.

Scientific programming with R MPhil in Computational Biology, Cambridge Computational Biology Institute, Cambridge, UK.

Advanced R Programming and Development (invited course), 28-29 November 2011 European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (course page, group picture) and 24-25 January 2013.

R object-oriented programming and package development, Since 2011, Graduate School of Life Sciences, University of Cambridge (course page).

A beginner's guide to R, Since 2011, Graduate School of Life Sciences, University of Cambridge (course page).

Quantitative Proteomics, Quantitative proteomics practicals at the joint EBI - Wellcome Trust Proteomics Bioinformatics Workshop, 17 - 19 July 2011 and 5 - 9 November 2012, Hinxton, UK.

Data Analysis for Genome Biology (CSAMA), Yearly, since 2011, Brixen, Italy.

Supervisions, 2000 - 2005. Supervisions of the practical session of phylogenetic inference of the second year Zoology course (by Prof. Michel Milinkovitch) at the Free University of Brussels (ULB).

Teaching assistant, 1999 - 2000. Assisting student for the practical session of the second year Zoology course (by Prof. Michel Milinkovitch) at the Free University of Brussels (ULB).

Education

September 2005 - September 2009, Evening classes at the Faculty of Computer Science of the University of Namur (FUNDP).

October 2000 - September 2005, PhD at the Institute of Molecular Biology and Medicine (IBMM), in the Unit of Evolutionary Genetics, with Prof. Michel Milinkovitch. PhD grants by the FRIA and FNRS. See past research in evolutionay biology for a brief description.

September 2000 - September 2001, Master of Advanced Studies (DEA) in Sciences at the Free University of Brussels (ULB), Belgium

September 1996 - September 2000, Master in Biology (Licence) at the Free University of Brussels (ULB), Belgium.