I am currently carrying bioinformatic and cellular signaling network research as an Assistant Professor in the Linding lab group at the University of Copenhagen, Denmark. I am specialized in the analysis of Mass Spectrometry data, data integration and Deep Learning methods.

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Areas of expertise

• Deep Learning
• Network biology (cellular signaling networks)
• Mass Spectrometry and NGS (Whole Exome and RNA-seq) data processing and integration
• Data analysis (ROC curves, biomarkers, supervised learning)
• Bioinformatics programming
• Web development (including database design)

Publications

⇒ See my bibliography.

Research experience

2016 – now, University of Copenhagen, Denmark

Assistant Professor, Linding lab

2014 – 2016, University of Copenhagen, Denmark

Post-doc, Linding lab

2014, Technical University of Denmark

Post-doc, Linding lab

2013, Technical University of Denmark

Bourse de chercheur débutant du Fond National

Post-doc, Linding lab

Scientific tools

MIAPEGelDB

a web interface to create MIAPE-gel-compliant documents

miapegeldb.expasy.org

pROC

a package for R and S+ to build and analyze ROC curves

www.expasy.org/tools/pROC

PanelomiX

find the best panel of biomarkers

www.panelomix.net

DeepLearning

a Deep Learning package for R

Restricted Bolzman Machines training with contrastive divergence and autoencoder fine-tuning with conjugate gradients

github.com/xrobin/DeepLearning

University degrees obtained

2012, University of Geneva

PhD in Science, interdisciplinary (bioinformatics)

2007, University of Geneva

Masters in proteomics and bioinformatics

2005, University of Geneva

Bachelor in biology

Public presentations

2009, UseR! conference, Rennes France

Combination of protein biomarkers

2010, Swiss Proteomics Society PhD students' symposium, Basel

How to combine biomarkers?

2011, HUPO Annual World Congress, Genève

PanelomiX – a bioinformatic tool to build biomarker panels

2012, 9th Siena Meeting, Sienne, Italy

PanelomiX: a web-based tool to create panels of biomarkers based on thresholds

Posters

2007, Congress of the Swiss Proteomics Society, Lausanne

MIAPEGelDB: a web-based submission tool and public repository for MIAPE gel electrophoresis documents

2008, 8^th Siena meeting, Siena, Italy

Comparison of statistical learning methods for biomarker combination

Swiss Proteomics Society Grant

2008, European BioAlpine Convention, Geneva

Comparison of statistical learning methods for biomarker combination

Award for the best poster in the session “beyond discovery in proteomics”

2012, Integrative Network Biology 2012: Network Medicine, Helsingør, Denmark

pROC: an open-source package for R and S+ to analyze and compare ROC curves

Teaching activities

2010, 2011, in masters in proteomics and bioinformatics

Biomarker validation part 2: statistical analysis (2h)

Combination of biomarkers (2h)

2014, Bachelor in IT and Health, KU / DTU

Course organizer: Introduction to Systems Biology

Associations

Association du corps intermédiaire de médecine fondamentale

Board member and webmaster

www.unige.ch/medecine/acimf

Geckozone community

Translation of extensions for Firefox and webmaster

extensions.geckozone.org

Education

Since 2007, University of Geneva

Preparation of a PhD thesis in sciences, mention interdisicplinary

“Combination of biomarkers”

2007, University of Geneva

Specialisation internship in the “stroke” project of the Biomedical Proteomics Research Group and University Hospital of Geneva

2005 – 2007, University of Geneva

Master's degree in proteomics and bioinformatics (jointly organized by the faculties of medicine and sciences and the Swiss Institute of Bioinformatics)

Practical work “Tools for proteomic standards” (web interface for MIAPE documents)

2002 – 2005, University of Geneva

Bachelor in biology (faculty of sciences)

Monograph “A dual role for Ded1p helicase?”

1998 – 2002, High school, Geneva

Federal maturity with scientific options

“with mention”

Distinction Denise Lecoultre for my maturity work about prion

1993 – 2007, Conservatoire populaire de musique de Genève

Piano (music studies certificate)

“with mention”

1987 – 1998, Geneva

Obligatory school

Professionnal background

Summer 2005, Geneva

Shop assistant at the fruit and vegetables department of Migros store.

Summer 2004, Geneva

Order assistant at the central purchasing agency of Migros, fruit and vegetables department.

Summer 2003, Geneva

Storekeeper in multimedia centre for Migros (CMR)

Summer 2002, Moudon

Military recruit school, hospital soldier

One-week placement at Delémont hospital (stewardship department)

Additional information

Peer-reviewed manuscripts for:

Journal of Proteomics

Biomarkers

The Open Proteomics Journal

Bioinformatics

Journal of Statistical Software

2012 – present

Member of the editorial board of the Journal of Proteomics

Spoken languages

French (mother tongue)

German (good level)

English (high school level)

Personal informations

Nationality : Switzerland

Date of birth : 9th January 1983

Birth place : Lancy, Geneva

Hobbies

Reading (Science-fiction, fantasy, computing)

Photography (macro)