Arthur Gilly | Principal Bioinformatician

Gilly, Arthur

Arthur's work focuses on the analysis of high-throughput sequencing data, with the objective of finding actionable targets for the prevention and treatment of common diseases. He designs pipelines, develops new statistical methods and performs bioinformatic follow-up of association discoveries.

In the past two years, I have been analysing very low-depth sequence data from the HELIC study (ca. 3000 participants). Typically, sequencing studies have a much higher depth, which meant that established analysis pipelines were not able to deal with the high amount of missingness and errors in this type of data. I have established a quality control and imputation pipeline for very low-depth sequence data, and am now carrying out association analysis with over 60 quantitative traits.

I am interested in every step of the omics data lifecycle, from acquisition and quality control, to statistical analysis and translation of results into clinical applications.

My background is in applied mathematics, so my main area of expertise is to develop and apply statistical methods to analyse large amounts of data. Recently, I developed a piece of software that corrects for overlapping samples in large-scale meta-analyses of genetic association studies.

Publications

  • Using population isolates in genetic association studies.

    Hatzikotoulas K, Gilly A and Zeggini E

    Briefings in functional genomics 2014;13;5;371-7

  • Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants.

    Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE et al.

    Nature communications 2014;5;5345

  • TE-Tracker: systematic identification of transposition events through whole-genome resequencing.

    Gilly A, Etcheverry M, Madoui MA, Guy J, Quadrana L et al.

    BMC bioinformatics 2014;15;377

  • Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants.

    Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE et al.

    Nature communications 2014;5;5345

  • Using population isolates in genetic association studies.

    Hatzikotoulas K, Gilly A and Zeggini E

    Briefings in functional genomics 2014;13;5;371-7

  • Mapping the epigenetic basis of complex traits.

    Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M et al.

    Science (New York, N.Y.) 2014;343;6175;1145-8

Career/Research Highlights

Gilly, Arthur
Arthur's Timeline
2013

Senior Bioinformatician/Statistical Geneticist, Wellcome Trust Sanger Institute

2012

Research Engineer, at National Sequencing Center, Evry, France

2011

R&D Engineer, at Misys Sophis, Paris, France

Junior Consultant, at Sophis Asia, Hong Kong, PRC

2010

Graduated from Grenoble INP - ENSIMAG, France (diplôme d'ingénieur, Applied Mathematics)