| I received a Ph.D. in Biostatistics and Bioinformatics applied to Cancer Research in 2011 from the University Paris Sud XI, I was working at the Curie institute under the supervision of Emmanuel Barillot and François Radvanyi. My Ph.D. was about the unsupervised analysis of cancer transcriptome. During my postdoctoral time, I worked on the computational and statistical analysis of NGS data.
My areas of interest and expertise include
|
Click to view graph
Connections
Click to view timeline
Timeline
About
Courses
Introduction to data analysis
This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data […]
2017-01-16 09:00:00
2017-02-17 13:00:00
Europe/Paris
Introduction to data analysis
This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data […]
28 Rue du Docteur Roux, Paris, France
Morning session – Introduction to NGS data analysis
The Hub of Bioinformatics and Biostatistics at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th […]
2016-05-10 09:00:00
2016-06-28 12:00:00
Europe/Paris
Morning session – Introduction to NGS data analysis
The Hub of Bioinformatics and Biostatistics at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th […]
28 Rue du Dr Roux, Paris, France
Morning session – Data analysis using R
This course is an introduction to data analysis. It is better to have a minimal knowledge of R. If not, an introductory tutorial is available on the course’s web page and the basics of […]
2016-03-08 09:00:00
2016-04-12 12:00:00
Europe/Paris
Morning session – Data analysis using R
This course is an introduction to data analysis. It is better to have a minimal knowledge of R. If not, an introductory tutorial is available on the course’s web page and the basics of […]
28 Rue du Docteur Roux, Paris, France
Introduction to Data Analysis
This four-week graduate level course will give participants basic skills and hands-on training in statistics and descriptive data analysis. This course is (primarily) dedicated to first year PhD students of the Institut Pasteur (each […]
2018-10-22 09:00:00
2018-11-20 00:00:00
Europe/Paris
Introduction to Data Analysis
This four-week graduate level course will give participants basic skills and hands-on training in statistics and descriptive data analysis. This course is (primarily) dedicated to first year PhD students of the Institut Pasteur (each […]
28 Rue du Dr Roux, Paris, France
Introduction to Data Analysis
This four-week graduate level course will give participants basic skills and hands-on training in statistics and descriptive data analysis. This course is (primarily) dedicated to first year PhD students of the Institut Pasteur (each […]
Bioinformatics and Biostatistics HUB
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Marie-Agnès Dillies
Stéphane Descorps-Declère
Vincent Guillemot
Emeline Perthame
Hugo Varet
Stevenn Volant
Thomas Obadia
Gaël Millot
Quentin Giai Gianetto
Anne Biton
Christophe Becavin
2018-01-08 09:00:00
2018-02-02 00:00:00
Europe/Paris
Introduction to Data Analysis
This four-week graduate level course will give participants basic skills and hands-on training in statistics and descriptive data analysis. This course is (primarily) dedicated to first year PhD students of the Institut Pasteur (each […]
28 Rue du Docteur Roux, Paris, France
Projects
Former Teams
CV
Education
Oct. 2007-June 2011: Ph.D. in bioinformatics and biostatistics.
Institut Curie / Inserm U900 / Mines ParisTech and CNRS UMR144, Institut Curie, France. Title: “Independent Component Analysis of Cancer Transcriptome”.
Supervisors: Dr. Emmanuel Barillot and Dr. François Radvanyi
Université Paris-Sud XI d’Orsay, France:
2005 – 2007: M. Sc. BIBS “Bioinformatics and Biostatistics”.
2004 – 2005: B. Sc. BIBS “Bioinformatics and Biostatistics”.
2002 – 2004: DEUG MIAS “Mathematics and Informatics applied to sciences”.
Work Experience
Since November 2015: Pasteur Institute, Paris, France.
Bioinformatics Research Scientist.
March 2014 – November 2015: University of California, San Francisco, USA.
Postdoctoral researcher with Dr. Noah Zaitlen. Study of allele-specific expression; data analysis of sequencing data (DNA-Seq, RNA-Seq) from functional genomics experiments, CrispR screens.
August 2011 – February 2014: University of California, Berkeley.
Postdoctoral researcher with Pr. Terry Speed in the Statistics Department. Correction of batch effects in miRNA-Seq and RNA-Seq data, analysis of transposable elements in RNA-Seq data from The Cancer Genome Atlas.
Spring 2007 (6 months): Genomic Science Department, Sanofi-Aventis, Vitry, France. Master internship with Dr. Arne Muller and Dr. Edgardo Ferran: Analysis of transcriptome data from treated cell lines.
Teaching
2007 – 2010: Université Paris Descartes V, France.
Biomathematics for undergraduate students in pharmaceutic sciences (46h per year): Algebra, Analysis, Probabilities and Statistics.
Biostatistics for undergraduate students in Biology (18h per year): Initiation to descriptive statistics and statistical tests.
From 2015: Institut Pasteur.
Teaching of statistics (multivariate analysis, statistical power, …) with practical sessions in R, RNA-Seq data analysis, and experimental design. Public: PhD students and researchers in biology.
Programming Skills
Progr. languages: python, java, shell scripting
Statistical packages: S-plus/R, Matlab
Softwares
GeneValorization. Java webstart application that gives a clear and handful overview of the bibliography corresponding to one particular gene list.
EMA. R package that proposes an analysis strategy and a selection of tools to investigate microarray gene expression data.
MineICA. R package whose goal is to facilitate the interpretation of an ICA decomposition of genomics data. Available in Bioconductor.
Publications
Download-
2024Smoking changes adaptive immunity with persistent effects., Nature 2024 Feb; 626(8000): 827-835.
-
2023Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum of Shank3 mutant mice., Front Mol Neurosci 2023 ; 16(): 1139118.
-
2022IRF8 regulates efficacy of therapeutic anti-CD20 monoclonal antibodies., Eur J Immunol 2022 Aug; (): .
-
2022Erythro-myeloid progenitor origin of Hofbauer cells in the early mouse placenta., Development 2022 Apr; 149(8): .
-
2021Megakaryocyte production is sustained by direct differentiation from erythromyeloid progenitors in the yolk sac until midgestation., Immunity 2021 May; (): .
-
2020The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection, Elife 2020 May;9.
-
2020Polygenic Architecture of Human Neuroanatomical Diversity., Cereb Cortex 2020 04; 30(4): 2307-2320.
-
2019Broad-Range Papillomavirus Transcriptome as a Biomarker of Papillomavirus-Associated Cervical High-Grade Cytology, J Mol Diagn 2019 Sep;21(5):768-781.
-
2019Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding, BMC Genomics 2019 Feb;20(1):107.
-
2019Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection, J Nanobiotechnology 2019 Jan;17(1):15.
-
+View full list of publications