20 YEARS OFGENOMICS

Past and futuredirections

March 28, 2019

PARIS, France

PROGRAM

INVITATION TO THE 20 YEARS OF GENOMICS: past and future directions

Dear Colleagues, dear Friends,

Twenty years ago, our genomics core facility has been established from a partnership

between the Institut Curie, the École Supérieure de Physique et Chimie Industrielles de la

ville de Paris (ESPCI) and the École normale supérieure (ENS). Since its inception, we

focused our activity on functional genomics analysis of eukaryotes to help laboratories

design and conduct state of the art high-throughput projects from the experimental

design to data analysis. We have been key players on many fields including yeast

sequencing genome project, microarrays development, single cell gene expression, high

throughput sequencing revolution and now nanopore technologies.

In order to celebrate this anniversary, we will organize in Paris on March the 28th 2019 a

half-day meeting entitled: “20 years of genomics past and future directions”. This event

will feature a series of talks covering key research fields in genomics. We will look at the

past of course, but we will also discuss the future of the field. The afternoon will be

followed by a reception at the Musée d’Orsay including a gala dinner and a guided tour of

the remarkable art collections.

The conference will be held at the École normale supérieure in Paris, with an exceptional

speaker line up including Clive Brown, Ana Conesa Cegarra, Denis Milan and CatherineNguyen. It will also be the occasion to meet biotech companies involved in future

applications for genomics.

Follow us on Twitter #20yearsofgenomics and LinkedIn

We are looking forward to that celebration where we expect great exchanges on past and

future challenges in genomics.

Stéphane LE CROM,

Scientific head of genomics core facility

PROGRAM | 2

TIME

13H-13H30 Welcome coffee and registration

13H30-13H40 Introduction

13H40-14H30

14H30-15H20 Catherine Nguyen, Inserm - Health genomics

15H20-16H10 Coffee break and meetings with biotech involved in genomics challenges

16H10-17H00

17H00-17H50 Ana Conesa Cegarra, Príncipe Felipe Research Center - Bioinformatics and transcriptomics

17H50-18H00 Closing remarks

19H-20H30 Orsay Museum guided visit

20H30 Anniversary gala dinner at the Orsay Museum

SESSIONS & SPEAKERS

PROGRAM OF THE CONFERENCE

PROGRAM | 3

Clive G Brown, Oxford Nanopore Technologies - Sequencing

Denis Milan, INRA - Agrogenomics

SPEAKERS

Clive BrownChief Technology Officer

Oxford Nanopore Technologies

Oxford – United Kingdom

20 years of sequencing

Clive is Chief Technology Officer at Oxford Nanopore. On the Executive team, he is

responsible for all of the Company’s product-development activities. Clive leads the

specification and design of the Company’s nanopore-based sensing platform, including

strand DNA/RNA sequencing and protein-sensing applications with a strong focus on

scientific excellence and successful adoption by the scientific community.

Clive joined Oxford Nanopore from the Wellcome Trust Sanger Institute (Cambridge, UK)

where he played a key role in the adoption and exploitation of 'next generation' DNA

sequencing platforms. This involved helping to set up the world’s largest single installation

of Illumina (formerly Solexa) Genome Analyzers in a production sequencing environment,

initially used to pioneer the 1000 genomes project.

From early 2003 he was Director of Computational Biology and IT at Solexa Ltd, where he

was central to the development and commercialisation of the Genome Analyzer (GA).

Solexa was sold to Illumina for $650m in early 2007 after the successful placement and

adoption of 12 instruments. The Solexa technology, now commercialised by Illumina, is the

market-leading DNA sequencing technology driving the renaissance in DNA-based

discovery.

He has a strong background in computer science and genetics/molecular biology and

manages interdisciplinary teams including mechanical engineering, electronics, physics,

surface chemistry, electrophysiology, software engineering and applications (of the

technology). Clive applies modern agile management techniques to the entire product-

development lifecycle.

Clive has also held various management and consulting positions at GlaxoWellcome,

Oxford Glycosciences and other EU- and US-based organisations. He has worked at the

interface between computing and science, ranging from genetics to proteomics. He holds

degrees in Genetics and Computational Biology from the University of York.

PROGRAM | 4

SPEAKERS

Ana ConesaProfessor of Bioinformatics

University of Florida

Gainesville – United States of America

Multi-omics and third generation sequencing strategies for the future ofgenome research

Ana Conesa is Professor of Bioinformatics at the Microbiology and Cell Science

Department at the University of and founder of the Bioinformatics company Biobam SL.

She graduated as Agricultural Engineer at the Polytechnical University of Valencia in 1993

and did her PhD in at the University of Leiden in the Netherlands. After a short

appointment as bioinformatics project leader at TNO Quality of Life (The Netherlands) she

obtained a Ramon y Cajal award and joined the Valencia Agricultural Research Institute in

2003. She moved to the Prince Felipe Research Center in 2007. She became UF Professor

in 2014.

Ana Conesa’s group is interested in understanding functional aspects of gene expression

at the genome-wide level and across different organisms. Her has developed statistical

methods and software tools that analyze the dynamics aspects transcriptomes, integrate

these with other types of molecular data and annotate them functionally, with a special

focus on Next Generation Sequencing (NGS) data. Some of our popular software tools are

Blast2GO, PaintOmics, maSigPro, NOISeq, Qualimap, SQANTI, tapppAS, etc. She has lead

international projects such as STATegra and DEANN where European and American

scientists developed new tools for the analysis of sequencing data. She has published over

110 research papers that have received more than 17,000 citations.

PROGRAM | 5

Denis MilanDirector of Research

France Genomics infrastructure deputy director

INRA - French National Institute for Agricultural Research

Castanet-Tolosan – France

20 years of agrigenomics: past and future directions

Denis Milan is an agricultural engineer from the Institut National Agronomique Paris

Grignon. After a thesis in retrovirology at the Institut Pasteur, he joined INRA at the

Toulouse research centre.

His scientific work focused on the knowledge of the porcine genome with the

development of genetic and physical maps of the porcine genome and then the

sequencing of this genome within the framework of an international consortium. He has

also worked on the mapping of QTL and major genes in pigs, including the identification of

a mutation in a gene involved in meat quality, the first strict positional cloning in species of

agronomic interest. He served as Head of the Animal Genetics Division at INRA from 2010

to 2017. Over the period 2011-2018 he also headed the INRA metaprogram dedicated to

genomic selection in animal and plant species.

Since 2003 he has been director and then scientific director of the Genomics platform that

became GeT (Genome and Transcriptome) in 2010, bringing together several sites in

Toulouse. In 2008-2009 he chaired the INRA national commission dedicated to platforms.

He has participated in the setting up of the France Genomics infrastructure, of which he is

deputy director.

SPEAKERS

PROGRAM | 6

Catherine NGuyenDirector of Research

Genetics, genomics and bioinformatics Institute (Aviesan) director

Inserm - French National Institute of Health and Medical research

Marseille – France

The impact of the transcriptomic to the exploration of the living and inmedical genomics

Director of Research at INSERM, Catherine Nguyen first led the ERITM and the ERM 206

from 2002 to 2008, then took over the leadership of TAGC-UMR 1090 (Advanced

Technologies for Genome and Clinic) from its creation in 2008 until 2018 as well as the co-

management of its platform IBiSA TGML (Transcriptomics and Genomics-Marseille

Luminy). In 2016, she is appointed Director of the Thematic Institute Multi-Organisms

"Genetics, Genomics and Bioinformatics" where she works to structure these disciplines in

the research landscape, and more specifically at INSERM.

Since joining INSERM, she has been involved in the development of genomics approaches

that she has applied to her research in immunology and oncology. She co-authored more

than a hundred articles and reviews in international publications.

Throughout her career, she fervently work on promoting technological deployment in

genomics for the benefit of the scientific advancement. She is a pioneer of the

transcriptomic by not only actively contributing to the development of its concept but also

to the evolution of its application. In addition, in 1998, she actively participated in

structuring the development of bioinformatics.

Always focused on the transmission of knowledge and its validation, she has actively

participated in the development of research in these areas. She provided training and

logistical support to many projects, and contributed to the networking of the development

of transcriptomic platforms at national and international level. Beyond the fundamental

aspect, her work led to the definition of new tools for diagnosis and/or prognosis thus

helping practitioners.

She has always been an advocate for spreading know-how, providing training at national

and international level (Brazil, Thailand), and participating in the establishment of research

Masters, particularly in Lebanon and in Vietnam (USTH program).

SPEAKERS

PROGRAM | 7

Philippe MarcDirector of Research

Global Head of Integrated Data Sciences

Novartis Institutes for BioMedical Research (NIBR)

Basel - Switzerland

Philippe MARC obtained a Ph.D. in Computational Science from Paris Diderot University

before completing a systems biology-oriented postdoctoral fellowship in the lab of George

Church at Harvard Medical School. He then worked for Aventis and Sanofi before joining

Novartis a decade years ago. At Novartis, his team developed tools to improve and

expedite Translational Medicine data analysis and decision-making. He is also leading the

data standardization and visualization work of the Innovative Medicine Initiative eTOX

project.

SCIENTIFIC ORGANIZING COMMITTEE

Frédéric DevauxProfessor of genomics

Sorbonne Université, IBPS – Institut de Biologie Paris Seine

Paris – France

F. Devaux got his PhD in functional genomics in 2001 at Université Pierre et Marie Curie

(UPMC, Paris, France). He was recruited as an assistant professor in 2002 in the laboratory

of Pr Claude Jacq (ENS, Paris, France). In 2008, he got a full professor position in microbial

genomics at UPMC and he created his research team at the laboratory of computational

and quantitative biology, studying transcriptional and post-transcriptional stress regulatory

networks in various yeast species.

PROGRAM | 8

Marie-Claude PotierDirector of Research

PhD, Pharm. D., Director of Research at CNRS

ICM - Brain & Spine Institute

Paris – France

Dr. Marie-Claude Potier is Director of Research at the French National Center for Scientific

Research (CNRS) and Co-Group Leader of the “Alzheimer’s and Prion Diseases” research

group at ICM-Institut du Cerveau et de la Moelle Epinière (Brain and Spine Institute), at the

Pitié-Salpêtrière Hospital, Paris, France.

Dr. Marie-Claude Potier and her team investigate the role of lipids, particularly cholesterol

and alipoprotein E in the secretion and neuronal transport, their involvement in endosomal

modifications that occur early during the course of the disease and novel mechanisms of

AB toxicity identified in vivo. She initiated translational research programs with on-site

clinicians and developed a microfluidic platform for studying the transcription of single

cells and producing microfluidic devices for neuronal cultures.

After a PharmD in Neuropharmacology at the University Réné Descartes, Paris, France and

a PhD at the University Pierre and Marie Curie, Paris, France, she was trained in molecular

and cellular biology during three years post-doct at the MRC Laboratory of Molecular

Biology, Cambridge, UK. She returned to the Alfred Fessard Institute when she obtained a

permanent scientific staff position at CNRS and later joined the School of Physic &

Chemistry (ESPCI), Paris France. She lately joined the ICM in 2008.

Dr. Marie-Claude Potier has been working for the past twenty-five years on Down

syndrome (DS) and is now developing pharmacological treatments for increasing

cognition in DS.

Dr. Marie-Claude Potier published more than one hundred papers in scientific journals and

is since 2017 Corresponding Member of the French Academy of Medicine. She received the

Dagnan-Bouveret Prize from The French Science Academy in 2005.

SCIENTIFIC ORGANIZING COMMITTEE

PROGRAM | 9

Stéphane Le CromProfessor of genomics

Sorbonne Université, IBPS – Institut de Biologie Paris Seine

Paris – France

Stéphane Le Crom is a Professor of Genomics at Sorbonne Université (ex Pierre et Marie

Curie, Paris, France). He got a Ph.D. in Cellular Neurobiology in 2000 at Paris-Sud Orsay

University. He performed two post-doctoral internships: one on yeast transcriptomics

(Claude Jacq’s team, Paris) and the other on protein-protein interaction analysis (Stephen

Michnick laboratory, Montréal). He has been recruited as an assistant professor in 2003 to

join the group of Patrick Charnay at École normale supérieure on genomic aspects of

development of the vertebrate nervous system.

Since 2007, he is the scientific director of the Genomics core facility at École normale

supérieure Biology Institute (IBENS in Paris. This facility has been created in 1999 for

providing access to functional genomics technologies with the main objectives to help

laboratories managing their genomic projects, disseminate genome-wide approaches

among the scientific community, and develop competence and diversified resources in

bioinformatics analyses of functional genomic data.

Since 2014 he is responsible for the Sorbonne Université Omics network that gathers 21

structures involved in data production in genomics (microarrays, high throughput

sequencing and qPCR), molecular analysis (proteomics, mass spectrometry, lipidomics and

metabolomics), biological resources’ management and associated bioinformatics.

SCIENTIFIC ORGANIZING COMMITTEE

PROGRAM | 10

MUSÉE D’ORSAY PRIVATE VISIT

PROGRAM | 11

19h – 20h30

Located in the heart of Paris, along the Seine river, in front of the Tuileries garden, the

Musée d’Orsay is the former Orsay railway station built in 1900 for the world exhibition. In

one of the historical place in Paris, the museum and its restaurant are awesome references

to French culture.

ANNIVERSARY GALA DINNER

20h30

The former restaurant of the Hôtel d’Orsay, on the first floor of the museum, is still as

magnificent as it was when it opened in 1900. The new furniture sets off the dazzling

chandeliers and the painted and gilded ceilings of this dining room, listed as a Historic

Monument. The chef Yann Landureau offers traditional French cuisine, interspersed with

original dishes that are linked to the museum’ current events.

INSTITUTIONAL PARTNERS

PROGRAM | 12

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