IGFL 2007 - ....

The 1990s

The scientific community considers that it is now possible to approach life sciences in an integrated manner “Integrative biology" no longer approaches the major biological functions in isolation, but attempts to break down the barriers between traditional scientific disciplines. The CNRS decided to set up several research centers in France to develop this new biology. Because of its solid experience in this field, Lyon was included in this program. A project to create a new European Institute of Developmental Biology and Integrative Physiology within the Claude Bernard Lyon 1 University (UCBL) emerged in the early 2000s, led by Jacques Samarut. At the same time, genomics became an established experimental approach and the arrival of Vincent Laudet in Lyon added the dimensions of comparative and evolutionary biology to the initial project. The creation of the Lyon Institute of Functional Genomics (IGFL) at the ENS de Lyon in partnership with the CNRS, the UCBL and the INRA was decided in 2006.

2007

The IGFL is officially created as a joint research unit of the ENS de Lyon, the Université Claude Bernard Lyon 1, the CNRS and the INRA (now a unit under contract to INRAE). The research conducted by several independent groups is devoted to Developmental Biology, Physiology and Integrative Biology. Integrative in vivo models are privileged. Jacques Samarut, director of research at the ENS of Lyon and professor at the University, is appointed director, Vincent Laudet is deputy director.

The first logo of the IGFL

Initially designed with teams from the Claude Bernard University and the Reproduction and Development of Plants (RDP) laboratory of the ENS of Lyon, the project is finally based on founding groups from the Laboratory of Molecular and Cellular Biology (LBMC)* directed by Vincent Laudet, Pierre Jurdic and Jacques Samarut. They were quickly joined by five new groups led by Françoise Bleicher, Jean-Marc Vanacker, Catherine Hänni, Frédéric Flamant and Philippe Durand. As there is no space dedicated to this new laboratory, the teams are scattered in different sites of the ENS. The construction of a new building to house the whole IGFL became a priority.

*We would like to thank the Laboratory of Molecular Biology of the Cell (LBMC), a laboratory created at the same time as the ENS of Lyon (1987) by Jacques Daillie with Jacques Samarut as its kingpin. The LBMC by a very open policy integrating the most recent approaches to biology of the time has been the catalyst of integrative biology and had a major role in the creation or relocation of biology laboratories at the ENS Lyon: The Reproduction and Development of Plants (RDP) laboratory in 1993 directed by Christian Dumas, the Virology laboratory with Jean-Luc Darlix and then Immunology with Chantal Rabourdin-Combes, which will merge into the International Center for Research in Infectiology (CIRI) in 2013 and finally the IGFL. Without the LBMC, its scientific success, its original organization (independent teams) and its very broad scientific policy, the IGFL would never have emerged.

2008

Vincent Laudet is appointed Director in May following the nomination of Jacques Samarut as Director of the ENS of Lyon (Monod site). He adds evolutionary biology to the previous scientific axes of the IGFL, which is concretized with the arrival of two future team leaders: Jean-Nicolas Volff, recruited as Professor at the ENS of Lyon and Laurent Viriot, recruited as Professor at the University Claude Bernard, and thus constitutes the thematic "tripod" of the unit, which is still relevant today: Developmental biology, Physiology and Evolution. The emergence of genomic and imaging approaches in the following years were very strong unifying factors that contributed to solidify the institute and to give a "scientific identity" to the IGFL. 

2009

The IGFL establishes a Scientific Advisory Board (SAB) composed of leading international scientific figures to accompany the IGFL in its growth through open and competitive calls for proposals for the creation of new research groups at the IGFL, both senior and junior. The management team has hired a research steering officer, Joanne Burden, who will set up the first 8 calls. The first president of the SAB is Prof. Manfred Schartl (University of Würzburg), followed by Prof. Ralf Sommer (Max-Plack-Gesellsahft), Dr. François Payre (University of Toulouse), Prof. Irene Miguel-Aliaga (Imperial College London) and finally Prof. Pavel Tomancak (Max-Plack-Gesellsahft). In 2022 our SAB was again chaired by Prof. Irene Miguel-Aliaga.

The first two calls for proposals allow the recruitment of Abderrahman Khila (2009) and Florence Ruggiero (2010). The ATIP-AVENIR 2010 program of the Institut National des Sciences Biologiques (INSB) of the CNRS allows the creation of the Khila team which will convert this label into an ERC CoG in 2014 and then into an FRM team label in 2021. The Ruggiero team, already active since 2003, comes from the Institute of Biology and Chemistry of Proteins (IBCP) on the Lyon-Gerland campus and will be continuously funded by the French National Research Agency (ANR). The IGFL project grows and diversifies during the years 2009-2010.

2011

Françoise Bleicher is appointed deputy director alongside Vincent Laudet, director, for a new 5-year mandate at the head of the unit. Under the leadership of efficient administrative services, the management and all the members of the unit are strongly committed to planning and organizing the development of the future building, the construction of which began in 2011. All of them are working hard to find the necessary funding to equip the new building, manage the calls for tender and select the best opportunities on the market. The tone is set by the management, all equipment must be new when entering the building and the support of the supervisory authorities, after many bitter negotiations, some setbacks and multiple twists, is finally there. This intense and collective preparatory period led to a fruitful gestation and a start-up of the IGFL project which created a strong feeling of belonging of the staff to this project. They responded and worked hard to prepare "their" future work tool. The 2011 call for tenders for the recruitment of new team leaders is unequalled in the history of the IGFL with the recruitment of 3 teams: Samir Merabet (FRM Amorçage young team 2012 then FRM team label 2017), François Leulier (ATIP-AVENIR 2012 then ERC StG 2013 then FRM team label 2018 renewed in 2022) and Michalis Averof (ANR Chair of Excellence 2012 then ERC AdG 2017). The IGFL project takes off!

2012

Thanks to the tenacity of its management, the commitment of its staff and the support of the supervisory authorities, the IGFL, which now has nearly 100 staff members, moved into a brand new building (future building M10 on the Monod campus) at the ENS de Lyon in September (which represents 10 years between the first discussions and the entry into the building!), 4500m2 fully equipped for molecular biology, cell biology, genomics and the use of animal models (housing and experimentation platform for rodents, fish animal house which, from the beginning, are made available to the SFR Biosciences, and terrestrial and aquatic arthropod animal houses). The construction and equipment were supported by Europe, the State, the Rhône General Council and the Rhône-Alpes Region, as well as the ENS of Lyon, the CNRS, the UCBL and the INRA. The Hänni and Durand teams are not maintained, and the IGFL is composed of 13 research groups when it enters the building:

Averof: Comparative biology of development and regeneration
Bleicher: Physiopathology of odontoblasts
Flamant: Neurodevelopment
Jurdic: Cell biology and bone physiopathology
Khila: Developmental genomics and evolution
Laudet: Molecular zoology

Leulier: Functional genomics of host-intestinal bacteria interactions
Merabet: Ontogeny and molecular interactions
Ruggiero: Biology and pathology of extracellular matrices
Samarut: Functional genomics of nuclear receptors
Volff: Evolutionary genomics of fish
Vanacker: Physiopathology of orphan nuclear receptors
Viriot: Evo-Devo of vertebrate dentition

Official inauguration of the IGFL building in October 2012                    The IGFL building ©Vincent Moncorgé

These teams use a variety of conventional animal models: mice, zebra and medaka fish, and drosophila, and non-conventional models from the wild: poecilid fish (guppies), crustaceans, and semi-aquatic insects (gerrids). When it entered the building, the IGFL invested in high-throughput sequencing technologies and the IGFL Sequencing Platform (PSI) was officially created shortly afterwards with Sandrine Hughes (CR CNRS) and Benjamin Gillet (IR CNRS) at its head and the support of the ENS of Lyon. The IGFL also acquired its own capacities in close-up imaging, complementary to those present in the advanced imaging platform of the SFR Biosciences on the Lyon-Gerland campus. Under the impetus of the management, a club of IGFL patrons was launched, but it received the support of only one company and was abandoned three years later because it was unable to include other partners. Let us thank here the company Silab which by its membership to the program allowed to co-finance the purchase of equipment including those of the IGFL sequencing and imaging platforms.

2013

The call for tenders launched that year allows the recruitment of two new teams, the building is complete (15 teams): Hugo Aguilaniu migrates locally from LBMC to the IGFL and brings a new model to the IGFL (the worm Caenorhabditis elegans), he obtains an ERC CoG in 2015, and Nicolas Goudemand (ANR Emergence and then recruited as a Professor at ENS Lyon) who strengthens the paleobiological dimension of the Institute. At the end of 2013, the IGFL organizes its inaugural scientific symposium focused on its DNA: evolution, development and animal physiology and their interfaces.

Inaugural scientific symposium of the IGFL in October 2013 

2014

A new era for the IGFL begins with the announcement of the first departures of "founding" team leaders (P.Jurdic then J.Samarut). Florence Ruggiero is asked to take a position in the next management and is appointed deputy director of the IGFL. She supervises the 2014 call for proposals during which Kiran Padmanabhan is recruited and who obtains ATIP-AVENIR funding to move to the IGFL in early 2016.

2015

Vincent Laudet is the last of the 3 founders to leave the IGFL to take the direction of the Oceanological Observatory of Banyuls-sur-mer. Florence Ruggiero assumes the interim management until the end of the unit's mandate in December 2015. 

2016

Florence Ruggiero is appointed director of the IGFL for the term 2016-2020. She is surrounded by Frédéric Flamant who has a very good knowledge of the history of the IGFL and the ENS site of Lyon as deputy director. Two new team leaders are recruited during her mandate during the 2016 call, Yad Ghavi-Helm, winner of an ATIP-AVENIR and then an ERC StG, and Jonathan Enriquez, winner of an ATIP-Avenir both also receive support from the MRF to start their group. The IGFL continues its successful recruitment momentum! During this period, the IGFL has 14 teams including 5 ERCs:

Aguilaniu: Aging, reproduction and metabolism
Averof: Comparative biology of development and regeneration
Bleicher: Physiopathology of odontoblasts
Enriquez: Development and function of the neuromuscular system
Flamant: Neurodevelopment
Ghavi-Helm: Developmental epigenomics
Goudemand: Biomodeling
Khila: Developmental genomics and evolution
Leulier: Functional genomics of host-gut bacteria interactions
Merabet: Ontogenesis and molecular interactions
Padmanabhan: Molecular and epigenetic control of biological rhythms
Ruggiero: Biology and pathology of extracellular matrices
Volff: Evolutionary genomics of fish
Vanacker: Physiopathology of orphan nuclear receptors
Viriot: Evo-Devo of vertebrate dentition

Florence Ruggiero has worked to create new work spaces, to upgrade the internal platforms, including imaging (overseen by two expert CNRS engineers Marilyne Duffraisse and Marilyne Malbouyres), to optimize interactions between experimenters and rationalize space, to equip them (new confocal on the IGFL imaging technical platform in 2018, Illumina equipment at the IGFL sequencing platform - with the help of our supervisors) and to re-structure the animal houses and animal experimentation rooms - those for aquatic invertebrates, enlargement of the rooms for drosophila and the mouse animal house with the creation of a black room for the Padmanabhan team. Responding to a call for tenders from the ENS of Lyon, the PSI platform expanded at the end of 2017 to be located on 2 sites (IGFL and Monod). In these new premises, the platform includes clean rooms dedicated to work on degraded, delicate or limited quantity DNA available to the local and external scientific community. During this period the IGFL also experienced two departures of team leaders, Hugo Aguilaniu in 2017 and Laurent Viriot in 2019. In 2018, the two candidates selected during a call for tenders for the recruitment of a new team that includes for the first time a sentence encouraging women to apply, do not finally join the unit, the international competition becomes increasingly tough!  

Florence Ruggiero institutes the first IGFL retreat to be organized in May 2018 by the unit's staff. It was essential to put a link between all these new recruited teams and new and old staff. Also at mid-term, while preparing a review for the retreat, it appeared that a brick was missing at the IGFL, obtaining a LABEX/EQUIPEX type project. Florence Ruggiero strongly encourages team leaders to respond to -EX calls for proposals.

First IGFL retreat in Aussois in June 2018 ©JF Metifiot

2019

Florence Ruggiero having announced her intention not to run for a second term at the head of the IGFL, François Leulier joins the management in September as second deputy in order to prepare himself to take over the leadership of the unit for the next term (2021-2025). The ERGO project, in which Frédéric Flamant's team is strongly involved, is the winner of a European H2020 call for proposals.

2020

At the opening of the PIA3 EQUIPEX+ call for proposals, Yad Ghavi-Helm and Jonathan Enriquez, responding to the call launched by Florence Ruggiero, raise their hands and work hard during the first COVID confinement to present an atypical multi-site federating project for an EQUIPEX linking imaging and genomics using spatial transcriptomics approaches. At the end of 2020, the project Spatial-Cell-ID, co-sponsored by the IGFL (Yad Ghavi-Helm and Jonathan Enriquez) and the RDP (Olivier Hamant) and managed by the ENS de Lyon, was funded. 
During this year of transition at the direction, the 3 candidates selected during the 2020 call for proposals for new teams do not integrate the IGFL, the national and international competition is still very strong. It was then decided to adjust our recruitment strategy by launching a series of targeted invitations before our calls for tenders and to add to our call for tenders the public announcement of an installation budget financed by the unit's own resources accumulated thanks to the success of the IGFL teams in European calls for tenders. The effort to recruit new team leaders is maintained. At the end of 2020, another team, that of Kiran Padmanabhan, is a winner of a European H2020 project. This is the REVEAL project for which the team is a partner. 
 

2021

François Leulier is appointed director for the new mandate of the unit extended by one year because of COVID (2021 - 2026). His proposal for a deputy director was not accepted by our supervisory authorities, and following the departure of our research coordinator, Joanne Burden, who has accompanied the various directions of the IGFL project with great skill and finesse since its inception, he is surrounded by an operational management team. This team is made up of Fabienne Rogowsky (administration and finance), Benjamin Gillet (logistics and security) and Jean-Louis Thoumas (technical and scientific infrastructures), as well as a number of task forces chosen from among the team leaders and researchers of the institute. A working group is also being set up to engage our ecological transition. The members of the IGFL respond very positively to these initiatives and are strongly committed to these groups which work in synergy with the laboratory council.

IGFL 2021-2026 Working Groups

Equipment / Store / Living well at the IGFL / Training / Sustainable development / International / Careers / Listening structure / Tech transfer.

In keeping with the historical investment of the IGFL (Florence Ruggiero then Pierre Jurdic) in the management team of the UMS/UAR Biosciences, Samir Merabet, team leader at the IGFL, is appointed director of the UAR Biosciences. A new fish model is welcomed at the IGFL, from the Cichlidae family, thanks to ANR funding obtained by the Goudemand and Ruggiero teams. A dedicated rearing and experimentation space was then set up with the help of the IGFL, the UAR Biosciences and the ENS of Lyon. In order to support its development, the management proposed that the IGFL Sequencing Platform move to new, more spacious premises on the second floor. In the same logic, the Goudemand team, initially on the first floor, will move to the third floor. At the end of 2021, Jean-Nicolas Volff's team stops its activities.

IGFL day in Sainte-Foy-lès-Lyon in June 2021

2022

The administrative service of the unit, helped by many members of the unit, starts the redesign of the intranet site of the unit in order to make our operating procedures more fluid. This is the occasion to thank our administrative and financial manager Fabienne Rogowsky and our webmaster Christelle Forcet and their colleagues for their efficient and vital help in the conduct of our research activities. 

The management and members of the IGFL are working on the integration of Clémence Bernard, winner of our 2022 call for proposals, which is expected by the end of 2023. Jean-Marc Vanacker's team is ending its activities. 3 lab spaces are again available to welcome new teams, a new recruitment dynamic must be initiated. 

2023

The unit is now composed of 10 teams and 3 technical platforms:

Averof: Comparative biology of development and regeneration
Enriquez: Development and function of the neuromuscular system
Flamant: Neurodevelopment
Ghavi-Helm: Developmental epigenomics
Goudemand: Biomodeling
Khila: Developmental genomics and evolution
Leulier: Functional genomics of host-gut bacteria interactions

Merabet: Ontogenesis and molecular interactions

Padmanabhan: Molecular and epigenetic control of biological rhythms
Ruggiero: Biology and pathology of extracellular matrices

Sequencing
Imaging-histology
Experimentation of living organisms

The IGFL is preparing to welcome the new high-resolution microscope of the Equipex+ Spatial-Cell-ID and its sequencing platform is continuing its developments around "nanopore" and "long fragment" sequencing technologies. The first carbon footprint of the unit established by the Sustainable Development WG with the help of the administrative services of the IGFL is presented at the General Assembly. Engaging our ecological transition, together with our supervisors, will be one of the strong objectives for 2023. The team leaders and the SAB of the IGFL are thinking about reorganizing the recruitment of new IGFL groups, it is decided to open a continuous call for tender with pre-evaluation of applications "as they come in" and organization of mini-symposia of recruitment every 6 months in the presence of our SAB.

In March 2023 the "10 years" anniversary symposium of the IGFL was held, initially planned for fall 2022 but delayed due to COVID. Formally our unit was created 16 years ago but our arrival in the new building dates from a little more than 10 years ago. This symposium was therefore an opportunity for us to celebrate this. Let's take this opportunity to congratulate the work of our logistics and security officer, Benjamin Gillet, recently assisted by our bursar and our prevention assistants, accompanied by the services of our host institution, the ENS de Lyon, who have been working every day for more than 10 years to ensure that our main work tool remains in compliance with safety standards, and is always as impeccable and functional as ever, so that we can carry out our missions in a comfortable and quality working environment.

This symposium was a strong scientific moment, of reflection on the science of today and tomorrow, but also of conviviality that we were pleased to celebrate with all those who have contributed and are contributing to the success of the IGFL and who, we have no doubt, will carry its future success.

12 March 2023. François Leulier with the help of Jacques Samarut, Frédéric Flamant, Vincent Laudet and Florence Ruggiero.