As France's leading biocluster, Genopole is an incubator for cutting-edge projects in biotechnology. Located in the city of Évry, just south of Paris, Genopole provides a unique environment for scientists and entrepreneurs seeking to advance research and innovation.

Discover >


Genopole accompanies researchers, postdocs and start-up entrepreneurs through all the phases of their projects to ensure the best possible conditions for business development.

Discover >

Genopole’s citizens

Every day, at Genopole, researchers, entrepreneurs and students cross paths, share ideas and unite forces in a veritable melting pot for innovation.

Discover >


Giving wings to research and empowering employment in our community are cornerstones of Genopole's mission. Catch up on recent scientific advances, the accomplishments of our biotech actors and the events that enliven the biocluster.

Discover >

Innovate with us

Discover >

A tool to digitize organs

Sysfate at Genoscope has combined image analysis and genomics to create MULTILAYER, a tool to digitize biological tissues and organs.

The Sysfate laboratory was created within the Genomics Metabolics unit at Genoscope through a Genopole Atige grant. The lab’s director, Marco Mendoza, and his team have developed MULTILAYER, a method for furnishing spatial digital images of activity in biological tissues. The team took inspiration from image analysis and admixed their expertise in “omics” (genomics, transcriptomics, etc.) to create the tool.

MULTILAYER thus reveals the functional structuration of an organ or tissue.

The method will be of particular interest for developing solutions in molecular diagnostics.

The function of a biological tissue or organ is determined by the activity of its constituent cells, or more precisely by the expression or non-expression of their genes.
Spatial transcriptomics* is a technique for analyzing the expression levels of a large group of genes simultaneously at the scale of a tissue or organ. From a histological section, the technique furnishes a two-dimensional image of gene expression therein, presented as points distributed evenly over the tissue. The functional map of the tissue can represent a thousand genes and several thousand positions, resulting together in millions of analyzable sequences. Such a quantity of data requires specific statistical and bioinformatics methods. To improve upon current methods, Marco Mendoza and his team at the Sysfate lab (Genoscope) have developed MULTILAYER and described its performance in an article published on 7 May 2021 in Cell Systems.

MULTILAYER analyzes a biological section and assigns to each spatial point in the tissue a measurement, called a gexel by the team for its analogousness with the pixels that make up a digital image. A gexel represents the expression of a thousand genes at a point in the tissue. Compared to conventional statistical methods, the novel nature of MULTILAYER is to be found in its analysis of gexels not as independent entities but as a continuity: adjacent gexels showing similar genetic expression profiles have weight in the analysis of any one gexel. Indeed, from a biological standpoint, contiguous cells should have a greater chance of a shared destiny and thus a shared genetic programming. The Sysfate team’s algorithm also mines known information centralized in databases, notably for gene co-expression, which can potentially indicate groups of genes associated with a given function.

MULTILAYER thus “digitizes” tissue into biologically pertinent substructures.

SysFate - Mapping a pancreas cut by Multilalayer
MULTILAYER has identified 6 functional cellular communities (6 colors) in the fabric, including strongly associated with tumor, cancer progression and ability to produce metastases.

In their article, the Sysfate researchers demonstrated MULTILAYER’s ability to identify functional zones from spatial transcriptomics data derived not only from heart tissue sections and a range of tumor tissues (below figure) but also from an entire mouse embryo, which the tool was able to stratify into regions corresponding perfectly to known anatomical structures (opposite figure).

MULTILAYER is freely available as an autonomous computer program:


An algorithm to obtain the functional cards of the organs

By uniting expertise in image analysis and in genomics, the Sysfate team was able to create a first version of an algorithm for the molecular analysis of tissues or organs that, when combined with spatial transcriptomics, may lead to functional maps of all of the organs in the human body. Such a feat would contribute to a better understanding of pathologies and the development of molecular diagnostics in the field of personalized medicine.

  • * Spatial transcriptomics

    Spatial transcriptomics produces spatial maps of gene expression within a tissue or organ. The method is built upon the fixation of groups of oligonucleotide mRNA (a product of gene expression) probes on a slide, upon which a tissue section will be placed.

    The mRNA are analyzed after separation, but a DNA barcode identifying the position of the trapped mRNA enables spatial reconstruction.

  • Reference

    Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer. Cell Systems (2021)

Article posted on 10 June 2021


Latest news

©Lionel Antoni - Plateforme d'irradiation expérimentale du LRGK - Plateforme génopolitaine mutualisée avec les acteurs de la communauté scientifique francilienne

The Experimental Irradiation Platform to serve the Île-de-France scientific community

Genopole is making available to the Île-de-France scientific community an Experimental Irradiation Platform equipped with a state of the art generator

Laina Freyer directrice scientifique, Felome

Felome Launches the Commercialization of Genetic Analyses for Companion Cats

Felome will begin the commercialization of a service offering genetic analyses for companion cats, to reveal their predispositions to over 50 diseases, identify their main physical traits, and their similarities with 14 types of breeds.

Lauréats de la promo 3 du programme Gene.iO - Genopole

Three Gene.iO whiz kids rewarded for their innovations

Three Gene.iO whiz kids, Alga Biologics, Fungu'it and Alt Biotech, rewarded for their innovations. Alga Biologics was among the 35 start-ups included in the French Blue Tech Index. Fungu'it and Alt Biotech, were selected to participate in 212 Founders, a start-up accompaniment and financing program by CDG Invest.

l'équipe iGEM 2023 Evry Paris-Saclay - Médaille d'or et p

A prize and gold for the 2023 Évry Paris-Saclay iGEM team

The international synthetic biology competition iGEM celebrated its 20th anniversary. From across the globe, the event drew more than 7,000 students in 400 teams from 66 countries. Genopole was there, among other actors in synthetic biology, to present the biocluster's advantages at its stand, and support the 17 students of the Évry Paris-Saclay team and their outstanding project, OptoGenEYEsis.

Genopole en mission exploratoire au Japon et en Corée du sud - octobre 2023

An exploratory mission to Japan and South Korea for Genopole

Genopole sent a team to Japan and South Korea to present itself and several of its accompanied businesses to major pharmaceutical corporations, investors and Asian bioclusters curious about biotechnological innovations and open to international partnerships.

Ibisc - Genopole's Laboratory

IBISC – Structure prediction for RNA complexes

passes a milestone in structure prediction for RNA complexes, key players in cell biology.

IBISC: A first predictive tool for the emerging field of bifunctional RNA

IBISC: A first predictive tool for the emerging field of bifunctional RNA

The IBISC laboratory has developed IRSOM2, an unprecedented bioinformatics tool for the prediction of bifunctional RNA, a relatively recently discovered class of RNA showing both an ability to code for proteins and an ability to perform biological roles.

Integrating informatics, structural biology and in vivo exploration for the discovery of new medicines

SABNP & Synsight: discovery of new medicines

SABNP and Synsight have validated an integrated, drug discovery approach uniting informatics, structural biology and in vivo exploration.

Alexis Biton and Paul Carouen - Genopole - visiting the Research Triangle Park (USA) accompanied by 3 Genopole's companies

Genopole strengthens its ties with the Research Triangle Park

From Monday March 20 to Thursday March 24, Genopole's Partnership & Business Development team visited the Research Triangle Park biopark in North Carolina to strengthen scientific and industrial collaborations.

Lambe - Genopole's laboratory

Lambe: Detecting coagulation biomarkers with a natural nanopore

The Lambe laboratory showed proof of concept for a coagulation biomarker detection technology based on a natural nanopore.

Andrew Tolonen's team within the unit of Genomics Metabolics (Genoscope - CEA)

Genoscope: Biomanufacturing with bacteria

A team led by Andrew Tolonen has developed a method to optimize the genetic engineering of Clostridium genus bacteria for biotech applications

l’équipe « Dystrophies musculaires progressives » du laboratoire Généthon

Shining light on a key mechanism of Duchenne muscular dystrophy

A Genethon team has provided new insights on a complex genetic mechanism involved in mitochondrial dysfunction in Duchenne muscular dystrophy.

A trio of genome sites associated with arterial hypertension

A trio of genome sites associated with arterial hypertension

Researchers from the CNRGH and PARCC have identified three loci associated with an increased risk of developing primary hyperaldosteronism, a leading cause of arterial hypertension.

Genoscope - CNS - Genopole's laboratory

The story of the domestic donkey told by its genome

Genoscope participated in the sequencing of the DNA of 250 donkeys in a study revealing the domestication of this species highly contributive to human activities to this day.

Galaxy-SynBioCAD: accelerating the arrival of green chemistry

Galaxy-SynBioCAD: accelerating the arrival of green chemistry

Conceived by the Genomics Metabolics Unit, Galaxy-SynBioCAD accelerates biological design and engineering for the production of next generation chemical compounds.

Equipe Sysfate de l'UMR 8030 - projet T-Fitness

T-FITNESS: Toward empowering CAR-T therapies for solid tumors

The Genopole team SysFate is participating in the international project T-FITNESS. The project, selected by the European Innovation Council, aims to resolve the difficulty of T-cell exhaustion in CAR-T therapies for solid tumors.

Ynsect & Genoscope : Vers la sélection génomique des insectes d’élevage

Toward the genomic selection of farmed insects

France is historically a land of livestock farming. Cows for meat or milk, sheep, pigs, fowl of all sorts; France rears them all. And insects! With its genomic selection project for Tenebrio molitor beetles, the Genopole company Ÿnsect and its biocluster partner, the sequencing center Genoscope, are making France a pioneer in insect farming.

Couverture de la revue Cell Genomics - Le plancton

A feat in the study of planktonic life

A Genoscope research team was part of a pioneering study in environmental genomics. The researchers were able to at least partially reconstitute the genomes of close to 700 eukaryote species.

Logos Istem & Généthon

A two-drug combination to treat limb-girdle muscular dystrophies and cystic fibrosis

The I-Stem and Genethon laboratories have identified a promising drug combination in the setting of three genetic diseases sharing similar molecular mechanisms.

IBISC - IA qui diagnostique et explique grâce à un réseau de neurones

An artificial intelligence to diagnose and explain

The IBISC laboratory has conceived an architecturally-innovative neural network able to provide not only a diagnostic prediction but also a biological explanation.

View all >
With the support from
Région île de France