About us
The BionomeeX journey originated from Gabriel Krouk's vision—a biologist deeply intrigued by the potential synergy between mathematics, AI, and biology. Post-doctorate, Gabriel collaborated with mathematician André Mas and AI researcher Clément Carré, publishing numerous scientific papers. Together, they crafted FRANK, a gene regulatory network simulation engine (DOI: 10.1038/s41540-017-0019-y) Enabling the simulation of large-scale gene networks with in vivo characteristics.
Driven by their collective passion, they founded BionomeeX, aiming to advance our understanding of intricate biological and environmental systems. Through computational biology, interdisciplinary collaborations, and cutting-edge technologies, Now BionomeeX explore bioinformatics, molecular genetics, and systems biology. Our mission spans diverse disciplines in life sciences, including comparative genomics, single-cell analysis, microbiology and enviromental studies.
At BionomeeX, we're committed to open-access publications and collaborative research, pushing the boundaries of discovery in biological research.
After two years of intense work, BionomeeX now offers two highly sophisticated data analysis technologies, as well as high-performance results processing software.
Indeed, the model developed in genomics (2D GWAS), has enabled us to obtain a significant quantity of results while considerably shortening the process time of the GWAS technology in order to associate genetic anomalies with specific traits or diseases. This breakthrough in genomics aids in the fields of genetics and cell biology. Furthermore, the development of NEO software has improved the prediction of phenotypes resulting from genomic analysis, This new technologic advancement provides accurate predictions at a reduced cost and analysis time.
In addition, our commitment to understanding complex systems, inspired us to create an artificial intelligence model essentially applied to biology and environment. This innovation automates, under human control and validation, the detection of target biological profiles available from medical imaging to microscopy or field data.
In the upcoming months, we eagerly anticipate unveiling novel software applications, showcasing diverse research themes in collaboration with our partners.
Concurrently, our focus remains on broadening our expertise to evolve and refine our AI tools for future advancements. Our team is committed to integrating mathematics and artificial intelligence to amplify and facilitate human expertise. We believe this convergence will drive a revolutionary transformation in science, advancing domains such as biomedicine, research in biology and ecoevolution.
We actively engage in seminars, symposiums, and collaborations to advance the frontiers of bioscience. In essence, the BionoTeam embodies BionomeeX's unwavering commitment and adopts a multidisciplinary approach aimed at transforming the landscape of life sciences through innovative AI tools and revolutionary methodologies, paving the way for groundbreaking discoveries and advancements.
Challenging lifetime
A Start fraught with Challenges
A journey marked by challenges: from its inception, BionomeeX encountered several obstacles. Our team, stemming from the scientific research realm, is keenly aware of the intricacies and expectations within this field. That's why our researchers have committed themselves to supporting fellow researchers in the fields of medicine, biology, and environmental sciences by integrating artificial intelligence through partnerships with public laboratories.
Bridging Worlds
The prospect of collaborating with the public sector elicited both allure and apprehension. Nevertheless, we persisted. Firmly believing that the fusion of artificial intelligence and public science was the way forward, we overcame these initial hurdles with unwavering determination. Today, we take pride in collaborating closely with several trusted and prestigious partners, both from the public (CNRS & INRAE) and private sectors, to jointly explore AI solutions to enhance scientific research.
Our projects and collaborations
CBGP NGS-OLICIT
In public collaboration with the CBGP team of
- Jean-Yves Rasplus & Astrid Cruaud.
ANR project aimed at preventing the impact of pests on citrus and olive crops by detecting and establishing relationships between the pests and their parasites.
BionomeeX's role is to develop an artificial intelligence for the detection and classification steps, as well as provide support in scientific deliberations.
Entomology: Small Insect Detection and Classification
In public collaboration with the CBGP team of
- Jean-Yves Rasplus & Astrid Cruaud.
Research project to test the feasibility of detecting and classifying small insects using artificial intelligence. This project is conducted using HitLoop, our internal AI toolbox.
Dendrite explorer
In public collaboration with
- the Eric Hosy CNRS team.
Bionomeex developped an application which automatize the detection of spines and generate automatic skeletons for dendrites.
Ladybugs CBGP
In public collaboration with
- CBGP team of Arnaud Estoup.
BionomeeX has launched a collaborative project with CBGP, led by Arnaud Estoup, to undertake an intriguing investigation into the geographic distribution of ladybug color morphs.
Our primary objective is to ascertain whether color variation is governed by distinct genetic markers, environmental temperatures and/or gender.
HITLOOP
In-house developed software.
BionomeeX has developed Hitloop, an innovative toolbox that revolutionizes the classification and analysis of imaging data through AI-powered methods.
Hitloop streamlines the data labeling process by allowing users to import their own data and build a powerful model with a small portion of it.
Simulation of shading and radiance.
In collaboration with
- Davele.
BionomeeX has designed a shading simulation alongside direct and indirect radiance to support Davele's research in agro-photovoltaics.
ANR ULTIM
In public collaboration with
- Laurent Nussaume of CEA.
BionomeeX collaborates as a partner in the Ultim ANR project.
Ultim project is a PRCE supported by ANR, led by CEA Cadarache (Dr. Laurent Nussaume).
BionomeeX uses advanced image analysis powered by deep learning to find and track nuclei, then locate transcription sites within them.
RNA-SEQ
In public collaboration with
- Marie Barberon from the University of Geneva.
BionomeeX developped a RNA-Seq software that involved applying differentiated treatments to RNA, requiring the analysis of large databases of RNA sequences.
Luciol
In-house developed software
To complement the NEXT GEN GWAS, our researchers developed Luciol.
Specially designed to navigate billions of epistatic interactions, Luciol stands as a meticulously crafted cutting-edge software to decode the complexities of epistatic interactions.
Bird protection by AI for Wind Farms
In collaboration with
- BioDivWind
BionomeeX co-developped an AI solution with Klanik for BioDivWind to detect protected birds around wind farms.
Creation of BionomeeX
BionomeeX was created through collaboration and innovation projects.
With their combined experience and expertise, the team focused their efforts on supporting research in biology, medicine, and ecology.
Super Resolution Microscopy Enhancement
In public collaboration with
- CNRS team of Eric Hosy
AI algorithm developed in collaboration with CNRS researchers to enhance the accuracy of Single-Particle Tracking Photoactivated Localization Microscopy (SptPALM). This algorithm enables the recovery of particle tracks three times longer than those achieved with high-power lasers, using very low laser conditions.
DEEPIRON
In public collaboration with
- IPSiM team of CNRS
Software for detection and classification of iron concentration in plant cells of the first stage (cotyledons).
Next Gen Gwas
Research thesis
Our three founders worked on an ambitious project: a thesis on NEXT GEN GWAS (NGG).
NGG offers a solution to the 'missing heritability' problem of first-generation studies, allowing for efficient decoding of billions of genetic interactions in genomic analysis.
The fruitful encounter of 3 researchers
Before giving birth to BionomeeX, three researchers from the world of public research met and collaborated on various research projects. Their paths crossed in the hallways of laboratories, driven by a passion to enhance scientific research.
Motivated by their desire to push the boundaries of knowledge, these researchers pooled their skills and innovative ideas to bring ambitious projects to life.
Our partners & collaborations
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