Computation biology and Bioinformatics lab in Bordeaux

TrialMatchAI: Harnessing Large Language Models (LLMs) to Match Cancer Patients with Molecularly-driven Clinical Trials – Part of the European Open Science Cloud for Cancer Project

Introduction In the fast-growing landscape of cancer treatment, the paradigm is shifting towards personalized medicine—a tailored approach that recognizes the unique genetic and clinical characteristics of cancer patients. At the core of this paradigm shift are precision clinical trials that drive advancements in personalized cancer therapeutics. By matching patients

Projects

LncRNA expression during cell differentiation

Studying cell differentiation has been revolutionized by the advent of single cell technologies. Moving beyond a stepwise view, we now depict a continuum process containing a range of intermediate cell states expressing different transcriptomic programs. Up to now, the annotation and understanding of these intermediate states mostly relied on protein-coding

Open Positions

Stage M2: Regulation of the suppressive function of myeloid cells by long noncoding RNAs in cancer.

We are looking for a highly motivated M2 student willing to explore how lncRNAs regulate the acquisition of functions and cell differentiation process using temporal transcriptomic data.

Seminars

25/04 Florian Mueller : Exploring spatial transcriptional regulation by quantitative imaging

Integrated quantitative imaging analysis approaches to study sub-cellular RNA localization and its link with translation. Spatial transcriptomics data analysis will be covered too

Seminars

14/03 Human and viral genomics of infections

In this talk Vincent Pedergnana will present results from his research on hepatitis C virus and dengue virus using novel biostatistical approaches.

Seminars

21/02 Professor Daniel Gautheret : RNA discovery in tumor samples through k-mer analysis

Orateur : Daniel Gautheret, Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Sud, Orsay Lieu : Centre de Génomique Fonctionnelle (salle des conférences, 1ème étage) Titre: "RNA discovery in tumor samples through k-mer analysis" Abstract: I will present the use of k-mer tools for reference-free analysis of RNA-seq samples. Applying

Seminars

24/01 Antonin Marchais : Spatial characterization of the immune infiltrate in Osteosarcoma

In this seminar, Antonin MARCHAIS from the Pediatric Precision Medicine and Experimental Therapeutics at Institut Gustave Roussy will present his work on spatial organization of infiltrate in Osteosarcoma at the Computational Biology and Bioinformatics Lab in Bordeaux

Seminars

29/11 Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

Seminar by Laurent Jacob (CNRS Lyon) "Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks"

Seminars

8/11 - Fridolin Gross: Predicting microRNA targets using a biochemical model combined with machine learning

In this seminar Fridolin Gross will present his work on predicting microRNA targets using a biochemical model combined with machine learning

3rd poster prize at 9th Immunotherapy of Cancer Conference

Domitille Chalopin received the 3rd poster prize at the 9th Immunotherapy of Cancer Conference (ITOC, September 22 to 24, 2022).

Machine Learning for antimicrobial resistance (AMR) prediction

Ulysse Guyet will be giving a talk titled "ARSENAL: Antimicrobial ReSistance prEdictioN by mAchine Learning approach" at the ML Microbial Genomics workshop on Friday 23/09.

Seminars

31/05 - Kateryna Makova: Explaining and predicting disease occurrence from omics data

In this seminar, Pr. Kateryna Makova from Penn State University will present her work on the prediction of disease occurrence from omics data at the Computational Biology and Bioinformatics Lab in Bordeaux

Publications

Deep Learning for automatic signal enhancement in biological imaging

Deep Learning for mRNA spot enhancement in fluorescent microscopy FISH images

Projects

Exploiting innate immunity of hepatocellular carcinoma to improve patients treatment

Analysis of HCC tumour etiology based on multi-omic datasets including scRNAseq, spatial scRNAseq, bulk RNAseq and 16S microbiome sequencing

Illsutration of a cybernetic antibiotic pill

Projects

Antimicrobial resistance prediction by machine learning approach

AI method for predicting the minimum inhibitory concentration (MIC) of several antibiotics for antimicrobial resistance (AMR)

Projects

Bioinformatics for the study of metabolism in glioblastoma

Development of omics data integration methods to elucidate the GBM invasiveness

Projects

Unsupervised segmentation of nuclei in fluorescence microscopy images using Deep Learning

Development of unsupervised Deep Learning methods for segmentation of liver spheroids acquired with the soSPIM in 3D and prediction of temporal phenotypes of spheroids

Publications

Population genomics of apricots unravels domestication history and adaptive events

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent

Projects

Tumoral heterogeneity and multi-omics data integration

Tumour heterogeneity analysis by deconvolution and multi-omic data integration to elucidate cancer phenotypes

Team

À propos de l'équipe de bio-informatique et de biologie computationelle de Bordeaux

Permettre la convergence entre "l'imagerie microscopique" et les "omiques" à travers la biologie computationelle

Seminars

12/04 - Samuel Chaffron (Tara Oceans) : Les Modèles De Réseau De Plancton

Présentation de SAMUEL CHAFFRON au Computational Biology and Bioinformatics Lab de bordeaux sur la communauté microbienne dans l'océan mondial

Seminars

22/03 - Laurent Tichit (IMM) : Random Walk with Restart on Multilayer Biological Networks

In this seminar, Dr. Laurent Tichit from Université D’aix-Marseille will present his work on random walk with restart on multilayer biological networks at Computational Biology and Bioinformatics Lab in Bordeaux

Team

Lab Publications

List of our recent publications

Seminars

01/03 - Emilien Peltier (ISVV) : Inheritance, Phenotypic Variation, And Missing Heritability Hidden Behind The Mitochondrial Genome

Seminars

18/01 - Clémence Frioux (PLEIADE) : Modélisation discrète du métabolisme, des organismes individuels aux écosystèmes microbiens

In this seminar, Clémence FRIOUX from the INRIA research team PLEIADE will present her work on Discrete modeling of metabolism, from individual organisms to microbial ecosystems at the Computational Biology and Bioinformatics Lab in Bordeaux

CB&B