CBiB

Address

146 Rue Léo Saignat 33076 Bordeaux France
44.824860, -0.608450

Attachment

Structure
Unit

Outlinks

homepage: [long name is missing in model]
legacy catalog: Try opening in it

Scientific Leaders

Nikolski Macha

Technical Leaders

Groppi Alexis

Certificats

Label IBiSA
ISO 9001
CNOC (INRA)
NF X50-900

Team

Groppi Alexis
Dartigues Benjamin
Barré Aurélien
Nikolski Macha

Data

Linda

biotoolsID: xeml-lab
homepage: https://services.cbib.u-bordeaux.fr/linda/
last_update: Sept. 27, 2022, 2:48 p.m.
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Description

The web application Linda offers a complete tool for entering and managing metadata associated with a phenotyping experiment on plants. It thus makes it possible to intuitively describe experimental related information such as, for example, the experimental design, the growth protocols, the environmental variable measurements, etc. Linda is coupled with a database that stores this information in a structured manneer using oriented graphs. This database uses reference ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type of experiment such as the Minimal Information About Plant Phenotyping Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the FAIR principles (Findable Accessible Interoperable Reusable) and oon the other hand, by exporting this metadata relating to the experiment in tabulated formats or formatted for submission in the international databases (ISA-tab).

Mix

biotoolsID: mix
homepage: https://github.com/cbib/MIX
last_update: Nov. 25, 2024, 2:18 p.m.
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Description

Tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

Molligen

biotoolsID: molligen
homepage: https://services.cbib.u-bordeaux.fr/molligen4/
last_update: Nov. 24, 2024, 3:35 p.m.
more: ...

Description

Database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes. It provides annotated sequence data and analysis for 72 genomes belonging to 51 species. The database provides genome and genetic element pages, homology relationship defined by various methods, pre-computed statistics, metabolic pathways, and a huge collection of tools for exploring and comparing genomes.

Tango

biotoolsID: tango
homepage: http://tango.crg.es/
last_update: Dec. 10, 2018, 12:58 p.m.
more: ...

Description

A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. The model used here, is designed to predict cross-beta aggregation in peptides and denatured proteins and consists of a phase-space encompassing the random coil and 4 possible structural states: beta-turn, alpha-helix, beta-sheet aggregation and alpha-helical aggregation.

xHeinz

biotoolsID: xheinz
homepage: https://github.com/ls-cwi/xheinz
last_update: March 12, 2019, 2:52 p.m.
more: ...

Description

Software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions. Active subnetwork modules are sets of genes, one for each species, which: - induce a connected subnetwork in a species-specific interaction network, - show overall differential behavior, and - contain a large number of orthologous genes.

Domains of activity

Biologie
Biomédical
Agro-alimentaire
Environnement

Description of expertise domains

The Bordeaux Bioinformatics Centre (CBiB) is a technology platform specialized in the analysis of high-throughput biological data (genomics, transcriptomics, proteomics, metabolomics, imaging). With strong expertise and the integration of advanced technologies, including artificial intelligence, CBiB supports academic and industrial partners in extracting value from complex data. Its services cover the full data lifecycle, supported by high-performance infrastructures and a multidisciplinary team in bioinformatics.

Keywords

Artificial Intelligence
cancer
Image analysis
spatial transcriptomics
Metabolomics
proteomics
Integration of heterogeneous data
Single-Cell Analysis
Comparative genomics
NGS Sequencing Data Analysis

Analyses Single Cell RNA-seq (ScRNA-seq) avec R

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DifficultyLevel: Intermediate
OpenTo: Everyone
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Description

Cette formation introduira notamment la librairie Seurat permettant la manipulation et l'analyse de données Single Cell RNA-seq ainsi que la visualisation des résultats d'analyse

- Rappels des concepts du séquençage Single Cell RNA-seq
- Importation des données Single Cell dans R
- Intégration de données Single Cell multiples
- Quality Check et pré-traitement des données
- Normalisation de données
- Identification de marqueurs
- Clustering et assignation cellulaire
- Analyse différentielle des groupes cellulaires
- Savoir intégrer les données de spatialisation
- Savoir intégrer les données de trajectoire
- Savoir intégrer les données de communication cellulaire
- Savoir intégrer les données d'épigénétique (ATAC-seq)

Analyses NGS avec R

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Description

Cette formation introduira les paquetages Bioconductor permettant l'analyse de données issues du séquençage nouvelle génération.

- Rappels des concepts du séquençage NGS
- Les outils d'annotation et de conversion d'identifiants
- L'analyse des reads et du résultat d'alignement
- L'analyse d'expression différentielle en RNA-seq
- Les techniques d'enrichissement
- Les outils de visualisation pour les NGS

La fin du stage (2 h) sera consacrée à un atelier pédagogique d'analyse et de réflexion sur les données apportées par les stagiaires.

Analyses Single Cell RNA-seq (ScRNA-seq) avec R

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Description

Langage R : introduction

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Description

Cette formation introduira le langage R et les techniques de fouille et de visualisation de données.

- Installation et configuration de R
- Notions et commandes essentielles (variables, fonctions...)
- Les formats de fichiers, la lecture et l'écriture de données tabulées
- Les outils de manipulation et de transformation de grands tableaux
- Les constructions modernes pour la création de graphiques

Analyses NGS avec R

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Description

Analyses Single Cell RNA-seq (ScRNA-seq) avec R

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Description

Langage R : introduction

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Description

None None. None, None.

Genetic and epigenetic interplay allows rapid transgenerational adaptation to metal pollution in zebrafish Pierron Fabien, Heroin Débora, Daffe Guillemine, Daramy Flore, Barré Aurélien, Bouchez Olivier, Romero-Ramirez Alicia, Gonzalez Patrice, Nikolski Macha. 2022, Environmental Epigenetics. 10.1093/eep/dvac022

DeepSpot: A deep neural network for RNA spot enhancement in single-molecule fluorescence in-situ hybridization microscopy images Bouilhol Emmanuel, Savulescu Anca F., Lefevre Edgar, Dartigues Benjamin, Brackin Robyn, Nikolski Macha. 2022, Biological Imaging. 10.1017/S2633903X22000034

VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data Sukhorukov Grigorii, Khalili Maryam, Gascuel Olivier, Candresse Thierry, Marais-Colombel Armelle, Nikolski Macha. 2022, Frontiers in Bioinformatics. 10.3389/fbinf.2022.867111

Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images Lefevre Edgar, Bouilhol Emmanuel, Chauvière Antoine, Souleyreau Wilfried, Derieppe Marie-Alix, Trotier Aurélien J., Miraux Sylvain, Bikfalvi Andreas, Ribot Emeline J., Nikolski Macha. 2022, Frontiers in Bioinformatics. 10.3389/fbinf.2022.999700

Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis Guyon Joris, Fernandez‐Moncada Ignacio, Larrieu Claire M, Bouchez Cyrielle L, Pagano Zottola Antonio C, Galvis Johanna, Chouleur Tiffanie, Burban Audrey, Joseph Kevin, Ravi Vidhya M, Espedal Heidi, Røsland Gro Vatne, Daher Boutaina, Barre Aurélien, Dartigues Benjamin, Karkar Slim, Rudewicz Justine, Romero‐Garmendia Irati, Klink Barbara, Grützmann Konrad, Derieppe Marie‐Alix, Molinié Thibaut, Obad Nina, Léon Céline, Seano Giorgio, Miletic Hrvoje, Heiland Dieter Henrik, Marsicano Giovanni, Nikolski Macha, Bjerkvig Rolf, Bikfalvi Andreas, Daubon Thomas. 2022, EMBO Molecular Medicine. 10.15252/emmm.202115343

Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation Pierron Fabien, Daffe Guillemine, Daramy Flore, Heroin Débora, Barré Aurélien, Bouchez Olivier, Clérendeau Christelle, Romero-Ramirez Alicia, Nikolski Macha. 2023, Journal of Hazardous Materials. 10.1016/j.jhazmat.2023.131579

Sex-specific DNA methylation and transcription of zbtb38 and effects of gene–environment interactions on its natural antisense transcript in zebrafish Pierron Fabien, Daramy Flore, Heroin Débora, Daffe Guillemine, Barré Aurélien, Bouchez Olivier, Nikolski Macha. 2023, Epigenetics. 10.1080/15592294.2023.2260963

Synthesis of Flavonol-Bearing Probes for Chemoproteomic and Bioinformatic Analyses of Asteraceae Petals in Search of Novel Flavonoid Enzymes Kempf Karl, Kempf Oxana, Capello Yoan, Molitor Christian, Lescoat Claire, Melhem Rana, Chaignepain Stéphane, Génot Elisabeth, Groppi Alexis, Nikolski Macha, Halbwirth Heidi, Deffieux Denis, Quideau Stéphane. 2023, International Journal of Molecular Sciences. 10.3390/ijms24119724

SalienceNet: An Unsupervised Image-to-Image Translation Method for Nuclei Saliency Enhancement in Microscopy Images Bouilhol Emmanuel, Lefevre Edgar, Barry Thierno, Levet Florian, Beghin Anne, Viasnoff Virgile, Galindo Xareni, Galland Rémi, Sibarita Jean-Baptiste, Nikolski Macha. 2023, Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies. 10.5220/0011623500003414

Effects of Lumacaftor-Ivacaftor on Airway Microbiota-Mycobiota and Inflammation in Patients with Cystic Fibrosis Appear To Be Linked to Pseudomonas aeruginosa Chronic Colonization Enaud Raphael, Lussac-Sorton Florian, Charpentier Elena, Velo-Suárez Lourdes, Guiraud Jennifer, Bui Stéphanie, Fayon Michael, Schaeverbeke Thierry, Nikolski Macha, the LumIvaBiota Study Group, Burgel Pierre-Régis, Héry-Arnaud Geneviève, Delhaes Laurence. 2023, Microbiology Spectrum. 10.1128/spectrum.02251-22

Systemic Convergent Multitarget Interactions of Plant Polyphenols Revealed by Affinity-Based Protein Profiling of Bone Cells Using C-Glucosidic Vescal(ag)in-Bearing Chemoproteomic Probes Kempf Karl, Capello Yoan, Melhem Rana, Lescoat Claire, Kempf Oxana, Cornu Anaëlle, Fremaux Isabelle, Chaignepain Stéphane, Groppi Alexis, Nikolski Macha, Deffieux Denis, Génot Elisabeth, Quideau Stéphane. 2023, ACS Chemical Biology. 10.1021/acschembio.3c00440

Roadmap for a European cancer data management and precision medicine infrastructure Nikolski Macha, Hovig Eivind, Al-Shahrour Fatima, Blomberg Niklas, Scollen Serena, Valencia Alfonso, Saunders Gary. 2024, Nature Cancer. 10.1038/s43018-023-00717-6

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data Galvis Johanna, Guyon Joris, Dartigues Benjamin, Hecht Helge, Grüning Björn, Specque Florian, Soueidan Hayssam, Karkar Slim, Daubon Thomas, Nikolski Macha. 2024, Bioinformatics. 10.1093/bioinformatics/btae282

Exploiting metabolic vulnerability in glioblastoma using a brain-penetrant drug with a safe profile Burban Audrey, Tessier Cloe, Larroquette Mathieu, Guyon Joris, Lubiato Cloe, Pinglaut Mathis, Toujas Maxime, Galvis Johanna, Dartigues Benjamin, Georget Emmanuelle, Luchman H Artee, Weiss Samuel, Cappellen David, Nicot Nathalie, Klink Barbara, Nikolski Macha, Brisson Lucie, Mathivet Thomas, Bikfalvi Andreas, Daubon Thomas, Sharanek Ahmad. 2025, EMBO Molecular Medicine. 10.1038/s44321-025-00195-6

THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1 Giraud Julie, Chalopin Domitille, Ramel Eloïse, Boyer Thomas, Zouine Atika, Derieppe Marie-Alix, Larmonier Nicolas, Adotevi Olivier, Le Bail Brigitte, Blanc Jean-Frédéric, Laurent Christophe, Chiche Laurence, Derive Marc, Nikolski Macha, Saleh Maya. 2024, Cell Reports. 10.1016/j.celrep.2024.113773

CellsFromSpace: a fast, accurate, and reference-free tool to deconvolve and annotate spatially distributed omics data Thuilliez Corentin, Moquin-Beaudry Gaël, Khneisser Pierre, Marques Da Costa Maria Eugenia, Karkar Slim, Boudhouche Hanane, Drubay Damien, Audinot Baptiste, Geoerger Birgit, Scoazec Jean-Yves, Gaspar Nathalie, Marchais Antonin. 2024, Bioinformatics Advances. 10.1093/bioadv/vbae081

Mobilization of an ICEclc-Like Element as a Potential Mechanism for the Spread of IMP-13 Carbapenemase in Pseudomonas aeruginosa Bientz Léa, Guyet Ulysse, Guiraud Jennifer, Metifiot Mathieu, Moulieras Mikeldi, Aillerie Sabine, Coulange-Mayonnove Laure, Boureima-Abdou Bachir, Groppi Alexis, Nikolski Macha, Bébéar Cécile, Pereyre Sabine, Dubois Véronique. 2025, Journal of Global Antimicrobial Resistance. 10.1016/j.jgar.2024.12.006

TrialMatchAI: An End-to-End AI-powered Clinical Trial Recommendation System to Streamline Patient-to-Trial Matching Abdallah Majd, Nakken Sigve, Bierkens Mariska, Galvis Johanna, Groppi Alexis, Karkar Slim, Meiqari Lana, Rujano Maria Alexandra, Canham Steve, Dienstmann Rodrigo, Fijneman Remond, Hovig Eivind, Meijer Gerrit, Nikolski Macha. 2025, None. 10.48550/arXiv.2505.08508

Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning Pham Nguyen-Phuong, Gingras Hélène, Godin Chantal, Feng Jie, Groppi Alexis, Nikolski Macha, Leprohon Philippe, Ouellette Marc. 2024, mBio. 10.1128/mbio.01360-24

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