BRANEpower : bioinformatics tools for omics data

#BRANEpower, our series of bioinformatics tools for network inference, biological graph learning, multi-omics data integration, function prediction etc.

BRANE papers (BRANE: Biologically-Related Apriori Network Estimation or Biologically-Related Adapted Node Embeddings)

• BRANEmf: Integration of Biological Networks for Functional Analysis of Proteins, Bioinformatics, December 2022
• BRANEnet: embedding multilayer networks for omics data integration, BMC Bioinformatics, October 2022
• BRANE Clust: cluster-assisted gene regulatory network inference refinement, IEEE/ACM Transactions on Computational Biology and Bioinformatics, May-June 2018 [doi|preprint|biorxiv|page|code|hal|blog|rnaseq-blog|omic tools|wikipedia]
• BRANE Cut: Biologically-Related A priori Network Enhancement with Graph cuts for Gene Regulatory Network inference, BMC Bioinformatics, 2015 [doi|preprint|biorxiv|page|code|hal|blog|rnaseq-blog|omic tools|wikipedia]
• BRANE Relax: Fast convex optimization for connectivity enforcement in gene regulatory network inference, ICASSP 2015
• BRANE HK (aka BRANE Cone): work in progress

BRANE codes, data & results

• BRANEmf (for matrix factorization)
• BRANEnet (BRANEnet ZENODO repository)
• BRANEcut (BRANE Cut) 
• BRANErelax (BRANErelax)
• BRANEclust (BRANE Clust) 

BRANE Tunes

• BRANE Tunes, songs related to our BRANE bioinformatics tools: Amstel trio: Sacrifice (Michael Nyman), EST Classical: When god created the coffeebreak (Esbjorn Svensson Dan Berglund Magnus Ostrom), Radiohead: On the Beach (Neil Young), M83: Lower your eyelids to die with the sun, Loney Dear: Everything turns to you, Nils Landgren Pat Metheny Michael Brecker: Fragile (Sting), Opeth: Patterns in the Ivy, Archive: End of our days, Petrucciani, Michel: Brazilian like

BRANE Applications

• Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain, Dante Poggi-Parodi, Frédérique Bidard, Aurélie Pirayre, Thomas Portnoy, Corinne Blugeon, Bernhard Seiboth, Christian P. Kubicek, Stéphane Le Crom and Antoine Margeot. Biotechnologies for Biofuels, 2014
• Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30, Aurélie Pirayre, Laurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot, Frédérique Bidard. BMC Genomics, 2020
• Genome-Wide (TSS) Distribution in Three Related Clostridia with Normalized Capp-Switch Sequencing, Rémi Hocq, Surabhi Jagtap, Magali Boutard, Andrew C. Tolonen, Laurent Duval, Aurélie Pirayre, Nicolas Lopes Ferreira, François Wasels. Microbiology Spectrum, 2022.

BRANE People, first generation

• Aurélie Chataignon-Pirayre
• Frédérique Bidard-Michelot
• Camille Couprie
• Antoine Margeot
  
• Jean-Christophe Pesquet
• Laurent Duval

BRANE People, second generation

• Surabhi Jagtap
• Fragkiskos Malliaros

BRANE Mentions & awards

• Wikipedia: List of RNA-Seq bioinformatics tools
• OMIC tools: BRANE Cut, BRANE Clust
• RNA-seq blog (twitter): BRANE Cut, BRANE Clust
• IPFEN 2018 Yves Chauvin PhD prize is awarded to Aurélie Pirayre, for IFPEN's first thesis on bioinformatics (graph optimization for gene networks). A short description is available in ‘‘BRANE Power’’: of genes and algorithms, an alliance for green chemistry. along with Three questions to Aurélie Pirayre, IFPEN's 2018 Yves Chauvin prize-winner. BRANE POWER stroke again!

Aurélie Pirayre, Grégoire Allaire, Didier Houssin, Pierre-Henri Bigeard, Eric Heintzé

Globally, we call the above BRANE POWER. Series of optimization, data science and machine methodologies combined with biologically-related a-priori for genomic/transcriptomic data analysis, gene network inference, omics data integration, downstream taks (): BRANE Cut, BRANE Clust, BRANE Relax, BRANEexp, BRANEnet, BRANEmf and more to come. They are being developed at IFP Energies nouvelles, see The development of "omic" technologies: gene expression, digital style, or bioinformatics serving more sustainable chemistry.

BRANE: Biologically-related A priori Network Enhancement for gene regulation network

We are developing a suite of bioinformatics tools based on graphs and optimization, dedicated to -omics gene expression data (from RNA-seq or microarrays). They are meant for Gene Regulatory Network (GRN) inference and genomic data analysis. Genomic and transcription data is complicated. Especially, gene-condition and transcription factor-target gene ratios are not favorable. Data counts are even biased, noisy and variable.

There exists therefore a large number of solutions. One needs to introduce a priori (co-regulation,  co-expression, clustering, modularity, sparsity) to improve the graph structure, for instance around modules, or using gene clustering. We use biologically-plausible assumptions, and propose a couple of Biologically-Related A priori Network Enhancement (BRANE) techniques. They can be used in post-processing of other network inferences techniques like CLR (Context Likelihood of Relatedness) or GENIE3 (GEne Network Inference with Ensemble of trees). They have been successfully tested on DREAM4 and DREAM5 challenges, Escherichia coli, Trichoderma reesei. Graph inference in the inferred Escherichia coli network is evaluated using the STRING database. Clustering is compared to SIMONE, WGCNA, X-means and RegulonDB.

The BRANE approach notably uses image processing and computer vision algorithms (dual thresholding, proximal methods, graph cuts, maximization-majorization, variable metrics), as noted in Enhancing gene regulatory network inference through data integration with markov random fields, Banf & Rhee, Nature Scientific Reports, 2017.

Borrowing concepts from the field of Computer Vision to infer gene regulatory networks in prokaryotes has recently gained some attention

The related results are detailed in Aurélie Pirayre PhD Thesis (Defense: Monday 3 July 2017): Reconstruction and clustering with graph optimization and priors on gene networks and images (PhD manuscript and slides). 

A note in passing: on Gilles Azzoni, wine producer (Le Raisin et l'Ange), who inspired our BRANE tools with his biodynamic Bran wines.