Journal Papers

• Aurélie Pirayre, Camille Couprie, Laurent Duval and Jean-Christophe Pesquet
• "BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement"
• In IEEE/ACM Transactions on Computational Biology and Bioinformatics , March 2017
• [ Article | Preprint | biorxiv | HAL | RNA-seq blog | OMIC tools | Software ]

• Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval and Jean-Christophe Pesquet
• "BRANE Cut: Biologically-Related Apriori Network Enhancement with Graph cuts for Gene Regulatory Network Inference"
• In BMC Bioinformatics , 2015, 16:369
• [ Article | Preprint | biorxiv | HAL | RNA-seq blog | OMIC tool | Software ]

• Dante Poggi-Parodi, Frédérique Bidard, Aurélie Pirayre, Thomas Portnoy, Corinne Blugeon, Bernhard Seiboth, Christian P. Kubicek, Stéphane Le Crom and Antoine Margeot
• "Kinetic transcriptome reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain"
• In Biotechnology for Biofuels , 2014, 7:173
• [ Article ]

Conference Papers

• Aurélie Pirayre, Yuling Zheng, Laurent Duval and Jean-Christophe Pesquet
• "HOGMep: variational bayes and higher-order graphical models applied to joint image recovery and segmentation"
• Accepted for the International Conference on Image Processing (ICIP) , September 2017, Beijing, China
• [ Preprint ]

• Aurélie Pirayre, Dimitri Ivanoff, Etienne Jourdier, Antoine Margeot, Laurent Duval and Frédérique Bidard
• "Growing Trichoderma reesei on a mix of carbon sources reveals links between development and cellulase production"
• Presented at the Fungal Genetics Conference (FGC) , March 2017, Pacific Grove, USA

• Laurent Duval, Aurélie Pirayre, Xiaoran Ning and Ivan W. Selesnick
• "Suppression de ligne de base et débruitage de chromatogrammes par pénalisation asymétrique de positivité et dérivées parcimonieuses"
• Presented at the 25e colloque GRETSI , September 2015, Lyon, France
• [ Preprint | Poster ]

• Aurélie Pirayre, Camille Couprie, Laurent Duval and Jean-Christophe Pesquet
• "Graph Inference Enhancement with Clustering: Application to Gene Regulatory Network Reconstruction"
• Presented at the European Signal Processing Conference (EUSIPCO) , September 2015, Nice, France
• [ Preprint | Article | Poster ]

• Aurélie Pirayre, Camille Couprie, Laurent Duval and Jean-Christophe Pesquet
• "Fast Convex Optimization for Connectivity Enforcement for Gene Regulatory Network Inference"
• Presented at the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) , 19-24 April 2015, Brisbane, Australia
• [ Preprint | Article | Poster ]

• Aurélie Pirayre, Camille Couprie, Laurent Duval and Jean-Christophe Pesquet
• "Discrete vs Continuous Optimization for Gene Regulatory Network Inference"
• Presented at the International Biomedical and Astronomical Signal Processing (BASP) Worshop , 25-30 January 2015, Switzerland
• [ Preprint | Poster ]

Others oral communications

• Aurélie Pirayre, Camille Couprie, Laurent Duval and Jean-Christophe Pesquet
• "Gene Regulatory Network inference refinement using clustering"
• Presented at the GdR ISIS, Apprentissage et/ou traitement du signal et des images sur graphes , June 2016, Paris, France

• Aurélie Pirayre, Dimitri Ivanoff, Etienne Jourdier, Antoine Margeot, Laurent Duval and Frédérique Bidard
• "Growing Trichoderma reesei on a mix of carbon sources reveals links between development and cellulase production"
• Presented at the 1st Trichoderma Workshop , April 2016, Paris, France

• Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, and Jean-Christophe Pesquet
• "BRANE Cut: integrating biological a priori in Gene Regulatory Network inference with Graph cuts"
• Presented at Statomique , November 2015, Paris, France

• Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, and Jean-Christophe Pesquet
• "Incorporating structural a priori in Gene Regulatory Network inference using Graph cuts"
• Presented at the International Workshop on Algorithmics, Bioinformatics and Statistics for NGS data analysis (ABS4NGS) , June 2015, Paris, France

• Aurélie Pirayre, Camille Couprie, Laurent Duval, and Jean-Christophe Pesquet
• "Graph enhancement via clustering: application to Gene Regulatory Network inference"
• Presented at the GdR MaDICS, One-day Worshop on Emerging Trends in Clustering , June 2015, Orléans, France

• Aurélie Pirayre, Camille Couprie, Laurent Duval, Frédérique Bidard and Jean-Christophe Pesquet
• "Incorporating structural a priori in Gene Regulatory Network Inference using Graph cuts"
• Presented at the European Student Council Symposium 2014 (ESCS'14), Strasbourg, France
• [ Poster, Awarded 2nd best poster ]