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Section: Software
PepLine
Participants : Jérôme Garin, Alain Viari [EPI, Contact, alain.viari@inria.fr] .
Pipeline for the high-throughput analysis of proteomic data.
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
- Partial Enumeration of Traces
- De-novo calling alternative splicing events from RNA-seq data
- Efficient bubble and/or cycle enumeration in directed/undirected graphs
- Simulating RNA-seq experiments
- Chimeric Transcripts may be Translated
- Transcriptomics of symbiosis in the Asobara tabida-Wolbachia association
- MicroRNA predictor
- Genomics of symbiosis
- Representation and curation of metabolic data: UniPathway, Rhea and MNX
- Annotation of the proteins of Angomonas deanei and Strigomonas culicis
- Finding candidate genes for orphan enzymes
- Metabolic cooperation of symbionts and their host trypanosomatids
- Structural and dynamical analysis of biological networks
- Network distance analysis
- Information spreading in dynamic graphs
- Metabolic network comparison
- Core and periphery of metabolic networks
- Metabolic stories
- Minimal precursor sets
- Minimum ratio cover of matrix columns by extreme rays of its induced cone
- Optimal flux spaces of genome-scale stoichiometric models
- Lateral gene transfer as a support for the tree of life
- Comparative approximability of hybridization number and directed feedback vertex set
- Influence of symbionts on antagonistic interactions
- Mod/Resc Parsimony Inference
- On the genetic architecture of cytoplasmic incompatibility
- Viral population structure and dynamics
- Charge group partitioning in biomolecular simulation
Partnerships and Cooperations
Bibliography
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
- Partial Enumeration of Traces
- De-novo calling alternative splicing events from RNA-seq data
- Efficient bubble and/or cycle enumeration in directed/undirected graphs
- Simulating RNA-seq experiments
- Chimeric Transcripts may be Translated
- Transcriptomics of symbiosis in the Asobara tabida-Wolbachia association
- MicroRNA predictor
- Genomics of symbiosis
- Representation and curation of metabolic data: UniPathway, Rhea and MNX
- Annotation of the proteins of Angomonas deanei and Strigomonas culicis
- Finding candidate genes for orphan enzymes
- Metabolic cooperation of symbionts and their host trypanosomatids
- Structural and dynamical analysis of biological networks
- Network distance analysis
- Information spreading in dynamic graphs
- Metabolic network comparison
- Core and periphery of metabolic networks
- Metabolic stories
- Minimal precursor sets
- Minimum ratio cover of matrix columns by extreme rays of its induced cone
- Optimal flux spaces of genome-scale stoichiometric models
- Lateral gene transfer as a support for the tree of life
- Comparative approximability of hybridization number and directed feedback vertex set
- Influence of symbionts on antagonistic interactions
- Mod/Resc Parsimony Inference
- On the genetic architecture of cytoplasmic incompatibility
- Viral population structure and dynamics
- Charge group partitioning in biomolecular simulation
Partnerships and Cooperations
Bibliography