BAMBOO - 2012 - Annual activity report

BAMBOO

BAMBOO - 2012

Project-Team Bamboo

Members

Overall Objectives

Highlights of the Year

Scientific Foundations

Formal methods
Symbiosis
Intracellular interactions

Application Domains

Biology with a focus on symbiosis

Software

AcypiCyc
AlViE
Cassis
Cravela
C3P
CycADS
Gobbolino
kisSNP
kisSplice
LASAGNE
MetExplore
Migal
MotusWEB
Motus
PhEVER
PepLine
Pitufo and family
PSbR
Repseek
Smile
Tuiuiu
UniPathway

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

Regional Initiatives
National Initiatives
European Initiatives
International Initiatives
International Research Visitors

Dissemination

Scientific Animation
Teaching - Supervision - Juries
Popularization

Bibliography

Publications of the year

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Section: Software

kisSplice

Participants : Rayan Chikhi, Janice Kielbassa [EPI] , Vincent Lacroix [Contact, EPI] , Pierre Peterlongo [Contact, pierre.peterlongo@inria.fr] , Gustavo Sacomoto [EPI] , Marie-France Sagot [EPI] , Raluca Uricaru.

Algorithm for de-novo calling alternative splicing events from RNA-seq data.

http://alcovna.genouest.org/kissplice/

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