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Research activities: Bioinformatics


Keywords:
  - Information integration
  - Ontologies
  - Data mining
  - Workflows

Groups


Joint Inria project teams


Research highlights
  The Average Complexity of Tree Alignment
  A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency
  GenoQuery: a new querying module for functional annotation in a genomic warehouse
  Automated motif extraction and classification in RNA tertiary structures
  Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm
  VARNA software distinguished
  Automated prediction of three-way junction topological families in RNA secondary structures
  Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots
  Chromosome Replication in Escherichia coli: Life on the Scales. Vic NORRIS and Patrick AMAR
  The Mimic Chain Reaction. V. Norris, A. Thierry, P. Amar, B. Holland, F. Molina
  Sensor potency of the moonlighting enzyme-decorated cytoskeleton: the cytoskeleton as a metabolic sensor
  Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene in Streptomyces lividans.

Contracts & grants
  RAFALE
  Microbiogenomics
  Brasero
  RNA_RECOD
  PASAPAS
  Bioinformatics and biomathematic
  RegRNAs

Software & patents
  GenRGenS
  VARNA
  HSIM
  BioGuide
  Sequential Nuggets of Knowledge - DeeVee
  GenoQuery
  NestedAlign
  Rna3Dmotif
  GeneValorization
  Cartaj
  SPFlow
  SPChecker

Collaborations
  Swiss Institute of Bioinformatics (Genève)

Members
  AZE Jérôme
  HERRBACH Claire
  GENTILS Lucie
  ZHOU Yu
  RANCE Bastien
  LEMOINE Frédéric
  SAULE Cédric
  THEVENIN Annelyse
  TOFFANO-NIOCHE Claire
  DJELLOUL Mahassine
  PONTY Yann
  LOU Feng
  ASLAOUI-ERRAFII Zahira
  RINAUDO Philippe
  MEUNIER David

Ph.D. dissertations & Faculty habilitations
  Etude algorithmique et statistique de la comparaison de structures secondaires d'ARN
  Intégration d'informations pour les bases de données génomiques
  Random structures, models, and genome analysis
  Application of RNA Bioinformatics in decoding RNA structure and regulation
  "Recherche d'associations séquentielles et alignement d'ontologies biologiques."
  Intégration, Interrogation et analyse de données de génomique comparative
  Modélisation de la complexité et de la dynamique des simulations entités centrées. Application pour l'analyse des phénomènes émergents
  Algorithmic Aspects of Genome Rearrangements: Duplications and Partial Orders


Research activities
° Algorithm control and hyper-parameter tuning
° Algorithms for networked systems
° Automated Proof, SMT and Applications
° Automated Reasoning
° Combinatorics
° Compilation and code optimization
° Data-Centric Languages and Systems
° Deductive Verification of Programs
° Distributed algorithms
° Engineering of interactive systems
° Formal Model-Based Testing
° Formalisation and Proof of Numerical Programs
° Formalisation of (Specification and Programming) Languages in Proof Assistants
° Generative design methods
° Graph Theory
° Green networks
° Heterogeneous Wireless Networks
° High-performance computing
° Human-Computer Interaction
° Integration of Data and Knowledge
° Interaction and visualization paradigms
° Large scale modelling
° Massively distributed algorithms for complex data
° Mediated collaboration
° Multi-hop wireless networks