Baobab Group
Members
Post-doc
CNRS
Tel: 04 72 44 81 42
Doctorante
INRIA
Doctorant
UCBL
Ingénieur de recherche
INRIA
Tel: 04 72 44 81 42
Maître de conférences
UCBL
Tel: 33 04 72 43 15 52
Maître de conférences
UCBL
Tel: 04 72 43 15 52
Professeur des universités
UCBL
Tel: 04 72 44 81 42
Technicienne
INRIA
Tel: 04 72 44 81 54
Directrice de recherche
INRIA
Tel: 33 04 72 44 82 38
Doctorante
UCBL
Baobab is a French research team of the Laboratoire de Biométrie et Biologie Évolutive, and at the same time represents the core of a European research team of Inria called Erable. Besides the members of Baobab, Erable has thus members in three institutions in Italy (Sapienza University of Rome, Luiss University, and University of Pisa) and two institutions in the Netherlands (CWI and Free University of Amsterdam).
Baobab has two main sets of research goals that currently cover four axes:
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Goals:
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The first is related to the original areas of expertise of the team, namely combinatorial and statistical modelling and algorithms, although more recently the team has also been joined by members that come from biology including experimental.
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The second set of goals concern its main Life Science interest which is to better understand interactions between living systems and their environment. This includes close and often persistent interactions between two living systems (symbiosis), interactions between living systems and viruses, and interactions between living systems and chemical compounds.
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Axes:
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(pan)genomics and transcriptomics in general,
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metabolism and (post)transcriptional regulation,
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(co)evolution
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health in general, of living systems and environmental.
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A longer objective of the team is to become able in some cases to suggest the means of controlling for or of re-establishing equilibrium in an interacting community by acting on its environment or on its players, how they play and who plays.
Two major steps are constantly involved in the research done by the team: a first one of modelling (i.e. translating) a Life Science problem into a mathematical one, and a second of algorithm analysis and design. The algorithms developed are then applied to the questions of interest in Life Science using data from the literature or from collaborators. More recently, thanks to the recruitment of young researchers (PhD students and postdocs) in biology, the team has become able to start doing experiments and producing data or validating some of the results obtained on its own.
From a methodological point of view, the main characteristic of the team is to consider that, once a model is selected, the algorithms to explore such model should, whenever possible, be exact in the answer provided as well as exhaustive when more than one exists for a more accurate interpretation of the results. More recently, the team has become interested in exploring the interface between exact algorithms on one hand, and probabilistic or statistical ones on the other such as used in machine learning approaches. More in particular, the team is interested in investigating an area of research called “interpretable machine learning” that has been developing more recently and its potential relations with exact, combinatorial approaches.
Besides being at the core of a European team, Baobab has a number of other collaborations at the international level.
Baobab is also strongly involved in teaching at the University of Lyon and Insa-Lyon, well as in other research institutions in Europe, directly or through the members of Erable that are not in France.
For more information, you may also visit the site of the Inria team Erable here: http://team.inria.fr/erable/en/.
Publications
Display of 61 to 90 publications on 291 in total
Computing EFMs consistent with equilibrium constants
Metabolic Pathway Analysis MPA 2017 .
Conference paper
see the publicationHSM a reduced model of Central Carbon Metabolism: a dynamical approach
advances in Systems and Synthetic Biology .
Conference paper
see the publicationHow important is thermodynamics for identifying elementary flux modes?
PLoS ONE . 12 ( 2 )
Journal article
see the publicationBacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits
Phytochemistry Reviews . : 1-36
Journal article
see the publicationAlgorithms for k-meet-semidistributive lattices
Theoretical Computer Science . 658 : 391 - 398
Journal article
see the publicationAnnotation and differential analysis of alternative splicing using de novo assembly of RNAseq data
DOI: 10.1101/074807
Preprint
see the publicationPlaying hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
Algorithms for Molecular Biology . 12 ( 1 ) : 2
Journal article
see the publicationOptPipe - a pipeline for optimizing metabolic engineering targets
BMC Systems Biology . 11 : 1-9
Journal article
see the publicationOn Bubble Generators in Directed Graphs
WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science . 10520 : 18-31
Conference paper
see the publicationIdentification of misexpressed genetic elements in hybrids between Drosophila-related species
Scientific Reports . 7 : 40618
DOI: 10.1038/srep40618
Journal article
see the publicationToken Jumping in minor-closed classes
International symposium on fundamentals of computer theory (FCT 2017) . 10472 : 136-149
Conference paper
see the publicationHow Long Does Wolbachia Remain on Board?
Molecular Biology and Evolution . 34 ( 5 ) : 1183 - 1193
Journal article
see the publicationThe Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect
Metabolites . 6 ( 4 ) : 12 p.
Journal article
see the publicationMinimality of Metabolic Flux Modes under Boolean Regulation Constraints
12th International Workshop on Constraint-Based Methods for Bioinformatics WCB’16 .
Conference paper
see the publicationReprésentation systémique multi-échelle des processus biologiques de la bactérie
IC2016 - Ingénierie des Connaissances .
Conference paper
see the publicationReprésentation systémique multi-échelle des processus biologiques de la bactérie
IC201: 27es Journées francophones d'Ingénierie des Connaissances .
Conference paper
see the publicationHuman-Scale Metabolic Network of Central Carbon Metabolism: application to serine metabolism from glutamine in Cancer Cells
advances in Systems and Synthetic Biology .
Conference paper
see the publicationMetabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract
JOBIM 2016 .
Poster
see the publicationA Combinatorial Algorithm for Microbial Consortia Synthetic Design
Scientific Reports .
DOI: 10.1038/srep29182
Journal article
see the publicationA Polynomial Delay Algorithm for Enumerating Minimal Dominating Sets in Chordal Graphs
WG 2015: Graph-Theoretic Concepts in Computer Science . : 138-153
Book chapter
see the publicationColib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
GigaScience . 5 ( 1 )
Journal article
see the publicationSNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
Nucleic Acids Research .
DOI: 10.1093/nar/gkw655
Journal article
see the publicationInsights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling
BMC Genomics . 17 ( 1 ) : 353
Journal article
see the publicationDegreeCox – a network-based regularization method for survival analysis
BMC Bioinformatics . 17 ( Suppl 16 ) : 109-121
Journal article
see the publicationEnumeration of minimal stoichiometric precursor sets in metabolic networks
Algorithms for Molecular Biology . 11 ( 1 ) : 25
Journal article
see the publicationRobustness of the Parsimonious Reconciliation Method in Cophylogeny
Lecture Notes in Computer Science . 9702 : 12
Journal article
see the publicationComputing and Listing st-Paths in Subway Networks
CSR 2016 - 11th International Computer Science Symposium in Russia . 9691 : 102-116
Conference paper
see the publicationIntroduction to the Special Theme - Tackling Big Data in the Life Sciences
Other publication
see the publicationSplicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy
Nature Communications . 7 : 11067
DOI: 10.1038/ncomms11067
Journal article
see the publicationMultiPus: Conception de communautés microbiennes pour la production de composés d'intérêt
Jobim .
Poster
see the publication