Baobab Group
Members
Post-doc
CNRS
Tel: 04 72 44 81 42
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/CrsiciE.jpg?itok=6TODeH3k)
Doctorante
INRIA
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/DarmonS.jpg?itok=ljjc2l3-)
Doctorant
UCBL
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/GindraudF.jpg?itok=aWKiUyWc)
Ingénieur de recherche
INRIA
Tel: 04 72 44 81 42
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Maître de conférences
UCBL
Tel: 33 04 72 43 15 52
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Maître de conférences
UCBL
Tel: 04 72 43 15 52
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/PeresS.jpg?itok=fi8Vla5f)
Professeur des universités
UCBL
Tel: 04 72 44 81 42
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/RoncerayA_2021.jpg?itok=fGDlKEsJ)
Technicienne
INRIA
Tel: 04 72 44 81 54
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/SagotMF.jpg?itok=CUVOyhcG)
Directrice de recherche
INRIA
Tel: 33 04 72 44 82 38
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/SiharathC.jpg?itok=ZREuT6sq)
Doctorante
UCBL
![baobab team](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__320x240__crop_main/public/media/images/baobab-team3.jpeg?itok=Hi4wVejN)
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 31 to 60 publications on 293 in total
MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network
Bioinformatics . 36 ( 2 ) : 514-523
Journal article
see the publicationMycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells
Scientific Reports . 10 ( 13707 )
Journal article
see the publicationInfluenza virus infection induces widespread alterations of host cell splicing
NAR Genomics and Bioinformatics . 2 ( 4 )
Journal article
see the publicationCapybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
Bioinformatics . 36 ( 14 ) : 4197-4199
Journal article
see the publicationAlgorithms for the quantitative Lock/Key model of cytoplasmic incompatibility
Algorithms for Molecular Biology . : 1-16
Journal article
see the publicationClinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene
PLoS ONE . 15 ( 7 ) : e0235655
Journal article
see the publicationA kinetic metabolic study of lipid production in Chlorella protothecoides under heterotrophic condition
Microbial Cell Factories . 18 ( 1 )
Journal article
see the publicationMetabolic therapies inhibit tumor growth in vivo and in silico
Scientific Reports . 9 ( 1 )
Journal article
see the publicationModulating mitochondria horsepower for biotechnological applications
Metabolic Pathway Analysis 2019 .
Conference paper
see the publicationUsing a hybrid approach to model central carbon metabolism across the cell cycle
International Workshop on Hybrid Systems Biology . 11705
Conference paper
see the publicationExploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny
IEEE/ACM Transactions on Computational Biology and Bioinformatics . : 1-11
Journal article
see the publicationA Distance-based block searching algorithm
Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) . 3 : 322-331
Conference paper
see the publicationThe Perfect Matching Reconfiguration Problem
MFCS 2019 - 44th International Symposium on Mathematical Foundations of Computer Science . : 1-14
Conference paper
see the publicationEfficient enumeration of solutions produced by closure operations
Discrete Mathematics and Theoretical Computer Science . : 1-30
Journal article
see the publicationNew insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients
RNA . : 1-21
Journal article
see the publicationAdvances in Analyzing Virus-Induced Alterations of Host Cell Splicing
Trends in Microbiology . 27 ( 3 ) : 268-281
Journal article
see the publicationTranscriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
Scientific Reports . 9 ( 1 ) : 14908
Journal article
see the publicationMetabolic Games
Frontiers in Applied Mathematics and Statistics . 5 : 1-13
Journal article
see the publicationThermodynamic constraints for identifying elementary flux modes
Biochemical Society Transactions . 46 ( 3 ) : 641-647
DOI: 10.1042/BST20170260
Journal article
see the publicationIdentifying Biomarkers of Wharton’s Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect
Metabolites . 8 ( 1 ) : 18
Journal article
see the publicationMetabolic view of tumor growth: a kinetic model to screen potential therapeutic targets
Computational systems biology for cancer .
Conference paper
see the publicationBounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension
SIAM Journal on Discrete Mathematics . 32 ( 2 ) : 902 - 918
DOI: 10.1137/16M1097833
Journal article
see the publicationExploring and Visualising Spaces of Tree Reconciliations
Systematic Biology . : 1-36
Journal article
see the publicationPierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model
Frontiers in Microbiology . 9 : 1-23
Journal article
see the publicationHydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae
Molecular Microbiology . : 1-45
DOI: 10.1111/mmi.13957
Journal article
see the publicationA fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events
PLoS Genetics . 14 ( 11 ) : 1-28
Journal article
see the publicationComplementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data
Scientific Reports . 8 ( 1 )
Journal article
see the publicationGeometric medians in reconciliation spaces
Information Processing Letters . 136 : 96 - 101
Journal article
see the publicationReconfiguration of graphs with connectivity constraints
WAOA 2018 - International Workshop on Approximation and Online Algorithms . 11312 : 295-309
Conference paper
see the publication