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
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/LacroixV.jpg?itok=BWzG_xg1)
Maître de conférences
UCBL
Tel: 33 04 72 43 15 52
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/MaryA.jpg?itok=f2Qpcw09)
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:
-
Goals:
-
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.
-
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.
-
-
Axes:
-
(pan)genomics and transcriptomics in general,
-
metabolism and (post)transcriptional regulation,
-
(co)evolution
-
health in general, of living systems and environmental.
-
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 211 to 240 publications on 293 in total
Transcriptomique
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1
Conference paper
see the publicationEfficient representation and P-value computation for high-order Markov motifs
Bioinformatics . 24 : i160-i166
Journal article
see the publicationIdentification de motifs dans les réseaux métaboliques
incollection . -- : D1-D5
Journal article
see the publicationAn introduction to metabolic networks and their structural analysis.
IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 4 ) : 594-617
DOI: 10.1109/TCBB.2008.79
Journal article
see the publicationEvolution des organismes bactériens
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1
Conference paper
see the publicationCaractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum
Séminaire INRA AgroBI . : 1-1
Conference paper
see the publicationA multiple layer model to compare RNA secondary structures
Software: Practice and Experience . 38 ( 8 ) : 775-792
DOI: 10.1002/spe.846
Journal article
see the publicationIndexing gapped-factors using a tree
International Journal of Foundations of Computer Science . 19 ( 1 ) : 71-87
Journal article
see the publicationLossless filter for multiple repetitions with Hamming distance
Journal of Discrete Algorithms . 6 ( 3 ) : 497-509
Journal article
see the publicationPrecise detection of rearrangement breakpoints in mammalian chromosomes
BMC Bioinformatics . 9 ( 1 ) : 286
Journal article
see the publicationDevelopment of the Acyrthosiphon pisum Cyc database (ApsCyc): from genome sequence to metabolic network analyses
Integrative Post-Genomics - IPG'08 . : 1-1
Conference paper
see the publicationAnnotation of metabolism genes: towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses
4th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1" . : 1-1
Conference paper
see the publicationExact Transcriptome Reconstruction from Short Sequence Reads
International Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 50-63
Conference paper
see the publicationIdentification de motifs dans les réseaux métaboliques : définitions algorithmes et application au métabolisme d’Escherichia coli
Edilivre . 978-2-35607-642-7
Book
see the publicationStructure et modélisation des réseaux métaboliques
Biofutur . ( 275 ) : 29-33
Journal article
see the publicationEfficient learning of Bayesian network classifiers:An extension to the TAN classifie
20th Australian Joint Conference on Artificial Intelligence . 4830 : 16-25
Conference paper
see the publicationThe solution space of sorting by reversals
3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007) . 4463 : 293-304
Conference paper
see the publicationEvolution under Reversals: Parsimony and Conservation of Common Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics . 4 : 301-309
Journal article
see the publicationRegulation of expression following nutritional stresses in the reduced genome of Buchnera aphidicola, "Is there any life left?
Seminarios del Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE) - Univ. Valencia (ESP) . : 1-1
Conference paper
see the publicationMetabolic network visualization eliminating node redundance and preserving metabolic pathways
BMC Biology . 1 - n°29 : 1-19
Journal article
see the publicationAdvances on sorting by reversals
Discrete Applied Mathematics . 155 : 881-888
Journal article
see the publicationRepetition-free longest common subsequence
IV Latin-American Algorithms, Graphs and Optimization Symposium (LAGOS) . 30 : 243-248
Conference paper
see the publicationThe maximum agreement forest problem: Approximation algorithms and computational experiments
Theoretical Computer Science . 374 : 91-110
Journal article
see the publicationEnumerating precursor sets of target metabolites in a metabolic network
8th Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 233-244
Conference paper
see the publicationRecherche de précurseurs dans un réseau métabolique
Réseaux d'interaction : analyse, modélisation et simulation (RIAMS) . : 1-1
Conference paper
see the publicationAll Maximal Pairs in Step-Leap Representation of Melodic Sequences
Information Sciences . 177 ( 9 ) : 1954-1962
Journal article
see the publicationSymBioCyc: Metabolic data on endosymbiotic, parasitic and free bacteria
Integrative Post-Genomics - IPG'07 . : 1-1
Conference paper
see the publicationMycotoxin fumonisin B-1 selectively down-regulates the basal IL-8 expression in pig intestine: in vivo and in vitro studies
Food and Chemical Toxicology . 44 ( 10 ) : 1768-1773
Journal article
see the publicationUncovering structure in biological networks
incollection . -- : 471-483
Journal article
see the publication