Baobab Group

Members

baobab team

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 308 in total

CycADS: an annotation management system for the development and update of BioCyc metabolic network databases

A. Vellozo, Patrice Baa-Puyoulet, A. Veron, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay...

1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE .

Conference paper

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A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

Sabine Peres, Laurence Molina, Nicolas Salvetat, Claude Granier, Franck Molina

BMC Bioinformatics . 9 ( 1 ) : 460

DOI: 10.1186/1471-2105-9-460

Journal article

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Enumerating precursor sets of target metabolites in a metabolic network

L. Cottret, P.V. Milreu, Vicente Acuna, A. Marchetti-Spaccamela, F. Viduani Martinez, M.F. Sagot...

WABI 2008 - 8th International Workshop on Algorithms in Bioinformatics . 5251 : 233-244

Conference paper

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Evolution des organismes bactériens

Guillaume Beslon, Federica Calevro, Hubert Charles, Jean-Michel Fayard, Carole Knibbe, Stéphane Génieys...

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 12 diapos

Conference paper

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Benchmarking RNA secondary structure comparison algorithms

Julien Allali, Yves d'Aubenton-Carafa, Cedric Chauve, Alain Denise, Christine Drevet, Pascal Ferraro...

Actes des Journées Ouvertes de Biologie, Informatique et Mathématiques . : 67-68

Conference paper

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A small trip in the untranquil world of genomes a survey on the detection and analysis of genome rearrangement breakpoints

Claire Lemaitre, M.-F. Sagot

Theoretical Computer Science . 395 : 171-192

Journal article

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Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution

Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 3 ) : 348-356

DOI: 10.1109/TCBB.2008.16

Journal article

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Benchmarking RNA secondary structure comparison algorithms

J. Allali, Y. d'Aubenton-Carafa, C. Chauve, A. Denise, C. Drevet, P. Ferraro...

Proc. JOBIM . : 67-68

Journal article

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Development of the Acyrthosiphon pisum Cyc database (ApsCyc) : from genome sequence to metabolic network analyses

Augusto Vellozo, Stefano Colella, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé...

Integrative Post-Genomics - IPG'08 .

Conference paper

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Les réseaux métaboliques et génétiques

H. Charles, G. Beslon, Federica Calevro, Jean-François Boulicaut, J.M. Fayard, G. Febvay...

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1

Conference paper

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Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum

Hubert Charles, Federica Calevro, Stefano Colella, Jean-Michel Fayard, Gérard Febvay, Yvan Rahbé...

Séminaire INRA AgroBI .

Conference paper

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Annotation of metabolism genes : towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses

Stefano Colella, Augusto Vellozo, L. Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé...

4. Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1" .

Poster

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Modes and Cuts in Metabolic Networks:Complexity and Algorithms

Vicente Acuna, F. Chierichetti, Vincent Lacroix, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie

BioSystems . 95 - n°1 : 51-60

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

: 26

Report

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Transcriptomique

Jean-François Boulicaut, Federica Calevro, H. Charles, J.M. Fayard, G. Febvay, Olivier Gandrillon...

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1

Conference paper

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Efficient representation and P-value computation for high-order Markov motifs

P. Soares da Fonseca, Christian Gautier, K.S Guimarães, M.-F. Sagot

Bioinformatics . 24 : i160-i166

Journal article

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Identification de motifs dans les réseaux métaboliques

Vincent Lacroix

incollection . -- : D1-D5

Journal article

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An introduction to metabolic networks and their structural analysis.

Vincent Lacroix, Ludovic Cottret, Patricia Thebault, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 4 ) : 594-617

DOI: 10.1109/TCBB.2008.79

Journal article

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Evolution des organismes bactériens

G. Beslon, Federica Calevro, H. Charles, J.M. Fayard, C. Knibbe, S. Genieys...

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1

Conference paper

see the publication

Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum

H. Charles, Federica Calevro, Stefano Colella, J.M. Fayard, G. Febvay, Yvan Rahbé...

Séminaire INRA AgroBI . : 1-1

Conference paper

see the publication

A multiple layer model to compare RNA secondary structures

Julien Allali, Marie-France Sagot

Software: Practice and Experience . 38 ( 8 ) : 775-792

DOI: 10.1002/spe.846

Journal article

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Indexing gapped-factors using a tree

Pierre Peterlongo, Julien Allali, Marie-France Sagot

International Journal of Foundations of Computer Science . 19 ( 1 ) : 71-87

DOI: 10.1142/S0129054108005541

Journal article

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Lossless filter for multiple repetitions with Hamming distance

Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira Do Lago, Marie-France Sagot

Journal of Discrete Algorithms . 6 ( 3 ) : 497-509

DOI: 10.1016/j.jda.2007.03.003

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

BMC Bioinformatics . 9 ( 1 ) : 286

DOI: 10.1186/1471-2105-9-286

Journal article

see the publication

Development of the Acyrthosiphon pisum Cyc database (ApsCyc): from genome sequence to metabolic network analyses

A. Vellozo, Stefano Colella, L. Cottret, G. Febvay, Federica Calevro, Yvan Rahbé...

Integrative Post-Genomics - IPG'08 . : 1-1

Conference paper

see the publication

Annotation of metabolism genes: towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses

Stefano Colella, A. Vellozo, L. Cottret, G. Febvay, Federica Calevro, Yvan Rahbé...

4th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1" . : 1-1

Conference paper

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Exact Transcriptome Reconstruction from Short Sequence Reads

Vincent Lacroix, M. Sammeth, R. Guigo, A. Bergeron

International Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 50-63

DOI: 10.1007/978-3-540-87361-7_5

Conference paper

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Identification de motifs dans les réseaux métaboliques : définitions algorithmes et application au métabolisme d’Escherichia coli

Vincent Lacroix

Edilivre . 978-2-35607-642-7

Book

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Structure et modélisation des réseaux métaboliques

Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

Biofutur . ( 275 ) : 29-33

Journal article

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Efficient learning of Bayesian network classifiers:An extension to the TAN classifie

A. Carvalho, A. Oliveira, M.-F. Sagot

20th Australian Joint Conference on Artificial Intelligence . 4830 : 16-25

DOI: 10.1007/978-3-540-76928-6_4

Conference paper

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