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 181 to 210 publications on 298 in total

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Augusto Vellozo, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro, Yvan Rahbé...

4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New Approaches and Outcomes” . : 45 p.

Poster

see the publication

Identifying SNPs without a reference genome by comparing raw reads

Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix

String Processing and Information Retrieval . 6393 : 147-158

DOI: 10.1007/978-3-642-16321-0_14

Conference paper

see the publication

Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

Journal article

see the publication

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Iagc The International Aphid Genomics Consortium, Federica Calevro, Hubert Charles, Stefano Colella, Gérard Febvay, Caroline Anselme...

PLoS Biology . 8 ( 2 ) : e1000313

DOI: 10.1371/journal.pbio.1000313

Journal article

see the publication

Repetition-free longest common subsequence

S.S Adi, M. Braga, C.G. Fernandes, C.E. Ferreira, F.V. Martinez, M.-F. Sagot...

Discrete Applied Mathematics . 158 ( 12 ) : 1315-1324

DOI: 10.1016/j.dam.2009.04.023

Journal article

see the publication

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno Mendes, Ana Freitas, Ana Vasconcelos, Marie-France Sagot

BMC Genomics . 11 ( 1 ) : 529

DOI: 10.1186/1471-2164-11-529

Journal article

see the publication

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret, David Wildridge, Florence Vinson, Michael P Barrett, Hubert Charles, Marie-France Sagot...

Nucleic Acids Research . 38 ( Web Server issue ) : W132-7

DOI: 10.1093/nar/gkq312

Journal article

see the publication

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles...

PLoS Computational Biology . 6 ( 9 ) : epub ahead of print

DOI: 10.1371/journal.pcbi.1000904

Journal article

see the publication

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Lilia Brinza, José Viñuelas, Ludovic Cottret, Federica Calevro, Yvan Rahbé, Gérard Febvay...

Comptes Rendus Biologies . 332 ( 11 ) : 1034-49

DOI: 10.1016/j.crvi.2009.09.007

Journal article

see the publication

The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism

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

5th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 2, Barcelona, Espagne, juin 2009 .

Conference paper

see the publication

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

Journal article

see the publication

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

see the publication

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

Journal article

see the publication

Multiple alignment of biological networks: A flexible approach

Yves-Pol Deniélou, Frédéric Boyer, Alain Viari, Marie-France Sagot

Combinatorial Pattern Matching (CPM) . 5577 : 263-273

DOI: 10.1007/978-3-642-02441-2_23

Conference paper

see the publication

Assessing the exceptionality of coloured motifs in networks

Sophie S. Schbath, Vincent Lacroix, Marie-France Sagot

EURASIP Journal on Bioinformatics and Systems Biology . 2009 : 9 pages on line

DOI: 10.1155/2009/616234

Journal article

see the publication

Current tools for the identification of miRNA genes and their targets

N.D. Mendes, A.T. Freitas, M.-F. Sagot

Nucleic Acids Research . 2009 : 2419-2433

Journal article

see the publication

Lossless filter for multiple repeats with bounded edit distance

Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira Do Lago, Nadia Pisanti, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 3

DOI: 10.1186/1748-7188-4-3

Journal article

see the publication

An asymmetric approach to preserve common intervals while sorting by reversals

Marília D.V. Braga, Christian Gautier, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 16

DOI: 10.1186/1748-7188-4-16

Journal article

see the publication

AcypiCyc (Acyrthosiphon pisum Cyc database) and CycADS (Cyc Annotation Database System): moving from genome sequence annotation to metabolic network analyses

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

8th International Symposium on Aphids (8 ISA 2009) . : 1-1

Conference paper

see the publication

AcypiCyc (Acyrthosiphon pisum Cyc database) : a model database to visualize and study the metabolic network underlying the pea aphid-Buchnera symbiosis

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

6. International Symbiosis Society (ISS) Congress .

Conference paper

see the publication

AcypiCyc (Acyrthosiphon pisumCyc database) and CycADS (CycAnnotation Database System) : moving from genome sequence annotation to metabolic network analyses

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

8. International Symposium on Aphids (8 ISA 2009) .

Conference paper

see the publication

AcypiCyc (Acyrthosiphon pisumCyc database) and CycADS (CycAnnotation Database System) : moving from genome sequence annotation to metabolic network analyses

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

Réseau Français de Biologie Adaptative des Pucerons .

Conference paper

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication