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 241 to 270 publications on 298 in total

All Maximal Pairs in Step-Leap Representation of Melodic Sequences

Emilios Cambouropoulos, Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot

Information Sciences . 177 ( 9 ) : 1954-1962

DOI: 10.1016/j.ins.2006.11.012

Journal article

see the publication

SymBioCyc: Metabolic data on endosymbiotic, parasitic and free bacteria

L. Cottret, H. Charles, M.F. Sagot

Integrative Post-Genomics - IPG'07 . : 1-1

Conference paper

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Identification de motifs dans les réseaux métaboliques

Vincent Lacroix

Thesis

see the publication

Mycotoxin fumonisin B-1 selectively down-regulates the basal IL-8 expression in pig intestine: in vivo and in vitro studies

S Bouhet, E Le Dorze, Sabine Pérès, Jm Fairbrother, Isabelle P. Oswald

Food and Chemical Toxicology . 44 ( 10 ) : 1768-1773

Journal article

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Uncovering structure in biological networks

J.J. Daudin, Vincent Lacroix, M. Mariadassou, V. Miele, Franck Picard, S. Robin...

incollection . -- : 471-483

Journal article

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Motif search in graphs: application to metabolic networks.

Vincent Lacroix, C.G. Fernandes, M.-F. Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 3 - n°4 : 360-368

Journal article

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Longest Repeats with a Block of k Don't Cares

Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot

Theoretical Computer Science . 362 ( 1-3 ) : 248-254

DOI: 10.1016/j.tcs.2006.06.029

Journal article

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RISOTTO: Fast extraction of motifs with mismatches

N. Pisanti, A. Carvalho, L. Marsan, M.-F. Sagot

Latin American Symposium on Theoretical Informatics . 3887 : 757-768

DOI: 10.1007/11682462_69

Conference paper

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The Gapped-Factor Tree

Pierre Peterlongo, Julien Allali, Marie-France Sagot

Prague Stringology Conference 2006 . : 182--196

Conference paper

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An efficient algorithm for the identification of structured motifs in DNA promoter sequences

A.M. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 3 : 126-140

Journal article

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Lossless Filter for Long Multiple Repetitions with Edit Distance

Pierre Peterlongo, Nadia Pisanti, Alair Peirera Do Lago, Marie-France Sagot

Report

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Metabolic network visualization using constraint planar graph drawing Algorithm

Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan

Metabolic network visualization using constraint planar graph drawing Algorithm . : 489 - 496

Conference paper

see the publication

Metabolic network visualization using constraint planar graph drawing algorithm

Romain Bourqui, D. Auber, Vincent Lacroix, F. Jourdan

incollection . -- : 489-496

Journal article

see the publication

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques

Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques . : électronique

Conference paper

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Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array

Pierre Peterlongo, Nadia Pisanti, Frederique Boyer, Marie-France Sagot

String Processing and Information Retrieval, 12th International Conference, SPIRE 2005 . 3772 : 179-190

DOI: 10.1007/11575832

Conference paper

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Reaction Motifs in Metabolic Networks

Vincent Lacroix, Cristina Gomes Fernandes, Marie-France Sagot

: 14

Report

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Perfect Sorting by Reversals

Marie-France Sagot, Eric Tannier

: 13

Report

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A Comparative Study of Bases for Motif Inference

Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot

String Algorithmics . : 195-225

Conference paper

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A Pattern Extraction Algorithm for Abstract Melodic Representations that Allow Partial Overlapping of Intervallic Categories

Emilios Cambouropoulos, Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot

Proceedings of the 6th International Conference on Music Information Retrieval (ISMIR 2005) . : 167-174

Conference paper

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A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison

Julien Allali, Marie-France Sagot

String Processing and Information Retrieval 2005 (SPIRE 2005) . 3772 : 348--359

DOI: 10.1007/11575832_39

Conference paper

see the publication

Reaction motifs in metabolic networks

Vincent Lacroix, C.G. Fernandes, M.-F. Sagot

International Workshop on Algorithms in Bioinformatics (WABI) . 3692 : 178-191

DOI: 10.1007/11557067_15

Conference paper

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Perfect sorting by reversals

M.-F. Sagot, Eric Tannier

International Computing and Combinatorics Conference . 3595 : 42-51

DOI: 10.1007/11533719_7

Conference paper

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A new distance for high level RNA secondary structure comparison

Julien Allali, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 2 : 3--14

Journal article

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Bases of motifs for generating repeated patterns with wild cards

Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 2 : 40-50

DOI: 10.1109/TCBB.2005.5

Journal article

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A first approach to finding common motifs with gaps,

Costas Iliopoulos, J. Mchugh, Pierre Peterlongo, Nadia Pisanti, W. Rytter, Marie-France Sagot

International Journal of Foundations of Computer Science . 16 ( 6 ) : 1145--1155

Journal article

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Efficient Extraction of Structured Motifs Using Box-links

A. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

International Symposium on String Processing and Information Retrieval : SPIRE . 3246 : 267-268

DOI: 10.1007/978-3-540-30213-1_37

Conference paper

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A first approach to finding common motifs with Gaps

Costas S. Iliopoulos, James Mchugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot

Prague Stringology Conference 2004 . : 88-97

Conference paper

see the publication

A parallel algorithm for the extraction of structured motifs

A. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

ACM Symposium on Applied Computing . -- : 147-153

Conference paper

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The at-most $k$-deep factor tree

Julien Allali, Marie-France Sagot

Report

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Motifs in Sequences: Localization and Extraction

Maxime Crochemore, Marie-France Sagot

Compact Handbook of Computational Biology . : 47-97

Book chapter

see the publication