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 91 to 120 publications on 308 in total

Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

Mariana G Ferrarini, Franciele Maboni Siqueira, Scheila G Mucha, Tony L Palama, Elodie E Jobard, Bénédicte Elena-Herrmann...

JOBIM 2016 .

DOI: 10.1186/s12864-016-2644-z

Poster

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A Combinatorial Algorithm for Microbial Consortia Synthetic Design

Alice Julien-Laferrière, Laurent Bulteau, Delphine Parrot, Alberto Marchetti-Spaccamela, Leen Stougie, Susana Vinga...

Scientific Reports .

DOI: 10.1038/srep29182

Journal article

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A Polynomial Delay Algorithm for Enumerating Minimal Dominating Sets in Chordal Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

WG 2015: Graph-Theoretic Concepts in Computer Science . : 138-153

DOI: 10.1007/978-3-662-53174-7_11

Book chapter

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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre...

GigaScience . 5 ( 1 )

DOI: 10.1186/s13742-015-0105-2

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

Journal article

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Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

Mariana G. Ferrarini, Franciele M. Siqueira, Scheila G. Mucha, Tony Lionel Palama, Elodie Jobard, Bénédicte Elena-Herrmann...

BMC Genomics . 17 ( 1 ) : 353

DOI: 10.1186/s12864-016-2644-z

Journal article

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DegreeCox – a network-based regularization method for survival analysis

André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga

BMC Bioinformatics . 17 ( Suppl 16 ) : 109-121

DOI: 10.1186/s12859-016-1310-4

Journal article

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Enumeration of minimal stoichiometric precursor sets in metabolic networks

Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu...

Algorithms for Molecular Biology . 11 ( 1 ) : 25

DOI: 10.1186/s13015-016-0087-3

Journal article

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Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot

Lecture Notes in Computer Science . 9702 : 12

DOI: 10.1007/978-3-319-38827-4_10

Journal article

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Computing and Listing st-Paths in Subway Networks

Kateřina Böhmová, Matúš Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot, Peter Widmayer

CSR 2016 - 11th International Computer Science Symposium in Russia . 9691 : 102-116

DOI: 10.1007/978-3-319-34171-2_8

Conference paper

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Introduction to the Special Theme - Tackling Big Data in the Life Sciences

Roeland M.H. Merks, Marie-France Sagot

Other publication

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Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy

Fernande Freyermuth, Frédérique Rau, Yosuke Kokunai, Thomas Linke, Chantal Sellier, Masayuki Nakamori...

Nature Communications . 7 : 11067

DOI: 10.1038/ncomms11067

Journal article

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MultiPus: Conception de communautés microbiennes pour la production de composés d'intérêt

A Julien-Laferrière, Laurent Bulteau, D Parrot, A Marchetti-Spaccamela, L Stougie, S Vinga...

Jobim .

Poster

see the publication

Efficient Enumeration of Solutions Produced by Closure Operations

Arnaud Mary, Yann Strozecki

33rd Symposium on Theoretical Aspects of Computer Science, STACS 2016 . 47

DOI: 10.4230/LIPIcs.STACS.2016.52

Conference paper

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On Maximal Chain Subgraphs and Covers of Bipartite Graphs

Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Combinatorial Algorithms - 27th International Workshop, IWOCA 2016 . 9843 : 137-150

DOI: 10.1007/978-3-319-44543-4_11

Conference paper

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Mycoplasma non-coding RNA: identification of small RNAs and targets

Franciele Maboni Siqueira, Guilherme Loss de Morais, Susan Higashi, Laura Scherer Beier, Gabriela Merker Breyer, Caio Padoan de Sá Godinho...

BMC Genomics . 23 : 1289 - 26

DOI: 10.1186/s12864-016-3061-z

Journal article

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Cell cycle progression is regulated by intertwined redox oscillators

Jorgelindo da Veiga Moreira, Sabine Pérès, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, Marcel Levy Nogeira...

Theoretical Biology and Medical Modelling . 12 ( 1 ) : 10

DOI: 10.1186/s12976-015-0005-2

Journal article

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Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

Qiong Rao, Pierre-Antoine Rollat-Farnier, Dan-Tong Zhu, Diego Santos-Garcia, Francisco J Silva, Andrés Moya...

BMC Genomics . 16 : 226

DOI: 10.1186/s12864-015-1379-6

Journal article

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Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

Pierre-Antoine Rollat-Farnier, Diego Santos-Garcia, Qiong Rao, Marie-France Sagot, Francisco J Silva, Hélène Henri...

Genome Biology and Evolution . 7 ( 3 ) : 839-855

DOI: 10.1093/gbe/evv030

Journal article

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MeDuSa: A multi-draft based scaffolder.

Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Lió...

Bioinformatics . : pii: btv171 [Epub ahead of print]

DOI: 10.1093/bioinformatics/btv171

Journal article

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Gustavo Sacomoto, Vincent Lacroix, Marie‑france Sagot

Algorithms for Molecular Biology . : 10

DOI: 10.1186/s13015-015-0046-4

Journal article

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Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Allan C. Azevedo-Martins, A. C. L. Machado, Cecilia Coimbra Klein, L. Ciapina, Luiz Gonzaga, Ana Tereza Ribeiro Vasconcelos...

Parasitology . 142 ( 2 ) : 352-362

DOI: 10.1017/S0031182014001139

Journal article

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Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

Algorithms and Data Structures (WADS) . 9214 : 446-457

Conference paper

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Incremental complexity of a bi-objective hypergraph transversal problem

Ricardo Andrade, Etienne E. Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot

Fundamentals of Computation Theory (FCT2015) . 9210 : 202-213

DOI: 10.1007/978-3-319-22177-9_16

Conference paper

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EUCALYPT: efficient tree reconciliation enumerator

Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot

Algorithms for Molecular Biology . 10 ( 1 ) : 11

DOI: 10.1186/s13015-014-0031-3

Journal article

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Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot

BMC Bioinformatics . 16 ( 1 ) : 179

DOI: 10.1186/s12859-015-0594-0

Journal article

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Cophylogeny Reconstruction via an Approximate Bayesian Computation

Christian Baudet, Béatrice Donati, Blerina Sinaimeri, Pierluigi Crescenzi, Christian Gautier, Catherine Matias...

Systematic Biology . 64 ( 3 ) : 416-431

DOI: 10.1093/sysbio/syu129

Journal article

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An average study of hypergraphs and their minimal transversals

Julien David, Loïck Lhote, Arnaud Mary, François Rioult

Theoretical Computer Science . 596 : 124-141

DOI: 10.1016/j.tcs.2015.06.052

Journal article

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SAT-Based Metabolics Pathways Analysis without Compilation

Sabine Pérès, Morterol Martin, Laurent Simon

CMSB 2014 .

Conference paper

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Systematic study of a metabolic network

Bertrand P Beauvoit, Sophie Colombié, Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

advances in Systems and Synthetic Biology . 978-2-7598-1201-1 : 173 p.

Conference paper

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