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 1 to 30 publications on 289 in total

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

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

Systematic Biology . : syad058

DOI: 10.1093/sysbio/syad058

Journal article

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Hybrid modelling to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres

BIOSTEC 2023 .

Conference paper

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Polynomial Delay Algorithm for Minimal Chordal Completions

Caroline Brosse, Vincent Limouzy, Arnaud Mary

49th International Colloquium on Automata, Languages, and Programming (ICALP) .

DOI: 10.4230/LIPIcs.ICALP.2022.33

Conference paper

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Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Fatimat Almentina Ramos Shidi, Audric Cologne, Marion Delous, Alicia Besson, Audrey Putoux, Anne-Louise Leutenegger...

Nucleic Acids Research .

DOI: 10.1093/nar/gkac1182

Journal article

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Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres, Marc Dinh, Vincent Fromion

International Conference on System Biology .

Conference paper

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Special Issue on “Frontiers in Connecting Steady-State and Dynamic Approaches for Modelling Cell Metabolic Behavior”

Sabine Peres, Mario Jolicoeur

Processes . 10 ( 8 ) : 1612

DOI: 10.3390/pr10081612

Journal article

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Hybrid metabolic modeling to identify new control strategies of living organisms

Sabine Peres

Hybrid models and methods in systems medicine .

Conference paper

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Mod ́elisation m ́etabolique pour identifier de nouvelles strat ́egies de contrˆole des organismes vivants

Sabine Peres

Meetochondrie .

Conference paper

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BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Carol Moraga, Evelyn Sanchez, Mariana Galvão Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot

GigaScience . 11

DOI: 10.1093/gigascience/giac093

Journal article

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Efficiently sparse listing of classes of optimal cophylogeny reconciliations

Yishu Wang, Marie-France Sagot, Arnaud Mary, Blerina Sinaimeri

Algorithms for Molecular Biology . 17 ( 1 ) : 1-16

DOI: 10.1186/s13015-022-00206-y

Journal article

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Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César...

Frontiers in Genetics . 13 : 1-12

DOI: 10.3389/fgene.2022.815476

Journal article

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CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

Bioinformatics .

DOI: 10.1093/bioinformatics/btac238

Journal article

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Answer set programming to compute constraint elementary flux modes

Maxime Mahout, Laurent Simon, Sabine Peres

Computational Methods in System Biology .

Conference paper

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Answer set programming to compute constraint elementary flux modes.

Maxime Mahout, Laurent Simon, Sabine Peres

Metabolic Pathway Analysis .

Conference paper

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Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

Jorgelindo da Veiga Moreira, Mario Jolicoeur, Laurent Schwartz, Sabine Peres

Scientific Reports . 11 ( 1 )

DOI: 10.1038/s41598-020-79577-4

Journal article

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Combining Kinetic and Constraint-Based Modelling to Better Understand Metabolism Dynamics

Cecile Moulin, Laurent Tournier, Sabine S. Peres

Processes . 9 ( 10 ) : 1701

DOI: 10.3390/pr9101701

Journal article

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A General Framework for Enumerating Equivalence Classes of Solutions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

ESA 2021 - 29th Annual European Symposium on Algorithms . : 1-14

DOI: 10.4230/LIPIcs.ESA.2021.80

Conference paper

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Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis

Mariana Galvão Ferrarini, Lindice Mitie Nisimura, Richard Marcel Bruno Moreira Girard, Mayke Bezerra Alencar, Mariana Sayuri Ishikawa Fragoso, Carlla Assis Araújo-Silva...

MSphere . 6 ( 1 )

DOI: 10.1128/mSphere.01002-20

Journal article

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A family of tree-based generators for bubbles in directed graphs

Vicente Acuña, Leandro Ishi Soares de Lima, Giuseppe F Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri

Journal of Graph Algorithms and Applications . 25 ( 1 ) : 549-562

DOI: 10.7155/jgaa.00572

Journal article

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A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha...

NAR Genomics and Bioinformatics . 3 ( 1 )

DOI: 10.1093/nargab/lqab009

Journal article

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Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18

DOI: 10.4230/LIPIcs.WABI.2021.3

Conference paper

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Cancer and Alzheimer’s disease: intracellular pH scales the metabolic disorders

Laurent Schwartz, Sabine S. Peres, Mario Jolicoeur, Jorgelindo da Veiga Moreira

Biogerontology . 21 ( 6 ) : 683-694

DOI: 10.1007/s10522-020-09888-6

Journal article

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Efficient hybrid de novo assembly of human genomes with WENGAN

Alex Di Genova, Elena Buena-Atienza, Stephan Ossowski, Marie-France Sagot

Nature Biotechnology . 39 : 422–430

DOI: 10.1038/s41587-020-00747-w

Journal article

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MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie-France Sagot, Nuno P Mira, Susana Vinga

BMC Bioinformatics . 21 ( 1 ) : 1-13

DOI: 10.1186/s12859-020-3377-1

Journal article

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A Family of Tree-Based Generators for Bubbles in Directed Graphs

Vicente Acuña, Leandro Ishi Soares de Lima, Giuseppe F Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri

IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29

DOI: 10.1007/978-3-030-48966-3_2

Conference paper

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MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network

Taneli Pusa, Mariana G. Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie...

Bioinformatics . 36 ( 2 ) : 514-523

DOI: 10.1093/bioinformatics/btz584

Journal article

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Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells

Scheila Gabriele Mucha, Mariana G. Ferrarini, Carol Moraga, Alex Di Genova, Laurent Guyon, Florence Tardy...

Scientific Reports . 10 ( 13707 )

DOI: 10.1038/s41598-020-70040-y

Journal article

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Influenza virus infection induces widespread alterations of host cell splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Navratil, Cécile Ligneau, Guillaume Fournier, Sandie Munier...

NAR Genomics and Bioinformatics . 2 ( 4 )

DOI: 10.1093/nargab/lqaa095

Journal article

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Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Bioinformatics . 36 ( 14 ) : 4197-4199

DOI: 10.1093/bioinformatics/btaa498

Journal article

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