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 311 in total

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

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

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

DOI: 10.7155/jgaa.00571

Journal article

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Algorithmic investigations of the dynamics of species interactions

Yishu Wang

Thesis

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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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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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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 Ferrarini, Susana Vinga, Lilia Boucinha...

NAR Genomics and Bioinformatics . 3 ( 1 )

DOI: 10.1093/nargab/lqab009

Journal article

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Of Evolution, Systems and Complexity

Guillaume Beslon, Vincent Liard, David P. Parsons, Jonathan Rouzaud-Cornabas

Evolutionary Systems Biology II .

Book chapter

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

Book chapter

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A framework for modelling soil structure dynamics induced by biological activity

Katharina Meurer, Jennie Barron, Claire Chenu, Elsa Coucheney, Matthew Fielding, Paul Hallett...

Global Change Biology . 26 ( 10 ) : 5382-5403

DOI: 10.1111/gcb.15289

Journal article

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The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness

Vincent Liard, David Parsons, Jonathan Rouzaud-Cornabas, Guillaume Beslon

Artificial Life . 26 ( 1 ) : 38-57

DOI: 10.1162/artl_a_00312

Journal article

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Efficient hybrid de novo assembly of human genomes with WENGAN

Alex 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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Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Thierry Wirth, Marine Bergot, Jean-Philippe Rasigade, Bruno Pichon, Maxime Barbier, Patricia Martins-Simoes...

Nature Microbiology . 5 ( 5 ) : 735-745

DOI: 10.1038/s41564-020-0676-2

Journal article

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Accumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains

Loan Vaillant-Beuchot, Arnaud Mary, Raphaëlle Pardossi-Piquard, Alexandre Bourgeois, Inger Lauritzen, Fanny Eysert...

Acta Neuropathologica .

DOI: 10.1007/s00401-020-02234-7

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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Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

Laurent Jacob, Anke Witteveen, Inès Beumer, Leonie Delahaye, Diederik Wehkamp, Jeroen van den Akker...

Communications Biology . 3

DOI: 10.1038/s42003-020-1111-1

Journal article

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Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO+ and Light Sheet Fluorescence Microscopy

Laurent Jacob, Jose Brito, Jean-Leon Thomas

Journal of visualized experiments : JoVE . ( 159 ) : e61099 |

DOI: 10.3791/61099

Journal article

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

Vicente Acuña, Leandro Soares de Lima, Giuseppe Italiano, Luca 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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Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area

Stéphane Gaubert, Marianne Akian, Xavier Allamigeon, Marin Boyet, Baptiste Colin, Théotime Grohens...

Comptes Rendus. Mathématique . 358 ( 7 ) : 843-875

DOI: 10.5802/crmath.99

Journal article

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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene

Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Claire Benetollo, Clément Saccaro, Justine Guguin...

PLoS ONE . 15 ( 7 ) : e0235655

DOI: 10.1371/journal.pone.0235655

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 Mira, Susana Vinga

BMC Bioinformatics . 21 ( 1 ) : 1-13

DOI: 10.1186/s12859-020-3377-1

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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Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility

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

Algorithms for Molecular Biology . : 1-16

DOI: 10.1186/s13015-020-00174-1

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 Mucha, Mariana Ferrarini, Carol Moraga, Alex Genova, Laurent Guyon, Florence Tardy...

Scientific Reports . 10 ( 13707 )

DOI: 10.1038/s41598-020-70040-y

Journal article

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

Taneli Pusa, Mariana 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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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Journal article

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Convolutional Kernel Networks for Graph-Structured Data

Dexiong Chen, Laurent Jacob, Julien Mairal

ICML 2020 - 37th International Conference on Machine Learning . 119 : 1576-1586

Conference paper

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An IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis

Friederike Jönsson, Luc de Chaisemartin, Vanessa Granger, Aurélie Gouel-Chéron, Caitlin Gillis, Qianqian Zhu...

Science Translational Medicine . 11 ( 500 ) : eaat1479

DOI: 10.1126/scitranslmed.aat1479

Journal article

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RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

Hussein Ghazale, Chantal Ripoll, Nicolas Leventoux, Laurent Jacob, Safa Azar, Daria Mamaeva...

Current Stem Cell Reports . 12 ( 5 ) : 1159-1177

DOI: 10.1016/j.stemcr.2019.04.001

Journal article

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Anatomy and function of the vertebral column lymphatic network in mice

Laurent Jacob, Ligia Simoes Braga Boisserand, Luiz Henrique Medeiros Geraldo, Jose de Brito Neto, Thomas Mathivet, Salli Antila...

Nature Communications . 10 : 4594

DOI: 10.1038/s41467-019-12568-w

Journal article

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In vitro, in vivo and spectroscopic assessment of lead exposure reduction via ingestion and inhalation pathways using phosphate and iron amendments

Farzana Kastury, Euan Smith, Emmanuel Doelsch, Enzo Lombi, Martin Donnelley, Patricia Cmielewski...

Environmental Science and Technology . 53 ( 17 ) : 10329-10341

DOI: 10.1021/acs.est.9b02448

Journal article

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Data Standards for Artificial Life Software

Alexander Lalejini, Emily Dolson, Clifford Bohm, Austin Ferguson, David Parsons, Penelope Faulkner Rainford...

ALIFE 2019 - Conference on Artificial Life . : 507-514

DOI: 10.1162/isal_a_00213

Conference paper

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