Baobab Group
Members
Stagiaire
UCBL
Tel: 0472448142

Ingénieur de recherche
INRIA
Tel: 0472448142
Stagiaire
UCBL
Tel: 0472448142
Doctorant
INRA
Tel: 0472448308

Chargé de recherche
CNRS
Tel: 0472448598

Maître de conférences
UCBL
Tel: 330472431552

Doctorant
autre
Tel: 0472448142

Maître de conférences
UCBL
Tel: 0472431552

Professeur des universités
UCBL
Tel: 0472448142

Technicienne
INRIA
Tel: 0426234460

Directrice de recherche
INRIA
Tel: 330472448238
Stagiaire
UCBL
Tel: 0472448142

Ingénieur d'études CDD
CNRS
Tel: 0472448142

Doctorant
CNRS
Tel: 0472448487

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:
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Goals:
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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.
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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.
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Axes:
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(pan)genomics and transcriptomics in general,
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metabolism and (post)transcriptional regulation,
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(co)evolution
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health in general, of living systems and environmental.
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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 290 in total
Efficiently sparse listing of classes of optimal cophylogeny reconciliations
Algorithms for Molecular Biology . 17 ( 1 ) : 1-16
Journal article
see the publicationTotoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations
Frontiers in Genetics . 13 : 1-12
Journal article
see the publicationCALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS
Preprint
see the publicationWithin-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features
Preprint
see the publicationSLIT2/ROBO signaling in tumor-associated microglia and macrophages drives glioblastoma immunosuppression and vascular dysmorphia
The Journal of clinical investigation . 131 ( 16 )
DOI: 10.1172/JCI141083
Journal article
see the publicationA General Framework for Enumerating Equivalence Classes of Solutions
ESA 2021 - 29th Annual European Symposium on Algorithms . : 1-14
Conference paper
see the publicationDichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis
MSphere . 6 ( 1 )
Journal article
see the publicationA family of tree-based generators for bubbles in directed graphs
Journal of Graph Algorithms and Applications . 25 ( 1 ) : 549-562
DOI: 10.7155/jgaa.00572
Journal article
see the publicationA comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog
NAR Genomics and Bioinformatics . 3 ( 1 )
Journal article
see the publicationMaking Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations
WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18
Conference paper
see the publicationControlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial
Communications Biology . 3
Journal article
see the publicationThree-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO+ and Light Sheet Fluorescence Microscopy
Journal of visualized experiments : JoVE . ( 159 ) : e61099 |
DOI: 10.3791/61099
Journal article
see the publicationEfficient hybrid de novo assembly of human genomes with WENGAN
Nature Biotechnology . 39 : 422–430
Journal article
see the publicationCapybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
Bioinformatics . 36 ( 14 ) : 4197-4199
Journal article
see the publicationMOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network
Bioinformatics . 36 ( 2 ) : 514-523
Journal article
see the publicationAlgorithms for the quantitative Lock/Key model of cytoplasmic incompatibility
Algorithms for Molecular Biology . : 1-16
Journal article
see the publicationMycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells
Scientific Reports . 10 ( 13707 )
Journal article
see the publicationAccumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains
Acta Neuropathologica .
Journal article
see the publicationInfluenza virus infection induces widespread alterations of host cell splicing
NAR Genomics and Bioinformatics . 2 ( 4 )
Journal article
see the publicationClinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene
PLoS ONE . 15 ( 7 ) : e0235655
Journal article
see the publicationNiche specialization and spread of Staphylococcus capitis involved in neonatal sepsis
Nature Microbiology . 5 ( 5 ) : 735-745
Journal article
see the publicationA Family of Tree-Based Generators for Bubbles in Directed Graphs
IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29
Conference paper
see the publicationMOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
BMC Bioinformatics . 21 ( 1 ) : 1-13
Journal article
see the publicationConvolutional Kernel Networks for Graph-Structured Data
ICML 2020 - 37th International Conference on Machine Learning . 119 : 1576-1586
Conference paper
see the publicationRecurrent Kernel Networks
NeurIPS 2019 - Thirty-third Conference on Neural Information Processing Systems .
Conference paper
see the publicationBiological Sequence Modeling with Convolutional Kernel Networks
Bioinformatics . 35 ( 18 ) : 3294–3302
Journal article
see the publicationAn IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis
Science Translational Medicine . 11 ( 500 ) : eaat1479
Journal article
see the publicationRNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells
Current Stem Cell Reports . 12 ( 5 ) : 1159-1177
Journal article
see the publicationBiological Sequence Modeling with Convolutional Kernel Networks
RECOMB 2019 - 23rd Annual International Conference Research in Computational Molecular Biology . 11467 : 292-293
Conference paper
see the publicationHormonal pleiotropy and the evolution of allocation trade‐offs
Evolution - International Journal of Organic Evolution . 73 ( 4 ) : 661-674
DOI: 10.1111/evo.13693
Journal article
see the publication