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:
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.
(pan)genomics and transcriptomics in general,
metabolism and (post)transcriptional regulation,
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/.
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
Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations
Frontiers in Genetics . 13 : 1-12
CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS
Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features
SLIT2/ROBO signaling in tumor-associated microglia and macrophages drives glioblastoma immunosuppression and vascular dysmorphia
The Journal of clinical investigation . 131 ( 16 )
A General Framework for Enumerating Equivalence Classes of Solutions
ESA 2021 - 29th Annual European Symposium on Algorithms . : 1-14
Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis
MSphere . 6 ( 1 )
A family of tree-based generators for bubbles in directed graphs
Journal of Graph Algorithms and Applications . 25 ( 1 ) : 549-562
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog
NAR Genomics and Bioinformatics . 3 ( 1 )
Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations
WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18
Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial
Communications Biology . 3
Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO+ and Light Sheet Fluorescence Microscopy
Journal of visualized experiments : JoVE . ( 159 ) : e61099 |
Efficient hybrid de novo assembly of human genomes with WENGAN
Nature Biotechnology . 39 : 422–430
Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
Bioinformatics . 36 ( 14 ) : 4197-4199
MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network
Bioinformatics . 36 ( 2 ) : 514-523
Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility
Algorithms for Molecular Biology . : 1-16
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells
Scientific Reports . 10 ( 13707 )
Accumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains
Acta Neuropathologica .
Influenza virus infection induces widespread alterations of host cell splicing
NAR Genomics and Bioinformatics . 2 ( 4 )
Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene
PLoS ONE . 15 ( 7 ) : e0235655
Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis
Nature Microbiology . 5 ( 5 ) : 735-745
A Family of Tree-Based Generators for Bubbles in Directed Graphs
IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
BMC Bioinformatics . 21 ( 1 ) : 1-13
Convolutional Kernel Networks for Graph-Structured Data
ICML 2020 - 37th International Conference on Machine Learning . 119 : 1576-1586
Recurrent Kernel Networks
NeurIPS 2019 - Thirty-third Conference on Neural Information Processing Systems .
Biological Sequence Modeling with Convolutional Kernel Networks
Bioinformatics . 35 ( 18 ) : 3294–3302
An IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis
Science Translational Medicine . 11 ( 500 ) : eaat1479
RNA 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
Biological Sequence Modeling with Convolutional Kernel Networks
RECOMB 2019 - 23rd Annual International Conference Research in Computational Molecular Biology . 11467 : 292-293
Hormonal pleiotropy and the evolution of allocation trade‐offs
Evolution - International Journal of Organic Evolution . 73 ( 4 ) : 661-674