Here we list the most significant 20% of publications by the members of the CRI Collaboratory (UMR U1284), organized following the our main research themes. Full list will be made available shortly.
Dimitriu T, Misevic D, Lotton C, Brown SP, Lindner AB, Taddei F (2016). Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids. PLoS Biol. 2016 Jun 7;14(6):e1002478.
The two papers above provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods.
This paper provides quantitative data and mathematical model to demonstrate that aging-related protein aggregates polar localization in E. coli results from coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.
This work shows that the bacteria Escherichia coli follow the same death/hazard rate curve as humans, called the Gompertz Law. This is an important finding that tells us that the death rate curve that humans follow through their lifespan has been around since one of the very first living organisms that inhabited earth, although there are exceptions that need to be explained eventually. We also show that death and survival rates can be manipulated with increasing and/or decreasing the organisms stress response, much like humans´ longevity can be increased with a calorie-restricted diet, which increases the protective stress response.
This research project was conducted exclusively with a team of undergraduate researchers from the Paris Bettencourt iGEM team. In 2013, the project was awarded the Grand Prize at the international Genetically Engineered Machines (iGEM) competition.
In this paper we present a model describing the encapsulation of spherical particles bearing weakly acidic surface groups and investigate how charge regulation and size polydispersity impact upon the encapsulation efficiency of gold nanoparticles by model coat proteins.
M. Santolini, A-L Barabasi, (2018) Predicting perturbation patterns from the topology of biological networks. Proc Natl Acad Sci USA, 169, 201720589. Altmetric score: 147 (top 1% of all Altmetric scores). This paper is important in the Network medicine field as it provides a basis to quantify the importance of network topology in predicting the spread of perturbations (differential expression), without the need for sophisticated kinetic models.
Kilic,A., Santolini,M., Nakano,T., Schiller,M., Teranishi,M., Gellert,P., Ponomareva,Y., Braun,T., Uchida,S., Weiss,S.T., et al. (2018) A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. JCI Insight, 3. The major result of this paper resides in the fact that by prioritizing miRNAs by their impact on the gene interaction network instead of differential expression, we uncover and validate novel targets involved in asthma.
In this paper, we use 100 genetically diverse strains of mice to disentangle genetic from environmental effect of a cardiac stressor. We developed a novel method to extract “personalised” genes that are missed by traditional population wide methods.
This is an in-depth study exhibiting the synergy between Six and MyoD proteins taking place during myogenic differentiation, using bioinformatics tools developed during my PhD as well as extensive validation of 20 new enhancers and several novel transcription factor binding sites.
Heuer K and Toro R (2018) Role of mechanical morphogenesis on the development and evolution of the neocortex. Accepted in Physics of Life Reviews. Preprint: https://doi.org/10.31219/osf.io/d2bgr This review extends our discussion about the role of mechanical morphogenesis in neocortical development into brain evolution.
This article develops our theoretical framework for the role of mechanical morphogenetic processes on the development of the neocortex. We aim at introducing physicists to the problematic of brain development, and neurobiologist to the formalisation of non-linear elasticity theory and the biomechanical modelling of growth.
This article is the result of our participation into the 2nd installment of the ABIDE project. The production of this article required an important effort to find the legal and ethical framework that would allow French clinicians to share their data.
This analysis of the anatomy of the corpus callosum in autism is one of the first to use the open access ABIDE data. It provides negative evidence for the idea that the corpus callosum is smaller in patients with autism, and substantial evidence of lack of statistical power and publication bias in the previous literature.
This is the 2nd article of the ENIGMA consortium, a follow up of the original analyses proposed by the same analysis team. The sample is once again the largest ever studied, more than 30k subjects with brain imaging and genetics data, representing an important effort of international collaboration and coordination.
Until this article, imaging genetics analyses have looked for individual variants of strong effect (genome-wide significant). Here, I provide for the first time evidence of a strongly polygenic genomic architecture. The results have since been replicated and extended by several research groups.
This paper emphasizes the tracking technologies based on machine learning used to monitor gestures. This is the tool used in our collaboration on rehabilitation with Hopital Lariboisiere.
This is a physics paper based on research at UGA. It shows for the first time how it is possible to study the dynamics of a capillary nanobridge.
A method for molecular dynamics on curved surfaces; S. Paquay, R. Kusters; Biophysical Journal (2016): We combined standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface and developed it as an open source package for LAMMPS, a MD software package.
M. Adrian, R. Kusters, C. Wierenga, C. Storm, C. Hoogenraad, L. Kapitein; Barriers in the brain: resolving dendritic spine morphology and compartmentalization;Frontiers in Neuroanatomy (2014)
Santos AL, Sinha S, Lindner AB. The Good, the Bad, and the Ugly of ROS: New Insights on Aging and Aging-Related Diseases from Eukaryotic and Prokaryotic Model Organisms (2018). Oxid Med Cell Longev. 2018 Mar 18;2018:1941285. doi:10.1155/2018/1941285.
Santos AL, Lindner AB. Protein Posttranslational Modifications: Roles in Aging and Age-Related Disease. Oxid Med Cell Longev. 2017;2017:5716409. Doi: 10.1155/2017/5716409.