@ssoubeyrand.bsky.social
Researcher at INRAE - Model construction, statistical inference, and their application to epidemiology, ecology... BioSP - INRAE - Avignon, France https://samuel.biosp.org
New in Mol. Ecol.: integrating multiple data and methods, we show how seasonal fluctuations in pathogen strain composition, diversity and their climate-influenced fitness play a significant role in shaping severity and variability of bacterial disease outbreaks doi.org/10.1111/mec.... #PlantHealth
17.07.2025 13:38 — 👍 1 🔁 2 💬 0 📌 0Discover the newest release in the Tropolink video series: Uncovering the seasonal routes of a plant-pathogen insect vector: www.youtube.com/playlist?lis... This work made by Margaux Darnis et al. is based on tropolink doi.org/10.1029/2023... / pse.mathnum.inrae.fr/tropolink
25.06.2025 12:22 — 👍 2 🔁 1 💬 0 📌 0
mportance of variables. Top left: Matrix of correlations between the weighted meansof standardized importance values computed for each model family. Top right: Percentage of to-tal importance computed for each variable classified in variable types (the horizontal dashed lineshows the threshold we considered for selecting the 14 retained important variables). Bottom:Cumulated percentage of total importance computed for each variable with respect to variabletypes. In the bottom panel, the noticeable information is given by the heights (and colors) ofthe bottom slices in each bar (for each variable type, variables are ordered from bottom to topwith respect to importance value). The total height of the bar for each variable type is largelycorrelated with the number of variables included in it and does not bring important information.
Which model should be used? Which explanatory variables should be selected?... Let's use a model ensemble instead of a single model to characterize and predict spatio-temporal disease distributions. Read our ms in @phytopathology.bsky.social with application to virus yellows doi.org/10.1094/PHYT...
17.06.2025 16:26 — 👍 0 🔁 2 💬 0 📌 0
Take a First Look at the paper about "Opportunities and Challenges in Combining Optical Sensing and Epidemiological Modelling" by Alexey Mikaberidze et al., very recently published in @phytopathology.bsky.social: doi.org/10.1094/PHYT...
11.06.2025 12:48 — 👍 5 🔁 2 💬 0 📌 0
Watch the introduction to the new tropolink video series: youtu.be/L7K88Cz-Ezc, and tutorials showing how to use the tropolink webapp to compute air-mass trajectories and the connectivity between distant sites they generate forgemia.inra.fr/tropo-group/.... Ref. in GeoHealth: doi.org/10.1029/2023...
03.06.2025 17:28 — 👍 2 🔁 2 💬 0 📌 1
Très heureux d'annoncer que notre ouvrage "Crises sanitaires en agriculture" aux éditions Editions Quae, a remporté le Prix Jacques Delage, décerné par le Comité des prix de l'Académie vétérinaire de France.
www.quae.com/produit/1749...
#Bioinvasions
#Biosecurity
#Agriculture
#Health
Two axes of the BEYOND project (beyond.paca.hub.inrae.fr) about epidemiological surveillance presented in French (4:30-19:20): natural language processing for knowledge and alerts, and tropolink webapp (doi.org/10.1029/2023...) for long-distance wind-borne dispersal
www.youtube.com/watch?v=PoPG...
Explore our bioRxiv preprint where we investigate the contribution of pathogen genetic diversity, climatic variation and their interaction towards disease dynamics, using high resol. sequencing data and multiple analysis techniques (with StrainRanking as a guest tool!). doi.org/10.1101/2024...
22.11.2024 12:32 — 👍 3 🔁 0 💬 0 📌 0Interested in fast & non-equilibrium dynamics of within-host pathogen populations? Read our paper just published by @FrontiersIn Microbiology:Associated R code to simulate such dynamics coupling viral kinetics and microevolution:
doi.org/10.5281/zenodo… doi.org/10.3389/fmicb.…
Connecting places: inferring spatiotemporal #networks generated by the movements of air masses, with potential applications in #aerobiology - #AtmosphericHighways - #LongDistanceDispersal
doi.org/10.3389/fams.2…
Our approach for predicting #COVID19 mortality dynamics using data from abroad and comparing country-level dynamics is now published in @PLoS ONE
doi.org/10.1371/journa…
A mechanistic-stat approach yields a factor-7 reduction of the effective reproduction number Re of COVID-19 during lockdown in FR (@FrontMedicine:. The post-lockdown very-mild infection dynamics certainly partly explained by remaining distancing behaviors
doi.org/10.3389/fmed.2…
Visit the BioSP "data blog" about #COVID19 (posts are in French but several preprints in English are available):It includes inferences about #COVID19 epidemiological parameters and the effect of lockdown, as well as forecasts of mortality dynamics.
informatique-mia.inrae.fr/biosp/covid-19
In natura, spatial heterogeneity is more the rule than the exception. We precisely propose a class of log-gaussian Cox processes with high degree of spatial non-stationarity and an accompanying fast estimation approach
doi.org/10.1016/j.spas…
A Bayesian inference of the spatiotemporal spread of #Xylella in South Corsica, France,, to look beyond our temporal analysis- @xf_actors
doi.org/10.1111/nph.15… doi.org/10.1007/s00285…
We use #StatisticalLearning to infer epidemiological links from Deep Sequencing Data and test the approach on Ebola, Swine influenza and a plant potyvirus. See our paper in Philosophical Transactions B
royalsocietypublishing.org/doi/10.1098/rs…
When machine learning and network analysis are used to understand the main drivers of #Xylella fastidiosa infections, produce risk maps and identify lookouts for the design of future surveillance plans
doi.org/10.1094/PHYTO-…
Linking aerial connectivity with genetic compositions of a pathogen: the case of Sclerotinia sclerotiorum
frontiersin.org/articles/10.33…
Open positions at @Inra_PACA, BioSP, for an applied statistician and a computer scientist in information system:
informatique-mia.inra.fr/biosp/pesv-cdd… informatique-mia.inra.fr/biosp/pesv-cdd…
Offre d'emploi à BioSP (@Inra_France, @Inra_PACA, Avignon) dans le cadre de la création de la plateforme nationale d'épidémiosurveillance en santé végétale: Ingénieur de Recherche en épidémiologie et analyse de l’information / Pilotage d’équipe
informatique-mia.inra.fr/biosp/pilote-p…
How to unravel the hidden side(s) of pathogen emergence? Our paper about the emergence of #xylella in Corsica, France, published by @NewPhyt, is available at
doi.org/10.1111/nph.15…
Our simulation tool for assessing biological risk and impact in space and time has been published in Risk Analysis:- The associated R package briskaR is on the cran:
cran.r-project.org/web/packages/b… doi.org/10.1111/risa.1…
GMCPIC: Testing differences between pathogen compositions with small samples and sparse data. MS in @PhytopathologyJ:- Code embedded in the StrainRanking package:
cran.r-project.org/web/packages/S… doi.org/10.1094/PHYTO-…
PhD position at @Inra_PACA: Statistics and modeling for dispersal networks - Application to epidemiosurveillance
informatique-mia.inra.fr/biosp/node/62
Our review for characterizing plant virus spread using molecular epidemiology in Annual Review of Phytopathology:
doi.org/10.1146/annure…
Special issue in Ann. Zool. Fennicifor Ilkka Hanski: The Legacy of a Multifaceted Ecologist
annzool.net/anz/anz541-4.h… annzool.net
... This MCMC algorithm was used to fit a group dispersal model to data (lesions of a fungal disease on a leaf
doi.org/10.1016/j.spas…
T. Mrckvicka and I proposed a MCMC algorithm for estimating doubly inhomogeneous cluster point processes ...
doi.org/10.1016/j.spas…
PhD position in Statistics for Molecular Epidemiology available at BioSP, INRA. Request offer in English if needed.
informatique-mia.inra.fr/biosp/sites/in…
What future for the bees? Abeilles Road, the trailer: In Fr:- In En:
youtube.com/watch?v=2Jm86U… youtube.com/watch?v=41WvRm…
