Samuel Soubeyrand
@ssoubeyrand.bsky.social
Researcher at INRAE - Model construction, statistical inference, and their application to epidemiology, ecology... BioSP - INRAE - Avignon, France https://samuel.biosp.org
We are pleased to announce the Biology of Vector-Borne Diseases (BVBD) summer school, 1–5 June 2026, France (sister course of BVBD in Idaho). Apply here bvbd-france.workshop.inrae.fr to bridge disciplines (biology, ecology, epidemiology, modeling, policy) and work on real-world wicked challenges.
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
Discover 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
Samuel Soubeyrand@ssoubeyrand.bsky.social · last yr.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...
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...
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...
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...
Tropolink video series - Introduction
YouTube video by Samuel Soubeyrand
youtu.be
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
Crises sanitaires en agriculture - Les espèces invasives sous surveillance - (EAN13 : 9782759234837) | Librairie Quae : des livres au coeur des sciences
Crises sanitaires en agriculture - Les espèces invasives sous surveillance - (EAN13 : 9782759234837)
quae.com
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...
Avancées à mi-parcours : Développer des indicateurs précoces de surveillance pour la prophylaxie
YouTube video by PPR Cultiver et Protéger Autrement
youtube.com
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...
Interested 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.…
Frontiers | Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial comm...
doi.org
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…
Frontiers | Impact of Lockdown on the Epidemic Dynamics of COVID-19 in France
The COVID-19 epidemic was reported in the Hubei province in China in December 2019 and then spread around the world reaching the pandemic stage at the beginn...
doi.org
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…
Dating and localizing an invasion from post-introduction data and a coupled reaction–diffusion–absorption model
Journal of Mathematical Biology - Invasion of new territories by alien organisms is of primary concern for environmental and health agencies and has been a core topic in mathematical modeling, in...
doi.org
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…
Inferring pathogen dynamics from temporal count data: the emergence of Xylella fastidiosa in France is probably not recent
Unravelling the ecological structure of emerging plant pathogens persisting in multi-host systems is challenging. In such systems, observations are often heterogeneous with respect to time, space ...
doi.org
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…
A Spatio‐Temporal Exposure‐Hazard Model for Assessing Biological Risk and Impact
We developed a simulation model for quantifying the spatio-temporal distribution of contaminants (e.g., xenobiotics) and assessing the risk of exposed populations at the landscape level. The model is...
doi.org
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-…
Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data | Phytopathology®
The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791. A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.
doi.org
PhD position at @Inra_PACA: Statistics and modeling for dispersal networks - Application to epidemiosurveillance informatique-mia.inra.fr/biosp/node/62
Bio-Bayes-Book | Biostatistique & Processus Spatiaux
Suite à l'école chercheur BioBayes (organisée en novembre 2011 à La Rochelle et renouvelée en octobre 2013 à Mandelieu) par un collectif de l'Inra, le projet d'un livre associé a émergé sous la coordination d'Eric Parent. Le titre projeté en est :
informatique-mia.inra.fr
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
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…
Abeilles Road - trailer
Depuis neuf ans l'Observatoire des lavandes en collaboration avec l'INRA d'Avignon et l'ADAPI suit des centaines de ruches pour déterminer les paramètres qui peuvent influer sur la production de miel et la santé des abeilles...
youtube.com
