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
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.
November 13, 2025 at 1:57 PM
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
July 17, 2025 at 1:38 PM
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
June 25, 2025 at 12:22 PM
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
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...
June 17, 2025 at 4:26 PM
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...
June 11, 2025 at 12:48 PM
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...
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...
November 22, 2024 at 12:32 PM
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...
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…
doi.org/10.3389/fams.2…
December 22, 2024 at 4:23 PM
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…
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…
doi.org/10.1371/journa…
December 22, 2024 at 4:23 PM
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…
doi.org/10.1371/journa…
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
informatique-mia.inrae.fr/biosp/covid-19
December 22, 2024 at 4:23 PM
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…
doi.org/10.1016/j.spas…
December 22, 2024 at 4:23 PM
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…
doi.org/10.1016/j.spas…
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…
royalsocietypublishing.org/doi/10.1098/rs…
December 22, 2024 at 4:23 PM
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…
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-…
doi.org/10.1094/PHYTO-…
December 22, 2024 at 4:23 PM
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-…
doi.org/10.1094/PHYTO-…
Linking aerial connectivity with genetic compositions of a pathogen: the case of Sclerotinia sclerotiorum
frontiersin.org/articles/10.33…
frontiersin.org/articles/10.33…
December 22, 2024 at 4:23 PM
Linking aerial connectivity with genetic compositions of a pathogen: the case of Sclerotinia sclerotiorum
frontiersin.org/articles/10.33…
frontiersin.org/articles/10.33…
Our review for characterizing plant virus spread using molecular epidemiology in Annual Review of Phytopathology:
doi.org/10.1146/annure…
doi.org/10.1146/annure…
December 22, 2024 at 4:22 PM
Our review for characterizing plant virus spread using molecular epidemiology in Annual Review of Phytopathology:
doi.org/10.1146/annure…
doi.org/10.1146/annure…
... 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…
doi.org/10.1016/j.spas…
December 22, 2024 at 4:22 PM
... 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…
doi.org/10.1016/j.spas…
Nicolas Parisey et al. rearrange agricultural landscapes in silico for regulating pests
dx.doi.org/10.1016/j.ecoc…
dx.doi.org/10.1016/j.ecoc…
December 22, 2024 at 4:21 PM
Nicolas Parisey et al. rearrange agricultural landscapes in silico for regulating pests
dx.doi.org/10.1016/j.ecoc…
dx.doi.org/10.1016/j.ecoc…
Spatial limits & fragmentation shape freq. of indep., clump and group dispersal strategies
dx.doi.org/10.1007/s10682…
dx.doi.org/10.1007/s10682…
December 22, 2024 at 4:21 PM
Spatial limits & fragmentation shape freq. of indep., clump and group dispersal strategies
dx.doi.org/10.1007/s10682…
dx.doi.org/10.1007/s10682…
See our BvM-like theorem showing asymptotic normality of ABC-posteriors conditional on MPLE:
dx.doi.org/10.1016/j.spl.…
dx.doi.org/10.1016/j.spl.…
December 22, 2024 at 4:21 PM
See our BvM-like theorem showing asymptotic normality of ABC-posteriors conditional on MPLE:
dx.doi.org/10.1016/j.spl.…
dx.doi.org/10.1016/j.spl.…
A need for a review paper about sharka? Loup Rimbaud and colleagues made it:
dx.doi.org/10.1146/annure…
dx.doi.org/10.1146/annure…
December 22, 2024 at 4:21 PM
A need for a review paper about sharka? Loup Rimbaud and colleagues made it:
dx.doi.org/10.1146/annure…
dx.doi.org/10.1146/annure…
New introductory textbook about Bayesian stats that follows 2 @Inra_France training workshops
editions-ellipses.fr/product_info.p…
editions-ellipses.fr/product_info.p…
December 22, 2024 at 4:21 PM
New introductory textbook about Bayesian stats that follows 2 @Inra_France training workshops
editions-ellipses.fr/product_info.p…
editions-ellipses.fr/product_info.p…
Our US rainfall-feedback mapsleading to open questions, e.g. land use influence on #drought?
w3.avignon.inra.fr/rainfallfeedba…
w3.avignon.inra.fr/rainfallfeedba…
December 22, 2024 at 4:20 PM
Our US rainfall-feedback mapsleading to open questions, e.g. land use influence on #drought?
w3.avignon.inra.fr/rainfallfeedba…
w3.avignon.inra.fr/rainfallfeedba…
December 22, 2024 at 4:20 PM
Example of dispersal pattern obtained with the model for group dispersal in a fragmented habitat
December 22, 2024 at 4:20 PM
Example of dispersal pattern obtained with the model for group dispersal in a fragmented habitat
December 22, 2024 at 4:19 PM
#Lionel_Roques wrote a textbook in French about reaction-diffusion models for spatial ecology
quae.com/fr/r3099-model…
quae.com/fr/r3099-model…
December 22, 2024 at 4:19 PM
#Lionel_Roques wrote a textbook in French about reaction-diffusion models for spatial ecology
quae.com/fr/r3099-model…
quae.com/fr/r3099-model…