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28 results on '"Cros, Marie-Josée"'

1. Improving Pest Monitoring Networks in order to reduce pesticide use in agriculture

Author

Cros, Marie-Josée, Aubertot, Jean-Noël, Gaba, Sabrina, Reboud, Xavier, Sabbadin, Régis, and Peyrard, Nathalie

Subjects
Quantitative Biology - Populations and Evolution, Statistics - Applications, 62P10, 62P12
Abstract

Disease and pest control largely rely on pesticides use and progress still remains to be made towards more sustainable practices. Pest Monitoring Networks (PMNs) can provide useful information for improving crop protection by restricting pesticide use to the situations that best require it. However, the efficacy of a PMN to control pests may depend on its spatial density and space/time sampling balance. Furthermore the best trade-off between the monitoring effort and the impact of the PMN information may be pest dependent. We developed a generic simulation model that links PMN information to treatment decisions and pest dynamics. We derived the number of treatments, the epidemic extension and the global gross margin for different families of pests. For soil-borne pathogens and weeds, we found that increasing the spatial density of a PMN significantly decreased the number of treatments (up to 67\%), with an only marginal increase in infection. Considering past observations had a second-order effect (up to a 13\% decrease). For the spatial scale of our study, the PMN information had practically no influence in the case of insects. The next step is to go beyond PMN analysis to design and chose among sustainable management strategies at the landscape scale.

Published
2020

4. Exact and approximate inference in graphical models: variable elimination and beyond

Author

Peyrard, Nathalie, Cros, Marie-Josée, de Givry, Simon, Franc, Alain, Robin, Stéphane, Sabbadin, Régis, Schiex, Thomas, and Vignes, Matthieu

Subjects
Statistics - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Learning
Abstract

Probabilistic graphical models offer a powerful framework to account for the dependence structure between variables, which is represented as a graph. However, the dependence between variables may render inference tasks intractable. In this paper we review techniques exploiting the graph structure for exact inference, borrowed from optimisation and computer science. They are built on the principle of variable elimination whose complexity is dictated in an intricate way by the order in which variables are eliminated. The so-called treewidth of the graph characterises this algorithmic complexity: low-treewidth graphs can be processed efficiently. The first message that we illustrate is therefore the idea that for inference in graphical model, the number of variables is not the limiting factor, and it is worth checking for the treewidth before turning to approximate methods. We show how algorithms providing an upper bound of the treewidth can be exploited to derive a 'good' elimination order enabling to perform exact inference. The second message is that when the treewidth is too large, algorithms for approximate inference linked to the principle of variable elimination, such as loopy belief propagation and variational approaches, can lead to accurate results while being much less time consuming than Monte-Carlo approaches. We illustrate the techniques reviewed in this article on benchmarks of inference problems in genetic linkage analysis and computer vision, as well as on hidden variables restoration in coupled Hidden Markov Models., Comment: 47 pages, 3 tables, 12 figures

Published
2015

11. FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data.

Author

Nicol, Sam, Cros, Marie‐Josée, Peyrard, Nathalie, Sabbadin, Régis, Trépos, Ronan, Fuller, Richard A., and Woodworth, Bradley K.

Subjects
MIGRATORY birds, SHORE birds, BENCHMARK problems (Computer science), STRUCTURAL frames, HIDDEN Markov models, CITIZEN science, STATISTICAL models
Abstract

Copyright of Methods in Ecology & Evolution is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2023
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14. A hidden semi-Markov model for inferring the structure of migratory bird flyway networks

Author

Peyrard, Nathalie, Sabbadin, Régis, Cros, Marie-Josée, Trepos, Ronan, Nicol, Sam, Peyrard, Nathalie, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CISRO AUS, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [MATH] Mathematics [math], [MATH]Mathematics [math], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

16. A modeling approach to evaluate the influence of spatial and temporal structure of an epidemiological surveillance network on the intensity of phytosanitary treatments on crops

Author

Cros, Marie-Josée, Peyrard, Nathalie, Sabbadin, Régis, Aubertot, Jean-Noel, Gaba, Sabrina, Reboud, Xavier, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and ProdInra, Migration

Subjects
[SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [MATH] Mathematics [math], pesticides, [INFO] Computer Science [cs], pest monitoring, simulation, dynamic bayesian networks, [SHS]Humanities and Social Sciences, [SDV] Life Sciences [q-bio], supervised control, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SHS] Humanities and Social Sciences, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

18. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Author

Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, Romby, Pascale, Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, and Romby, Pascale

Abstract

Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism

Published
2017

19. Recherche reproductible et calcul scientifique

Author

Cros, Marie-Josée, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), and Institut National de la Recherche Agronomique (INRA)

Subjects
recherche reproductible, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

20. RNAspace: an integrated environment for the prediction, annotation and analysis of non-coding RNA

Author

Cros, Marie-Josée, de Monte, Antoine, Mariette, Jérôme, Bardou, Philippe, Gautheret, Daniel, Touzet, Hélène, Gaspin, Christine, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
ComputingMethodologies_PATTERNRECOGNITION, genome annotation, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], non-protein-coding RNA, ncRNA gene finder
Abstract

National audience; RNAspace is an environment that allows to create web sites dedicated to nonprotein- coding RNA (ncRNA) prediction, annotation and analysis. The web sites allow users to run a variety of tools in an integrated and flexible way. RNAspace is focused on the integration of complementary ncRNA gene finders. It also offers a set of tools for the comparison, visualization, edition and export of ncRNAs candidates. Predictions can be filtered according to a large set of characteristics. A public web site http://rnaspace.org has been created that allows for on line annotation of a complete bacterial genome or a small eukaryotic chromosome.

Published
2011

21. rnaspace.org - a web application for noncoding RNA identification

Author

Cros, Marie-Josée, de Monte, Antoine, Mariette, Jérôme, Bardou, Philippe, Gautheret, Daniel, Touzet, Helene, Gaspin, Christine, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Université des Sciences et Technologies (Lille 1) (USTL), Algorithms for large scale sequence analysis (SEQUOIA2), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Plateforme Bio-Informatique - Génotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Plateforme SIGENAE, Université Paris-Sud - Paris 11 (UP11), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Lille, Sciences et Technologies, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2010

26. A biophysical dairy farm model to evaluate rotational grazing management strategies

Author

Cros, Marie-Josée, Duru, Michel, Garcia, Frédérick, and Martin-Clouaire, Roger

Abstract

This paper describes a biophysical dairy farm model developed as part of the SEPATOU system that simulates pasture-dominated feeding strategies in a dairy cow enterprise. It can reproduce the effects of various technical management options applied to a set of grazing fields on a daily basis over a period of several months. The model is made up of three submodels that deal with the soil (availability of water), sward and animal (cow intake and milk yield) components. It includes as driving variables the main factors that farmers can control (nitrogen fertilizer rate, defoliation frequency and intensity, composition of cows' diet) in order to attain some objectives such as the intended grazing herbage contribution in the cows' diet or the amount of milk produced per cow or per ha. The intended purpose of the SEPATOU system has led to several original developments. In order to simulate various defoliation regimes, growth and senescence processes are dissociated as there is no longer synchronization between them, and the effect of grazing intensity is expressed in terms of the ratio between the herbage mass after and before grazing. The animal intake submodel that can deal with mixed feeding combines two approaches, one based on energy requirements and the other on the relationship between herbage mass, herbage digestibility and intake. The model of herbage digestibility is based on herbage mass and takes into account its variation down the sward profile; this latter aspect plays a key role in the plant-animal interaction. The model has been validated using typical farm cases in Brittany. It provides realistic estimates of the state variables involved in the processes, such as herbage mass and daily milk yield, and it credibly predicts the timing of key events (e.g. date of turnout to grass, end of first grazing cycle).

Published
2003

27. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Author

Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, Romby, Pascale, Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, and Romby, Pascale

Abstract

Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism

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