Marie-Josée Cros - Activities

Marie-Josée Cros

See my Google Scholar page or some traces of my past activities organized to reflect collaborations and chronology:

- Probabilistic Graphical Models (2015-): Inference, GMtoolbox, Dynamic Bayesian Network, Inference of marine network from counts
- Sequential decision making under uncertainty (2000-): GMDPtoolbox, MDPtoolbox, IDtoolbox, Dynamic Bayesian Network
- Identification of non-coding RNAs (2005-2012): RNaspace, ApolloRNA, Prediction, Studies
- Gene finding (2001-2005): EuGene
- Modeling and simulation in agricultural production (1990-2001)
- Simulation of rotational grazing management (1996-2001): SEPATOU
- Determination of greenhouse climate setpoints (1991-1996): SERRISTE

Probabilistic Graphical Models (2015-2022)

Hidden Semi-Markov Model
- - A hidden semi-Markov model for inferring the structure of migratory bird flyway networks. N. Peyrard, MJ. Cros, R. Sabbadin, R. Trépos, S. Nicol. Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes (JFRB), Porquerolles France, 2021.
  - A hidden semi-Markov model for inferring the structure of migratory bird flyway networks. N. Peyrard, R. Sabbadin, MJ. Cros, R. Trépos, S. Nicol. International Statistical Ecology Conference (ISEC), Sidney Australia, 2020.
Inference
- - Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited. N. Peyrard, MJ. Cros, S. de Givry, A. Franc, S. Robin, R. Sabbadin, T. Schiex, M. Vignes. Australian and NewZealand Journal of Statistics, vol 61(2), pp 89-133, 2019. (also on arXiv)
GMtoolbox : functions for inference in Graphical Models.
- - GMtoolbox code (MATLAB).
Dynamic Bayesian Network

- Improving Pest Monitoring Networks using a simulation-based approach to contribute to pesticide reduction. MJ. Cros, JN Aubertot, S. Gaba, X. Reboud, R. Sabbadin, N. Peyrard. Theoretical Population Biology 141, 2021. arXiv:2002.00951.
- A DBN model to study the influence of epidemio surveillance networks on phytosanitary treatments. JN. Aubertot, MJ. Cros, S. Gaba, N. Peyrard, X. Reboud, R. Sabbadin. Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes (JFRB), Toulouse France, 31 mai-1 juin 2018.
- A modelling approach to evaluate the influence of spatial density historic length of an Epidemio Surveillance Network on the intensity of phytosanitary treatments on crops. MJ. Cros, N. Peyrard, R. Sabbadin, JN. Aubertot, S. Gaba, X. Reboud. EFITA WCCA Congress, Montpellier, France, July 2017.

Inference of marine network from counts

- Le modèle Poisson log-normal : un cadre générique pour l’analyse de distributions jointes d’abondance. J. Chiquet , MJ. Cros , M. Mariadassou , N. Peyrard , S. Robin. In Approches statistiques pour les variables cachées en écologie – N. Peyrard, O. Gimenez - To be published by ISTE.
- Apprentissage d'un réseau écologique marin à partir de données de comptage. MJ. Cros, LT. Duong, N. Peyrard. MARAMI, Avignon, France, Oct. 2018.

Sequential decision making under uncertainty (2000-2022)

GMDPtoolbox : functions related to Graph-based Markov Decision Processes (GMDP) to represent and approximately solve Markov Decision Processes (MDP) problems with an underlying spatial structure allowing a factored representation.
- GMDPtoolbox code (MATLAB)
- GMDPtoolbox: A Matlab library for designing spatial management policies. Application to the long-term collective management of an airborne disease. MJ. Cros, JN. Aubertot, N. Peyrard, R. Sabbadin. PLoS ONE 12(10), 2017.
- Sustainable collective pest management using a Graph-based Markov Decision Processes framework. JN. Aubertot, MJ. Cros, N. Peyrard and R. Sabbadin. International Congress on Environmental Modelling and Software (iEMSs), Toulouse France, July 10-14, 2016.
- GMDPtoolbox: a Matlab library for solving Graph-based Markov Decision Processes. MJ. Cros, N. Peyrard and R. Sabbadin. Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes (JFRB), Clermont-Ferrand France, 27-28 juin 2016.
MDPtoolbox : functions related to the resolution of discrete-time Markov Decision Processes: backwards induction, value iteration, policy iteration, linear programming algorithms with some variants.
- MDPtoolbox code available on several environments: MATLAB, GNU Octave, Scilab and R.
- Multi-objective sequential forest management under risk using a Markov Decision Process-Pareto fontier approach. S. Couture, MJ. Cros, R. Sabbadin. Environmental Modeling & Assessment, 26, 2021.
- Multi-objective forest management under risk by exploring Pareto frontier. S. Couture, MJ. Cros, R. Sabbadin. World Conference on Natural Resource Modeling. Barcelona, Spain, June 2017.
- Risk aversion and optimal management of an uneven-aged forest under risk of windthrow: A Markov decision process approach. S. Couture, MJ. Cros, R. Sabbadin. Journal of Forest Economics 25, 94-114, 2016.
- Risk preferences and optimal management of uneven-aged forests in the presence of climate change: a Markov decision process approach. S. Couture, MJ. Cros, R. Sabbadin. World Congress of Environmental and Resource Economists. Istanbul, Turkey, July 2014.
- Risk preferences and optimal management of uneven-aged forests in the presence of climate change: a Markov decision process approach. S. Couture, MJ. Cros, R. Sabbadin. IUFRO symposium, Sopron, Hungary, May 2014.
- MDPtoolbox: a multi-platform toolbox to solve stochastic dynamic programming problems. I. Chades, G. Chapron, MJ. Cros, F. Garcia, R. Sabbadin. Ecography 37:916-920, 2014.
IDtoolbox : Influence Diagram toolbox (MATLAB, version beta)

Identification of non-coding RNAs (2005-2012)

RNAspace : environment that allows to create web sites dedicated to non-protein-coding RNA (ncRNA) prediction, annotation and analysis. An instance is the web site RNAspace.org
- RNAspace code (Python).
- RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. MJ. Cros, A. de Monte, J. Mariette, P. Bardou, B. Grenier-Boley, D. Gautheret, H. Touzet, C. Gaspin. RNA , 17(11):1947-56, 2011.
- RNAspace: an integrated environment for the prediction, annotation and analysis of non-coding RNA. MJ. Cros, A. de Monte, J. Mariette, P. Bardou, D. Gautheret, H. Touzet, C. Gaspin. Poster at JOBIM, Paris, 2011.
- rnaspace.org - a web application for noncoding RNA identification. MJ. Cros, A. de Monte, J. Mariette, P. Bardou, D. Gautheret, H. Touzet, C. Gaspin. Poster at JOBIM, Montpellier, 2010.
- RNAspace - non-coding RNA annotation web platform. MJ. Cros, A. de Monte, J. Mariette, P. Bardou, D. Gautheret, H. Touzet, C. Gaspin. Poster at JOBIM, Nantes, 2009.
- Développement d'une plateforme web avec CherryPy. MJ. Cros. Conférence Pycon, Paris, 2009.
ApolloRNA : extension for ncRNA identification of the Apollo environment, a genome annotation viewer and editor.
- ApolloRNA code (mainly Java).
- ApolloRNA - Visual genome environment to support ncRNA identification. MJ. Cros, A. Moisan, C. Cierco-Ayrolles, C. Gaspin. Poster at Congrès annuel SFBBM-SifrARN, Montpellier, France, 2008.
- ApolloRNA - Visual support to ncRNA identification and analysis. MJ. Cros, A. Moisan, C. Cierco-Ayrolles, C. Gaspin. Poster at the 5th Colmar Symposium: The New RNA Frontiers, Colmar, France, 2007.
- Visualizing and exploring genomic information for non-protein-coding RNA identification using ApolloRNA. MJ. Cros, E. Sallet, A. Moisan, C. Cierco-Ayrolles, C. Gaspin. Nature Protocol Exchange, doi:10.1038/nprot.2007.285, 2007.
- Visualizing genome information for ncRNA search. MJ. Cros, E. Sallet, A. Moisan, C. Cierco-Ayrolles, C. Gaspin. Poster at the Workshop RiboReg, Carry le Rouet, France, 2007.
- Non-Protein-coding RNA identification and analysis: Choice and extension of Apollo. MJ. Cros, E. Sallet, A. Moisan, C. Cierco-Ayrolles, C. Gaspin. Short presentation and poster at Jobim, Marseille, France, 2007.
Prediction of non-coding RNA
- Classification d'ARN non-codant-protéine par SVM. MJ. Cros. Poster at EPIT, 2008.
- Etude de classification d'ARN non-codants par SVM. MJ. Cros. Document interne INRA Toulouse, 2005.
- Prediction ab initio d'ARN non codant. C. Cierco-Ayrolles, MJ. Cros, C. Gaspin, A. Kozomara. Poster at Journée annuelle GenoToul, Toulouse, 2006.
- Prédiction d'ARNnc ab initio : Etude de l'apport en G et C en séquence et appariés dans une structure prédite. MJ. Cros. Document interne INRA Toulouse, 2006.
Studies on organisms :
- A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. T. Geissmann, C. Chevalier, MJ. Cros, S. Boisset, P. Fechter, C. Noirot, J. Schrenzel, P. François, F. Vandenesch, C. Gaspin, P. Romby. Nucleic Acids Res., 37(21):7239-57, doi: 10.1093/nar/gkp668, 2009.
- Identification and Characterization of new non-coding RNA in Pyrococcus abyssi. K. Phok, A. Moisan, MJ. Cros, C. Gaspin, B. Clouet D'Orval. Poster at the International Conference on Regulatory RNA in prokaryotes, Berlin, 2009.
- PeRNA code (Perl) to build a databank to analyze non-protein-coding RNA.
- Recherche de riboswitch par apprentissage sur Staphylococcus aureus. MJ. Cros. Document interne INRA Toulouse, 2007.
- Studies for ncRNA prediction in Staphylococcus aureus. C. Cierco, MJ. Cros, C. Gaspin, A. Moisan. Document interne INRA Toulouse, 2006.
- Studies for ncRNA prediction in Ralstonia solanacearum GMI100. C. Cierco, MJ. Cros, C. Gaspin, A. Moisan. Document interne INRA Toulouse, 2006.
- Studies for ncRNA prediction in Pyrococcus abyssi. C. Cierco, MJ. Cros, C. Gaspin, A. Moisan. Document interne INRA Toulouse, 2006.

Gene finding (2001-2005)

participation in EuGène : open integrative gene finder for eukaryotic and prokaryotic genomes.
- Medicagoo: Searching Medicago resources. In Medicago truncatula handbook, 2006.
- EuGène: an open gene finder for eukaryotes. P. Bardou, MJ. Cros, S. Foissac, J. Gouzy, and T. Schiex. User documentation, 2004.
- EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. S. Foissac, P. Bardou, A. Moisan, MJ. Cros, T. Schiex. Nucleic Acids Res., 31(13):3742-5, 2003.
- EuGene'Hom web site: a generic gene finder using multiple homologous sequences.
- Adaptation d'EuGène au génome du riz. P.Bardou, MJ. Cros, S. Foissac, A. Moisan, AM. Henry, B. Piégu, J. Salse, T. Schiex,R. Cooke. Poster at Séminaire GENOPLANTE, Poitiers, France, 2003.

Modeling and simulation in agricultural production (1990-2001)

Modeling and simulation. MJ. Cros, F. Garcia, R. Martin-Clouaire, JP. Rellier. CIGR Handbook of Agricultural Engineering, Vol.6, ch. 3, doi:10.13031/2013.21668, 2006.
Modeling management operations in agricultural production simulators. MJ. Cros, F. Garcia, R. Martin-Clouaire, JP. Rellier. Agricultural Engineering International: the CIGR electronic Journal of Scientific Research and Development (5), 2003.
Modeling and simulating agricultural production processes. MJ. Cros, F. Garcia, R. Martin-Clouaire, JP. Rellier. ASAE Annual Meeting, doi: 10.13031/2013.9620, 2002.
Management of agricultural production systems. MJ. Cros, R. Martin-Clouaire. 3rd International Congress for Computer Technology, 'Integrated Decision Support Systems in Agriculture', Franckfurt, Germany, 1990.

Simulation of rotational grazing management (1996-2001)

SEPATOU : simulation and optimization of rotational grazing management in a dairy production system
- SEPATOU and OPTI-SEPATOU code (C++), considered climates, elicited strategies..
- Simulating management strategies: the rotational grazing example. MJ. Cros, F. Garcia, R. Martin-Clouaire. Agricultural systems, 80 (2004).
- A biophysical dairy farm model to evaluate rotational grazing management strategies. MJ. Cros, M. Duru, F. Garcia, R. Martin-Clouaire. Agronomie, 23, 105-122, 2003.
- Modeling grazing systems in dairy production. M. Duru, MJ. Cros, F. Garcia, R. Martin-Clouaire. Proceedings of the Symposium Int. of Animal Production, Everling D., Ferreira de Quadros F., Viégas J. et al., editors, Santa Maria, Brazil, 2002.
- Modeling and simulating agricultural production processes. MJ. Cros, M. Duru, F. Garcia and R. Martin-Clouaire. In Proceedings of the 2002 ASAE Annual International Meeting, Chicago, 2002.
- Simulating rotational grazing management. MJ. Cros, M. Duru, F. Garcia, and R. Martin-Clouaire. In European Grass Congress, La Rochelle, France, 2002.
- News in a satirical Journal ! Le canard enchaîné, 31 juillet 2002.
- Validation du simulateur SEPATOU. MJ. Cros, F. Garcia, R. Martin-Clouaire, M. Duru. Ecole-Chercheurs Aide à la décision - Comment articuler connaissances et actions, La Londe-les-Maures, France, 2001.
- Simulation optimization of grazing management strategies. MJ. Cros, F. Garcia, R. Martin-Clouaire. In Proceedings of the 3rd Europ. Conf. On Information Technology in Agriculture (EFITA'01), Montpellier, France, 2001.
- Simulating rotational grazing management. MJ. Cros, M. Duru, F. Garcia, R. Martin-Clouaire. Environment International, 27, 139-145, 2001.
- SEPATOU, un simulateur de conduites du pâturage à l'épreuve des menus bretons. MJ. Cros, M. Duru, D. Peyre. Fourrages (167), 365-383, 2001.
- SEPATOU : simulation de conduites du pâturage - exemple des "menus" bretons. MJ. Cros, M. Duru, D. Peyre. Journées AFPF, Paris, France, 2001.
- Evaluation d'un simulateur de stratégies de pâturages de vaches laitières. MJ. Cros, M. Duru, F. Garcia, M. Grasset, A. Legall, R. Martin-Clouaire, Peyre, L. Delaby, JL. Fiorelli, JL. Peyraud. Rencontres autour des recherches sur les ruminants, Paris, 2000.
- SEPATOU : cadre général et composantes décisionnelles. MJ. Cros, F. Garcia, R. Martin-Clouaire. Document interne INRA Toulouse, 2000.
- SEPATOU : cadre général et composantes biophysiques. MJ. Cros, F. Garcia, R. Martin-Clouaire. Document interne INRA Toulouse, 2000.
- SEPATOU: a decision support system for the management of rotational grazing in a dairy production. MJ. Cros, F. Garcia, R. Martin-Clouaire. In Proceedings of the 2nd Europ. Conf. On Information Technology in Agriculture (EFITA), Bonn, Germany, 1999.
- A DSS for rotational grazing management: simulating both the biophysical and decision making processes. MJ. Cros, M. Duru, F. Garcia, R. Martin-Clouaire. In Proceedings of the International Congress on Modelling and Simulation (MODSIM), 759-764, Hamilton, New-Zealand, 1999.
- Expliciting and evaluating management strategies: a case study in dairy production . MJ. Cros, M. Duru, F. Garcia, R. Martin-Clouaire. BIO-DECISION, Montpellier, France, 1998.
- Characterizing and simulating a rotational grazing strategy. MJ. Cros, M. Duru, F. Garcia, R. Martin-Clouaire. In Proceedings of the 1st European Conference for Information Technology in Agriculture, Copenhagen, Denmark, 1997.

Determination of greenhouse climate setpoints (1991-1996)

SERRISTE : Determination of greenhouse climate setpoints.
- News in a newspaper ! Le Monde interactif, avril 2000.
- Determination of greenhouse climate setpoints by SERRISTE: the approach and its object-oriented implementation>. R. Martin-Clouaire, K. Kovats, MJ. Cros. AI Applications, 7 (1), 1993.
- Using empirical knowledge for the determination of climatic setpoints: An artificial intelligence approach. R. Martin-Clouaire, T. Boulard, MJ. Cros, B. Jeannequin. In The computerized greenhouse, Academic Press, 1993.
- Base de connaissance de SERRISTE. MJ. Cros, R. Martin-Clouaire. Document interne INRA Toulouse, 1994.
- SERRISTE: an object-oriented software for the determination of climatic setpoints. MJ. Cros, R. Martin-Clouaire. 4th International Congress for Computer Technology in Agriculture, Versailles, France, 1992.
- Choix de consignes climatiques par le logiciel SERRISTE. MJ. Cros, R. Martin-Clouaire. Document interne INRA Toulouse, 1992.
- Setpoint determination by constraint satisfaction. MJ. Cros, R. Martin-Clouaire. First IFAC/ISHS Workshop on Mathematical and Control Applications in Agriculture and Horticulture. Matsuyama, Japan, 1991.
- Détermination de consignes par satisfaction de contraintes. MJ. Cros, R. Martin-Clouaire. 11th International Worshop Expert systems and their applications, Avignon, France, 1991.

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