Data Mining, Databases, Data Science, Business Intelligence, Big Data,
Machine Learning, Data Integration, Data Quality, Master Data Management, Bioinformatics
CEPPPIA :
Centre Expérimental de Prévention Prédictive Participative Individualisée en Auvergne.
Projet porté par le Grand Clermont. Partenaires : CHU de Clermont-Fd, CRNH, Centre Jean Perrin.
RQL :
Rule Query Language platform.
Langage de requêtes pour l'inférence de règles. Collaboration : LIRIS (Lyon), LIAS (Poitiers).
DAG :
Declarative Approaches for Enumerating Interesting Patterns.
Projet ANR DAG. Partenaires : LIRIS (Lyon), CRIL (Lens).
RulNet :
Rule Inference and Network Visualization.
Plateforme de visualisation de réseaux biologiques. Collaboration : GDEC (INRA Crouël).
BREEDWHEAT :
Breeding for economically and environmentally sustainable wheat varieties: an integrated approach from genomics to selection.
Projet ANR Investissements d’avenir. Partenaires : INRA, Biogemma, Limagrain...
Genome reconstruction :
Stratégies de reconstruction de génomes microbiens à partir de métagenomes.
Thèse de Kevin Gravouil. Partenaires : MEDIS, LMGE.
dbWFA :
A Wheat Functional Annotation Database.
Base de données d'annotation fonctionnelle. Collaboration : GDEC (INRA Crouël).
DroPNet :
Bioinformatics platform for functional and proteomics data analysis.
Projet région/FEDER. Partenaires : GRED (INSERM Clermont-Fd), The Gurdon Wellcome Trust Institute (University of Cambridge).
PREFON_META :
Prédiction de domaines fonctionels de séquences de données métagénomiques.
Projet région/FEDER. Partenaires : LMGE (Clermont-Fd).
Publications
Revues internationales
T. Bonnot, P. Martre, V. Hatte, M. Dardevet, P. Leroy, C. Benard, N. Falagan, M-L. Martin-Magniette, C. Deborde, A. Moing, Y. Gibon, M. Pailloux, E. Bancel, C. Ravel.Omics data reveal putative regulators of einkorn grain protein composition under sulphur deficiency. Plant Physiology, 183(2):501-516, 2020.
T. Bonnot, E. Bancel, D. Alvarez, M. Davanture, J. Boudet, M. Pailloux, M. Zivy, C. Ravel, P. Martre.
Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. The Plant Journal, 91(5):894-910, 2017.
B. Chardin, E. Coquery, M. Pailloux, J-M. Petit.
RQL: A query language for rule discovery in databases. Theoretical Computer Science, Vol. 658, pp. 357–374, 2017.
Z. Dai, A. Plessis, J. Vincent, N. Duchateau, A. Besson, M. Dardevet, D. Prodhomme, Y. Gibon, G. Hilbert, M. Pailloux, C. Ravel, P. Martre.
Transcriptional and metabolic alternations rebalance wheat grain storage protein accumulation under variable nitrogen and sulfur supply. The Plant Journal, 83(2):326-43, 2015.
J. Vincent, P. Martre, B. Gouriou, C. Ravel, Z. Dai, J-M. Petit, M. Pailloux.
RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat -Omics Data. PLoS ONE, 10(5), 2015.
J. Vincent, Z. Dai, C. Ravel, F. Choulet, S. Mouzeyar, M.F. Bouzidi, M. Agier, P. Martre.
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. Database, Vol. 2013:bat014, Oxford, 2013.
Y. Renaud, A. Baillif, J-B. Perez, M. Agier, E. Mephu Nguifo, V. Mirouse.
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. Nucleic Acids Research, 40(Web Server issue):W134-9, Oxford, 2012.
N. Chalabi, D.J. Bernard-Gallon, Y.-J. Bignon; Breast Med Consortium, F. Kwiatkowski, M. Agier, V. Vidal, V. Laplace-Chabaud,
V. Sylvain-Vidal, V. Bertholet, F. de Longueville, M. Lacroix, G. Leclercq,
J. Remacle, C. Sibille, N. Zammateo, N. Ben Jaafar, A. Sefiani, K. Ouldim, A. Mégarbané,
N. Jalkh, W. Mahfoudh, W. Troudi, A. Ben Ammar-El Gaïed, L. Chouchane.
Comparative clinical and transcriptomal profiles of breast cancer between French and Mediterranean patients show minor but significative biological differences. Cancer Genomics and Proteomics, 5(5): 253-61, 2008.
M. Agier, J-M. Petit, E. Suzuki.
Unifying framework for rule semantics: Application to gene expression data. Fundamenta Informaticae, 78(4):543-59, special issue on "Best Papers from ISMIS 2005", IOS Press, 2007.
Conférences internationales
B. Chardin, E. Coquery, M. Pailloux, J-M. Petit.
RQL: A SQL-like Query Language for Discovering Meaningful Rules. 14th IEEE International Conference on Data Mining (ICDM), demo session, Shenzhen, China, 2014.
B. Chardin, E. Coquery, B. Gouriou, M. Pailloux, J-M. Petit.
Query Rewriting for Rule Mining in Databases. 1st International ECML/PKDD Workshop on Languages for Data Mining and Machine Learning (LML), Prague, République Tchèque, pp. 35-49, 2013.
M. Agier, C. Froidevaux, J-M. Petit, Y. Renaud, J. Wijsen.
On Armstrong-compliant logical query languages. 4th International EDBT/ICDT Workshop on Logic in Databases (LID), Uppsala, Sweden, pp. 33-40, 2011.
M. Agier and J-M. Petit.
A new and useful syntactic restriction on rule semantics for tabular datasets. 5th International Conference on Formal Concept Analysis (ICFCA), Clermont-Ferrand, France,
Lecture Notes in Computer Science (LNCS), Vol. 4390, pp. 39-50, Springer, 2007.
M. Agier, J-M. Petit, E. Suzuki.
Towards ad-hoc rule semantics for gene expression data. 15th International Symposium on Methodologies for Intelligent Systems (ISMIS), Saratoga Springs, NY, USA,
Lecture Notes in Computer Science (LNCS), Vol. 3488, pp. 494-503, Springer, 2005.
M. Agier and J-M. Petit.
Defining, mining and reasoning on rules in tabular data. 2nd International Workshop on Information Search, Integration and Personalization (ISIP), Lyon, France, 2005.
Brevets
V. Chabaud, C. D'Incan, V. Sylvain-Vidal, V. Vidal, M. Agier, Y.J. Bignon, C. Pradeyrol.
Biochip for determining sensitivity to an anticancer drug.
French Patent n°FR2874622 and International patent n°WO2006027463, 2006.
V. Chabaud, C. D'Incan, V. Sylvain-Vidal, V. Vidal, M. Agier, Y.J. Bignon, C. Pradeyrol.
Biochip for diagnosis of the metastatic or localized character of a mammary tumour, method and kit for use.
French patent n°FR2875512 and International patent n°WO2006032769, 2006.
Revues et conférences nationales
K. Gravouil, C. Hochart, B. Batut, C. Defois, C. Gasc, P. Peyret, D. Debroas, M. Pailloux, E. Peyretaillade.
Stratégies de reconstruction de génomes microbiens à partir de métagénomes. 17èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Lyon, France, pp. 304-7, 2016.
B. Chardin, E. Coquery, M. Pailloux, J-M. Petit.
RQL : un langage "à la SQL" pour découvrir des règles à partir des données. 30èmes journées Bases de Données Avancées (BDA), session démonstration, Grenoble, France, 2014.
J. Vincent, M. Agier, C. Ravel, M F. Bouzidi, S. Mouzeyar, P. Martre.
dbWFA: A Web-Based Database for Functional Annotation of Wheat Transcripts. 12èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Paris, France, pp. 327-8, 2011.
J. Vincent, P. Martre, C. Ravel, A. Baillif, M. Agier.
A Web-Oriented Platform for Gene Regulatory Network Inference. 12èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Paris, France, pp. 293-4, 2011.
R. Saidi, W. Dhifli, S. Aridhi, M. Agier, G. Bronner, D. Debroas, L. D'Orazio, F. Enault, S. Guillaume, E. Mephu Nguifo.
Protein classification in the case of large and many-class datasets: A comparison with BLAST and BLAT. 12èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Paris, France, pp. 221-2, 2011.
M. Agier.
Différents types de règles pour la reconstruction de réseaux de gènes à partir de données d'expression. Revue I3 Information - Interaction - Intelligence, numéro hors série, pp. 161-81, Cépaduès Editions, 2007.
M. Agier and J-M. Petit.
Un outil pour la visualisation de relations entre gènes. 7ème conférence Extraction et Gestion des Connaissances (EGC), session démonstration,
Namur, Belgique, Revue des Nouvelles Technologies de l’Information (RNTI), Vol. 1, RNTI-E-9, pp. 185-6, Cépaduès Editions, 2007.
M. Agier and J-M. Petit.
A new and useful syntactic restriction on rule semantics for tabular data. 21èmes journées Bases de Données Avancées (BDA), Saint-Malo, France, pp. 135-50, 2005.
M. Agier and J-M. Petit.
Notion de sémantiques bien-formées pour les règles. 5ème conférence Extraction et Gestion des Connaissances (EGC),
Paris, France, Revue des Nouvelles Technologies de l’Information (RNTI), Vol. 1, RNTI-E-3, pp. 19-30, Cépaduès Editions, 2005.
M. Agier, J-M. Petit, V. Chabaud, C. Pradeyrol, Y-J. Bignon, V. Vidal.
Vers différents types de règles pour les données d'expression de gènes - Application à des données de tumeurs mammaires. XXIIème congrès Informatique des Organisations et Systèmes d'Information et de Décision (INFORSID), Biarritz, France, pp. 351-67, 2004.
Divers
E. Bancel, T. Bonnot, M. Davanture, M. Pailloux, M. Zivy, P. Martre, C. Ravel.
Proteomic changes occuring in einkorn (Triticum monoccocum) grain during filling. Breeding cereals for sustainable agriculture Symposyum, EUCARPIA cereal section, Clermont-Ferrand, France, 2018.
T. Bonnot, E. Bancel, D. Alvarez, M. Dardevet, J. Boudet, M. Davanture, A. Moing, Y. Gibon, M. Zivy, M. Pailloux, P. Martre, C. Ravel.
Integration of "omics" data provides tools for understanding effects of variable nitrogen (N) and sulphur (S) supply during wheat grain development. 2nd Work Group 2 meeting of COST Action FA1306 "Diving into integrative cell phenotyping through 'omics'", Versailles, France, 2016.
J. Vincent, I. Romeuf, A. Besson, C. Ravel, Z. Dai, M. Dardevet, Y. Gibon, M. Pailloux, P. Martre.
Unravelling transcriptional regulators of grain development and their response to nitrogen and sulfur availability for wheat. 7th European Plant Science Organisation Conference (EPSO), Porto Heli, Greece, 2013.
A. Baillif, M. Agier, E. Mephu Nguifo, V. Mirouse.
DroPNet: Bioinformatics web platform for functional and proteomics data analysis. 11èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Montpellier, France, 2010.
R. Saidi, S. Aridhi, M. Agier, G. Bronner, D. Debroas, L. D'Orazio, F. Enault, S. Guillaume, E. Mephu Nguifo.
Functional prediction in the scope of large-scale multi-class learning. 11èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Montpellier, France, 2010.
M-L. Vuillaume, N. Uhrhammer, V. Vidal, V. Sylvain Vidal, V. Chabaud, M. Agier, Y-J. Bignon.
Search for a rapid pre-screening technique to identify heterozygous BRCA mutation carriers using gene expression profiling in peripheral blood lymphocytes. The European Human Genetics Conference, Nice, France, 2007.
A. Scalbert, R. Llorach, C. Manach, E. Pujos, J-F. Martin, M. Agier, J. Lampe.
Phytochemicals as prominent constituents of the human metabolome - From dietary exposure to health effects. 3rd International Conference of the Metabolomics Society, Manchester, UK, 2007.
M. Agier.
De l'analyse de données d'expression à la reconstruction de réseaux de gènes. Doctorat en informatique, Université Blaise Pascal-Société Imaxio, Clermont-Ferrand, France, 2006.
M. Agier, V. Chabaud, J-M. Petit, V. Sylvain, C. DIncan, V. Vidal, Y-J. Bignon.
Towards meaningful rules between genes from gene expression data. 6th International Meeting of the Microarray Gene Expression Data Society (MGED), Aix-en-Provence, France, 2003.