Projet PROSPECTOM — Appel d’offre Mastodons du CNRS

Liste des publications/communications pour 2014 :

• T. Burger. "Geometric Interpretations of conflict: A viewpoint",  The 3rd International Conference on Belief Functions (BELIEF 2014), LNCS Vol. 8764, pp. 412-421, Oxford, UK, September 2014.
• N. Courty, G. Xing, J. Vandel, T. Burger. "SAGA: Sparse And Geometry-Aware non-negative matrix factorization through non-linear local embedding". Machine Learning, 97(1-2), pp. 205-226, 2014.
• J. Estellon, S. Ollagnier de Choudens, M. Smadja, M. Fontecave M, Y. Vandenbrouck. Design and assessment of an integrative predictive model for large-scale identification of metalloproteins in prokaryotic genomes: iron-sulfur cluster proteins. Metallomics. 2014. 6(10):1913-30. Selected as "Hot Article 2014" by Metallomics
• F. Pichon, S. Destercke, T. Burger. "A consistency-specificity trade-off to select source behavior in information fusion". IEEE trans. on System, Man and Cybernetics - Part B, accepted for publication (06/2014).
• M. Tomizioli, C. Lazar, S. Brugiere, T. Burger, D. Salvi, L. Gatto, L. Moyet, L. M. Breckels, A.-M. Hesse, K. S. Lilley, D. Seigneurin-Berny, G. Finazzi, N. Rolland and M. Ferro. "Deciphering thylakoid sub-compartments using a mass spectrometry-based approach". Molecular and Cellular Proteomics, 2014.
• R. Blanch, R. Dautriche, G.Bisson. Dendrogramix: a Hybrid Tree-Matrix Visualization Technique to Support Interactive Exploration of Dendrograms. To appear in the proceeding of the 8th IEEE Pacific Visualization Symposium. April 14 to 17, 2015. Zhejiang University, China. 8 pages
• L. Gatto, L. M. Breckels, T. Burger, D. J. H. Nightingale, A. J. Groen, C. Campbell, C. M. Mulvey, A. Christoforou, M. Ferro and K. S. Lilley. "A foundation for reliable spatial proteomics data analysis". Molecular and Cellular Proteomics, 2014.
• L. Gatto, L. M. Breckels, S. Wieczorek, T. Burger and K. S. Lilley. "Mass-spectrometry based spatial proteomics data analysis using pRoloc and pRolocdata". Bioinformatics, application notes, 2014.
• Y. Vandenbrouck. Computational and mass spectrometry-based workflow for the discovery and validation of missing proteins: the case of human chromosomes 2 and 14. 13th Annual World Congress Human Proteome Organization (HUPO). Oral communication. Madrid, Spain. October 5-8th 2014.

Liste des publications/communications pour 2013 :

• T. Burger, S. Destercke. "How to randomly generate mass functions". International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems (IJUFKS), vol 21(5), pp. 645-673, October 2013.
• S. Destercke, T. Burger. "Toward an axiomatic definition of conflict between belief functions". IEEE trans. on System, Man and Cybernetics - Part B, (accepted 08/2012), vol. 43(2), pp. 585-596, April 2013.
• N. Courty, T. Burger. "A kernel view on manifold sub-sampling based on Karcher variance optimization", Geometric Sciences of Information (GSI 2013), LNCS 8085, pp. 751-758, Paris, France, July 2013.
• F. Pichon, S. Destercke, T. Burger. "Selecting source behavior in information fusion on the basis of consistency and specificity", The Twelfth European Conference on Symbolic and Quantitative Approaches to Reasoning with Uncertainty (ECSQARU 2013), LNAI 7958, pp. 473–484, Utrecht, The Netherlands, July 2013.
• Y. Vandenbrouck. “From mass spectrometry based proteomics data analysis to meaningful biological knowledge: practical use cases”s. Indian-French CeFiPRA “New trends in Proteomics » workshop. Bangalore, India. 6-8th April 2013. Invited speaker
• R. Blanch, R. Dautriche, G. Bisson. Les dendro-matrices : une alternative aux dendrogrammes pour visualiser les résultats d'une classification ascendante hiérarchique. Actes de l'atelier Visualisation d'information, interaction et fouille de données (GT-VIF), EGC 2013.
• C. Lazar, M. Matringe, S. Brugière, J. Dziekan, D. Salvi, N. Rolland, M. Ferro, T. Burger: "To which extent spectral counting can be used to predict protein localization ?", AdO'13 workshop (Apprentissage et données Omiques), CAP, PFIA, Lilles, France, July 2013.
• Bisson G., Blanch R. (2013). Alternative Visualization Methods to Explore Larger Dendrograms. In proceedings of the European Conference on Data Analysis. Luxembourg, 10-12 july 2013

Liste des publications/communications pour 2012 :

• N. Courty, T. Burger, P.-F. Marteau. "Geodesic analysis on the Gaussian RKHS hypersphere", The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD 2012), P. Flach et al. (Eds.): ECML PKDD 2012, Part I, LNCS 7523, pp. 299–313, Bristol, UK, September 2012.
• T. Burger, S. Destercke. "Random generation of mass functions: A short howto", The 2nd International Conference on Belief Functions (BELIEF 2012), Advances in Intelligent and Soft Computing, Volume 164/2012, pp. 145-152, Compiègne, May 2012.
• S. Destercke, T. Burger. "Revisiting the notion of conflicting belief functions", The 2nd International Conference on Belief Functions (BELIEF 2012), Advances in Intelligent and Soft Computing, Volume 164/2012, pp. 153-160, Compiègne, May 2012.
• S. Bouveret, T. Burger. "Identification de protéines et prise en compte des peptides partagé", Atelier Prospectom, November 2012. 
• T. Burger. "Les défauts du calcul du FDR (False Discovery Rate)", Atelier Prospectom, November 2012. 
• R. Blanch, C. Bruley. « La visualisation interactive d'information : une piste pour affronter la complexité des données d’identification par spectrométrie de masse ? », Atelier Prospectom, November 2012. 
• G. Bisson, R. Blanch. Stacked Trees: “a New Hybrid Visualization Method ». In Proceedings of the working conference on Advanced Visual Interfaces (AVI 2012). 
• R. Blanch. “La visualisation interactive d'information pour les biologistes » Invited Speaker, Atelier Prospectom, November 2012.
• G. Bisson, R. Blanch. “Improving Visualization of Large Hierarchical Clustering ».
• In Proceedings of the 16th International Conference on Information Visualisation (IV 2012).
• T. Burger, S. Wieczorek, C. Masselon, D. Salvi, N. Rolland, M. Ferro. "Prediction of subplastidial localization of chloroplast proteins from spectral count data - Comparison of machine learning algorithms",RECOMB Satellite Conference on Computational Proteomics, La Jolla, San Diego, CA, USA, april 2012.
• Bisson G., Grimal C. (2012). Co−clustering of Multi−View Datasets: a Parallelizable Approach. In proceedings IEEE International Conference on Data Mining (ICDM), 10-13 december, Brussels, Belgium. 828-833
• Bisson G., Grimal C. (2012). An Architecture to Efficiently Learn Co-Similarities from Multi-View Datasets. Proceedings of 19th International Conference on Neural Information Processing (ICONIP). LNCS 7663. 12-15 novembre 2012. Doha, Quatar. 184-193.