List of Publications
Bioinformatics
Jean-Luc Falcone, Renée Kreuter, Dominique Belin and Bastien Chopard (2007) Understanding Signal Sequences with Machine Learning in EvoBIO 2007, LNCS 4447, pp. 57-67, Springer Verlag.
Abstract: Protein translocation, the transport of newly synthesized proteins out of the cell, is a fundamental mechanism of life. We are interested in understanding how cells recognize the proteins that are to be exported and how the necessary information is encoded in the so called "Signal Sequences". In this paper, we address these problems by building a physico-chemical model of signal sequence recognition, using experimental data. This model was built using decision trees. In a first phase the classifier were built from a set of features derived from the current knowledge about signal sequences. It was then expanded by feature generation with genetic algorithms. The resulting predictors are efficient, achieving an accuracy of more than 99% with our wild-type proteins set. Furthermore the generated features can give us a biological insight about the export mechanism. Our tool is freely available through a web interface.
@InProceedings{falcone:evobio:07, author = {Jean-Luc Falcone and Ren\'ee Kreuter and Dominique Belin and Bastien Chopard}, title = {Understanding Signal Sequences with Machine Learning}, booktitle = {EvoBIO 2007}, pages = {57-67}, year = 2007, editor = {E. Marchiori and J.H. Moore and J.C. Rajapakse}, volume = 4447, and Simulations series = {LNCS}, address = {Berlin Heidelberg}, publisher = {Springer-Verlag}, }Jean-Luc Falcone and Paul Albuquerque (2004) A Correlation-Based Distance, arXiv.org, cs.IR/0402061.
Abstract: In this short technical report, we define on the sample space R^D a distance between data points which depends on their correlation. We also derive an expression for the center of mass of a set of points with respect to this distance.
@misc{falcone:arxiv:2004, author = {Jean-Luc Falcone and Paul Albuquerque}, title = {A Correlation-Based Distance}, number = {cs.IR/0402061}, url = {http://arxiv.org/abs/cs.IR/0402061}, year = {2004} }Jean-Luc Falcone and Paul Albuquerque (2004) Clustering of physico-chemical properties of amino acids in IEEE Proceedings of CCECE'04, 4, pp. 1881-1884.
Abstract: The data obtained from the sequencing of organisms necessitates the perfecting of methods of predicting the function and structure of proteins. For these methods to be effective, they must be based on the physico-chemical properties of the 20 amino acids (mass, charge, etc.) of which there are currently 484. Many of these properties are very strongly correlated. To regroup them, a measurement derived from the correlation is proposed. The physico-chemical properties are classified according to this distance, using the k-means and global k-means methods. A quality index has enabled the determination of of the 'natural' numbers of the groups. The results of the aggregations conform to the biochemical expectations. The centres of the groups thus produced constitute a new group of properties.
@InProceedings{falcone:ccece:04, author = {Jean-Luc Falcone and Paul Albuquerque}, title = {Agr\'egation des propri\'et\'es physico-chimiques des acides amin\'es}, booktitle = {IEEE Proceedings of CCECE'04}, pages = {1881--1884}, year = 2004, volume = 4, address = {Niagara Falls}, month = {May}, organization = {CCECE}, }
Modeling and Simulations
Alfons Hoekstra, Eric Lorenz, Jean-Luc Falcone and Bastien Chopard (2007) Towards a Complex Automata Framework for Multi-Scale Modeling.; Formalism and the Scale Separation Map in ICCS 2007, LNCS.
Jonas Lätt, Guy Courbebaisse, Bastien Chopard and Jean-Luc Falcone (2004) Lattice Boltzmann Modeling of Injection Moulding Process in ACRI 2004, LNCS 3305, pp. 345-354.
Abstract: Polymer injection in moulds with complicated shapes is common in todays industrial problems. A challenge is to optimize the mould design which leads to the most homogeneous filling. Current commercial softwares are able to simulate the process only partially. This paper proposes a preliminary study of the capability of a two- uid Lattice- Boltzmann model to provide a simple and exible approach which can be easily parallelized, will include correct contact angles and simulate the eect of the positioning of air-holes.
@inproceedings{latt:acri:04, author = {Jonas L{\"a}tt and Guy Courbebaisse and Bastien Chopard and Jean-Luc Falcone}, title = {Lattice Boltzmann Modeling of Injection Moulding Process}, booktitle = {ACRI}, year = {2004}, pages = {345-354}, series = {LNCS}, volume = {3305} }
Molecular Biology
Jean-Luc Falcone (2001) Le rôle des gènes rllA et rllB du phage T4, Master Thesis, University of Geneva.