Curriculum Vitae


Refined Agent Model Using Shape-Based Grained Structure: Application to Membrane Molecules
Francois Vallee, Marie Beurton-Aimar, Hien T. Tran and Nicolas Parisey in Journal of Computer and Communications 04(13):12-22. January 2016

Estimating landmarks on 2D images of beetle mandibles
Le Van, L., Beurton-Aimar, M., Salmon, J.P., Marie,A., Parisey,N. 24th WSCG Conference on Computer Graphics, Visualization and Computer Vision 30 may- 3 june 2016, Pilsen (Czech Republic).

Metabolic Networks: Visual Analysis of Elementary Flux Modes
Marie Beurton-Aimar, Joris Sansen, Tung Ngoc Vu Nguyen BioNetVisA 2016 workshop (joined to ECCB). The Hague (Netherlands), 4 september 2016

Metabolic Network Reconstruction and Their Topological Analysis
Marie Beurton-Aimar, Tung Vu-Ngoc Nguyen, Sophie Colombie Book chapter in Plant Metabolic Flux Analysis, in Methods in molecular biology 1090:19-38. October 2014

Fast Computation of Minimal Cut Sets in Metabolic Networks with a Berge Algorithm that Utilizes Binary Bit Pattern Trees
]C. Jungreuthmayer, M. Beurton-Aimar, J. Zanghellini IEEE/ACM Trans Comput Biol Bioinform 2013 Sep-Oct;10(5):1329-33.

ACoM: a classification method for elementary flux modes based on motif finding
Peres, S. and Vallée, F. and Beurton-Aimar, M. and Mazat, J.P. Biosystems, vol 103(3), p410- 419,2011.

Image processing for MRI brain images with social spiders
Richard moussa, Marie Beurton-Aimar and Pascal Desbarats. Multi-agent Systems - Modeling, Control, Programming, Simulations and Applications., Chapter 18-pp. 363-382 ,Edited by: Faisal Alkhateeb, Eslam Al Maghayreh and Iyad Abu Doush Publisher: InTech, April 2011, ISBN 978-953-307-174-9

Towards Noise Robust Edge Detection Using Ants Colonies In 3D Medical MR Images.
Richard Moussa, Pascal Desbarats and Marie Beurton-Aimar EEE Congress on Evolutionary Computation (IEEE CEC 2011) - june 5-8 2011 New Orleans, USA.

Elementary Flux Mode Analysis of the Central Metabolism of Plant Cells
F. Vallee, S. Colombie, B. Beauvoit, N. Parisey, M. Dieuaide-Noubhani, M. Beurton-Aimar Seventh International Workshop on Com- putational Systems Biology, WCSB 2010 June 16-18, 2010, Luxembourg.

On the use of social agents for image segmentation -
Moussa R., Beurton-Aimar M., Desbarats P. International Conference on complex systems and applications (iccsa 2009) - (2009)

Multi-agent segmentation for 3D medical images,
Moussa R., Beurton-Aimar M., Desbarats P Proceedings of the 9th International Conference on Information Technology and Applications in Biomedicine, ITAB 2009, Larnaca, cyprus, 5-7 November 2009.

Multi-Agent Model for Simulation at the Subcellular Level
Beurton-Aimar M., Parisey N., Vallee F. ECAL 2009 - Darwin Meets von Neumann (2009)

TIM/WIM: a set of tools to interface modelling in biology
Francois Vallee, Marie Beurton-Aimar, Nicolas Parisey, Florent Collot, Sophie Colombie Proceedings of the 6th European Lisp Workshop in con- junction with ECOOP ’09 European Conference on Object-Oriented Programming genova Italy. July 06 - 10, 2009.

Investigating Oxidoreduction Kinetics using Protein Dynamics. - Journal of Biological Physics and Chemistry
Parisey N., Beurton-Aimar M. JBPC Journal of Biological Physics and Chemistry 9 (2008) , 27-35.

Formal TCA cycle description based on elementary actions
Pierre Maziere, Nicolas Parisey, Marie Beurton-Aimar and Franck Molina Journal of BioSciences Vol 32, 1- feb. 2007, 145-155

Classification des modes élémentaires : application au métabolisme énergétique mitochondrial
S. Peres, M. Beurton-Aimar, JP Mazat Technique et Science Informatiques, ol 26 numéro 1-2 pp 197- 216,2007.

Les reseaux biochimiques,
M. Beurton-Aimar Standard pour la biologie systémique Chapitre 7- p167-182 ed.Ecrin 2007. ISBN 978-2- 916097-12-1

Mitochondrial OxydoReduction Simulation using Multi-Agent System
N. Parisey and J.P. Mazat, and M. Beurton-Aimar European Simulation and Modelling Conference,ESM’2007 October 22-24, 2007- Malta. ISBN 978-90- 77381-36-6 p385 - 390

An agent-based framework to simulate metabolic processes
Marie Beurton-Aimar, Nicolas Parisey ELW at European Conference on Object-Oriented Pro- gramming, 20th edition July 3-7, Nantes (France) 2006.

Modelling of biological complex systems in the context of genomics
Thierry A. R., Képès F., Amar P., Barlovatz-Meimon G., Bernot G., Beurton-Aimar M., Dutreix M., Giavitto J.-L., Guespin J., Mazat J.-P. et al. An account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005, Journal of Biological Physics and Chemistry 6 (2006) 103–107

Multi-Agent Design to Reduce Complexity of Biological Processes,
Parisey N., Beurton-Aimar M., Lales C. 7th German Workshop on Artificial Life, Allemagne (2006)

Simulation of mitochondrial metabolism using multi-agents system
C. Lales ,N. Parisey, J.P. Mazat, M. Beurton-Aimar Int. Workshop on Multiagent Systems for Bioin- formatics and Medicine, Conference on Autonomaus Agents and Multi-Agents Systems - AAMAS Utrecht, July 2005

Analysis of large set of elementary modes : application to energetic mitochondrial metabolism
Peres, S. Beurton-Aimar M. and Mazat, J.P. European Conference on Complex Systems Paris, novembre 2005

A hyperstructure approach to mitochondria
Mirella Trinei, Jean-Pierre Vannier, Marie Beurton-Aimar, Vic Norris. Molecular biology vol 53 (1) p 41-53, 2004

Towards computer-aided diagnosis for white matter abnormalities
Laurent Vallet, Marie Beurton-Aimar Pascal Desbarats, Colette Fabrigoule, Michèle Allard
International Conference on Computer Vision and GraphicsSeptember 22-24, 2004 Warsaw, Poland.

Virtual Mitochondria : Metabolic Modelling And Control
Marie Aimar, Stéphane Ludinard, Bernard Korzeniewski, Jean-Pierre Mazat and Christine Nazaret.
International Journal on Molecular and Cellular Biology(Kluwer Academic Publishers), vol 29:1-2, p227-232, 2002.

Virtual mitochondria and their control
Marie Aimar, Bernard Korzeniewski, Jean-Pierre Mazat and Christine Nazaret.
Modelling and simulation of biological processes in the context of genomics, Autrans (France), March 18 - 21, 2002.

PaLaDeM : a Pattern Language for a Decision Making System in Medicine (ps abstract).
M. Beurton-Aimar et B. Le Blanc. IPMU2000, 8th Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, Madrid (Espagne), July 3 - 7, 2000.

A Decision Making System in Inflammatory Rheumatology using Different Reasoning Methods (ps abstract).
M. Beurton-Aimar, B. Le Blanc. International Journal of Computers and their Applications, 6 (2): 73-77, 1999.

Medical KBS Design with Patterns (ps).
M. Beurton-Aimar. 9th Workshop for PhD Students in Object Oriented Systems. Object-Oriented Technology, ECOOP'99 Workshops, Panels, and Posters, Lisbonne (Portugal), 14-18 juin 1999.
Lecture Notes in Computer Science 1743.

Using Patterns into the Conception of a Medical KBS: LADRI, a Software for Diagnosis in Rheumatology. (ps)
M. Beurton-Aimar et B. Le Blanc. Object-Oriented Technology, ECOOP'99 Workshops, Panels, and Posters, Lisbonne (Portugal), 14-18 juin. Lecture Notes in Computer Science 1743,.

Designing Medical Knowledge-based System from Patterns. (ps abstract)
M. Beurton-Aimar et B. Le Blanc. Proceed. of the 14th Int. Conference on Computers And Their Applications, pp 218-221, Cancun (Mexique), 7-9 avril, 1999.

LADRI: a Decision Making System in Inflammatory Rheumatology. (ps abstract)
M. Beurton-Aimar, B. Le Blanc et J.P. Vernhes. Proceed. of the 7th Int. Conference on
Intelligent Systems
, pp 51-56, Paris, 1-2 juillet, 1998.

Création d'une base de connaissances objet pour l'aide au diagnostic en rhumatologie (1) (ps abstract).
M. Beurton-Aimar, J.P. Vernhes, B. Le Blanc, J. Dehais et R. Salamon. 10ème congrès français de rhumatologie. Rev. du rhumatisme, 11 : 762, 1997.

Logiciel d'aide au diagnostic en rhumatologie inflammatoire (2) (ps abstract).
J.P. Vernhes, M. Beurton-Aimar, B. Le Blanc, J. Dehais et R. Salamon. 10ème congrès français
de rhumatologie.
Rev. du rhumatisme, 11 : 763, 1997.

Modélisation Objet et Aide au Diagnostic : Application à la Rhumatologie Inflammatoire (ps abstract).
M. Beurton-Aimar, J.P. Vernhes, B. Le Blanc, J. Dehais, 2ème Colloque de Sciences Cognitives façade atlantique, COGNITIQUES/Cognitics, série des sciences cognitives appliquées, 2 : 175, 1996.

Multipoint linkage analysis using the WPC statistic (ps abstract).
D. Commenges, M. Beurton-Aimar. Genetic Epidemiology, 17 : 515-519, 1999.

WPC Test based on randomization for analyzing quantitative traits on simulated pedigrees (ps abstract).
D. Commenges, M. Beurton-Aimar. Genetic Epidemiology, 14 : 971-4, 1997.