Publications

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F
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2005.  Immersive graph-based visualization and exploration of biological data relationships. Data Sci. J.. 4:189–194.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  Exploration by visualization of numerical and textual genomic data. Journal of Biological Physics and Chemistry. 4:102–110.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  A Distributed Multimedia Database Visualization within An Immersive Environment for Bioinformatics. International Symposium on Multimedia Software Engineering (ISMSE 2004 - IEEE). :156–159.
Férey N, Gherbi R..  2006.  Visual Mining for Microarray Knowledge Discovery. International Conference on Information & Communication Technologies: from Theory to Applications (ICTTA 2006 - IEEE).
Férey N, Gros P.-E., Gherbi R..  2006.  An Immersive Visualization and Interaction Paradigm for Genomic Databases Exploration. Mediterranean Journal of Computers and Networks. 2:118–124.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  Visualization and Exploration of Factual and Textual Genomic Data. Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM 2004).
Férey N, Delalande O., Grasseau G., Baaden M.  2008.  A VR Framework for Interacting with Molecular Simulations. Symposium on Virtual Reality Software and Technology (ACM-VRST 2008). :91–94.
Férey N, Toffano-Nioche C, Matte-Taillez O, Gherbi R, Turner W.  2007.  REVIVOS: REalité VIrtuelle pour la construction de VOcabulaires Spécialisés. Journées Francophones d'Ingénierie des Connaissances (AFIA-IC 2007).
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  Immersive Graph-based Visualization and Exploration of Biological Data. International CODATA Conference - The Information Society: New Horizons for Science.
Férey N.  2006.  Exploration Immersive de Données Génomiques Textuelles et Factuelles : vers une approche par Visual Mining.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2005.  Visual data mining of genomic databases by immersive graph-based exploration. international Conference on Computer Graphics and interactive Techniques in Australasia and South East Asia (GRAPHITE 2005 - ACM-ACMSIGRAPH Sponsored). :143–146.
Férey N, Delalande O., Grasseau G., Baaden M.  2008.  From Interactive to Immersive Molecular Dynamics. Workshop on Virtual Reality Interaction and Physical Simulation (VRIPHYS 08 - Eurographics). :89–96.
Férey N, Bouyer G., Martin C., Bourdot P., Nelson J., Burkhardt andJM.  2008.  User Needs Analysis to Design a 3D Multimodal Protein-Docking Interface. Symposium on 3D User Interfaces 2008 (3DUI 2008 - IEEE). :125–132.
B Fas A, Sacquin-Mora S, Papaleo E.  2023.  Editorial: In Celebration of Women in Science: Biological Modeling and Simulation. Front Mol Biosci. 10:1175325.
Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP.  2004.  Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins: Struct., Funct., Bioinf.. 57:783–791.
E
Esque J, Sansom MSP, Baaden M, Oguey C.  2018.  Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.. Sci Rep. 8(1):13540.
Esmenjaud J-B, Stroebel D, Chan K, Grand T, David M, Wollmuth LP, Taly A, Paoletti P.  2019.  An inter-dimer allosteric switch controls NMDA receptor activity. The EMBO journal. 38
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.  2009.  Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. Plos Comput. Biol.. 5:e1000267.
Elyakova L.A, Mazur AK.  1982.  Mathematical modelling of endoglucanase-catalysed hydrolysis of a linear polysaccharide. Mol. Biol.. 16:499–510.
Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C.  2018.  Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution.. J Chem Theory Comput. 14(2):1045-1058.
Ebrahimi M, Hénin J.  2022.  Symmetry-Adapted Restraints for Binding Free Energy Calculations.. J Chem Theory Comput.
D
Durrieu M.P, Bond P.J, Sansom M.S, Lavery R., Baaden M.  2009.  Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.
Durrieu M-P, Lavery R, Baaden M.  2008.  Interactions between neuronal fusion proteins explored by molecular dynamics. Biophys. J.. 94:3436–3446.
Duboué-Dijon E, Hénin J.  2021.  Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H.  2020.  A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.. J Chem Phys. 153(5):050901.

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