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inria-00429607v1 Communication dans un congrès
Sebastien Loriot, Frédéric Cazals, Michael Levitt, Julie Bernauer. A geometric knowledge-based coarse-grained scoring potential for structure prediction evaluation
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2009, Nantes, France. 2009

hal-01071876v1 Article dans une revue
Adrien Guilhot-Gaudeffroy, Christine Froidevaux, Jérôme Azé, Julie Bernauer. Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities.
PLoS ONE, Public Library of Science, 2014, 9 (9), pp.e108928. <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0108928>. <10.1371/journal.pone.0108928>

hal-01201665v1 Article dans une revue
Mélanie Boudard, Julie Bernauer, Dominique Barth, Johanne Cohen, Alain Denise. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.
PLoS ONE, Public Library of Science, 2015, 10 (8), pp.e0136444

inria-00625000v1 Article dans une revue
Thomas Bourquard, Julie Bernauer, Jérôme Azé, Anne Poupon. A collaborative filtering approach for protein-protein docking scoring functions.
PLoS ONE, Public Library of Science, 2011, 6 (4), pp.e18541. <10.1371/journal.pone.0018541>

inria-00542791v1 Article dans une revue
Julie Bernauer, Samuel Flores, Xuhui Huang, Seokmin Shin, Ruhong Zhou. MULTI-SCALE MODELLING OF BIOSYSTEMS: FROM MOLECULAR TO MESOCALE - Session Introduction.
Pacific Symposium on Biocomputing, World Scientific, 2011, pp.177-80. <http://eproceedings.worldscinet.com/9789814335058/preserved-docs/9789814335058_0019.pdf>. <10.1142/9789814335058_0019>

inria-00536410v1 Article dans une revue
Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin. MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES - Session Introduction.
Pacific Symposium on Biocomputing, World Scientific, 2010, 15, pp.201-204. <http://eproceedings.worldscinet.com/9789814295291/preserved-docs/9789814295291_0022.pdf>. <10.1142/9789814295291_0022>

tel-01136261v1 HDR
Julie Bernauer. Geometric and statistical methods for the analysis and prediction of structural interactions between biomolecules
Bioinformatics [q-bio.QM]. Université Paris-Sud XI, 2015

hal-01257755v1 Communication dans un congrès
Julie Bernauer, Rasmus Fonseca, Henry Van den Bedem. KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids
RECOMB 2015, Apr 2015, Warsaw, Poland. 9029 2015, Research in Computational Molecular Biology. <www.recomb2015.pl>. <10.1007/978-3-319-16706-0_11>

hal-01016683v1 Communication dans un congrès
Adrien Guilhot-Gaudeffroy, Jérôme Azé, Julie Bernauer, Christine Froidevaux. Apprentissage de fonctions de tri pour la prédiction d'interactions protéine-ARN
Extraction et Gestion des Connaissances, Jan 2014, Rennes, France. 2014, <http://editions-rnti.fr/?inprocid=1001960>

inria-00624999v1 Article dans une revue
Julie Bernauer, Xuhui Huang, Adelene y L Sim, Michael Levitt. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.
RNA, Cold Spring Harbor Laboratory Press, 2011, 17 (6), pp.1066-75. <10.1261/rna.2543711>

hal-01058972v1 Article dans une revue
Ehsan Ranaei-Siadat, Cécile Mérigoux, Bili Seijo, Luc Ponchon, Jean-Michel Saliou et al. In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution.
RNA, Cold Spring Harbor Laboratory Press, 2014, 20 (10), pp.1607-20. <10.1261/rna.045674.114>

hal-00757761v1 Article dans une revue
Adelene y L Sim, Olivier Schwander, Michael Levitt, Julie Bernauer. Evaluating mixture models for building RNA knowledge-based potentials.
Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2012, 10 (2), pp.1241010. <10.1142/S0219720012410107>

hal-01058971v1 Article dans une revue
Rasmus Fonseca, Dimitar V Pachov, Julie Bernauer, Henry Van den Bedem. Characterizing RNA ensembles from NMR data with kinematic models
Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2014, 42 (15), pp.9562-72. <10.1093/nar/gku707>

inria-00637848v1 Article dans une revue
Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin et al. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.
Journal of Molecular Biology, Elsevier, 2011, in press. <10.1016/j.jmb.2011.09.031>

hal-01257437v1 Article dans une revue
Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer et al. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.
PLoS Computational Biology, Public Library of Science, 2015, 11 (7), pp.e1004404. <10.1371/journal.pcbi.1004404>

inria-00536404v1 Article dans une revue
Sébastien Loriot, Frédéric Cazals, Julie Bernauer. ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.
Bioinformatics, Oxford University Press (OUP), 2010, 26 (8), pp.1127-8. <http://bioinformatics.oxfordjournals.org/cgi/reprint/26/8/1127.pdf>. <10.1093/bioinformatics/btq083>

hal-00684530v1 Article dans une revue
Samuel C Flores, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang. Multiscale modeling of macromolecular biosystems.
Briefings in Bioinformatics, Oxford University Press (OUP), 2012, 13 (4), pp.395-405. <10.1093/bib/bbr077>

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