Bibliography

Major publications by the team in recent years

• 1F. Cazals, P. Kornprobst (editors)
  
  Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor, Springer, 2013. [ DOI : 10.1007/978-3-642-31208-3 ]
  
  http://hal.inria.fr/hal-00845616
• 2D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert, S. Pérennes.
  
  Connectivity Inference in Mass Spectrometry based Structure Determination, in: European Symposium on Algorithms (Springer LNCS 8125), Sophia Antipolis, France, H. Bodlaender, G. Italiano (editors), Springer, 2013, pp. 289–300.
  
  http://hal.inria.fr/hal-00849873
• 3D. Agarwal, C. Caillouet, D. Coudert, F. Cazals.
  
  Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems, in: Molecular and Cellular Proteomics, 2015, vol. 14, pp. 2274–2282. [ DOI : 10.1074/mcp.M114.047779 ]
  
  https://hal.archives-ouvertes.fr/hal-01078378
• 4J. Carr, D. Mazauric, F. Cazals, D. J. Wales.
  
  Energy landscapes and persistent minima, in: The Journal of Chemical Physics, 2016, vol. 144, n^o 5, 4 p. [ DOI : 10.1063/1.4941052 ]
  
  https://www.repository.cam.ac.uk/handle/1810/253412
• 5F. Cazals, F. Chazal, T. Lewiner.
  
  Molecular shape analysis based upon the Morse-Smale complex and the Connolly function, in: ACM SoCG, San Diego, USA, 2003, pp. 351-360.
• 6F. Cazals, T. Dreyfus.
  
  The Structural Bioinformatics Library: modeling in biomolecular science and beyond, in: Bioinformatics, 2017, vol. 7, n^o 33, pp. 1–8. [ DOI : 10.1093/bioinformatics/btw752 ]
  
  http://sbl.inria.fr
• 7F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.
  
  Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, in: J. of Computational Chemistry, 2015, vol. 36, n^o 16, pp. 1213–1231. [ DOI : 10.1002/jcc.23913 ]
  
  https://hal.archives-ouvertes.fr/hal-01076317
• 8F. Cazals, T. Dreyfus, S. Sachdeva, N. Shah.
  
  Greedy Geometric Algorithms for Collections of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining, in: Computer Graphics Forum, 2014, vol. 33, n^o 6, pp. 1–17. [ DOI : 10.1111/cgf.12270 ]
  
  http://hal.inria.fr/hal-00777892
• 9T. Dreyfus, V. Doye, F. Cazals.
  
  Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 9, pp. 2125–2136.
• 10T. Dreyfus, V. Doye, F. Cazals.
  
  Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Sub-complexes, in: Proteins: structure, function, and bioinformatics, 2013, vol. 81, n^o 11, pp. 2034–2044. [ DOI : 10.1002/prot.24313 ]
  
  http://hal.inria.fr/hal-00849795
• 11N. Malod-Dognin, A. Bansal, F. Cazals.
  
  Characterizing the Morphology of Protein Binding Patches, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 12, pp. 2652–2665.
• 12S. Marillet, P. Boudinot, F. Cazals.
  
  High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, in: Proteins: structure, function, and bioinformatics, 2015, vol. 1, n^o 84, pp. 9–20. [ DOI : 10.1002/prot.24946 ]
  
  https://hal.inria.fr/hal-01159641
• 13A. Roth, T. Dreyfus, C. Robert, F. Cazals.
  
  Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes, in: J. Comp. Chem., 2016, vol. 37, n^o 8, pp. 739–752. [ DOI : 10.1002/jcc.24256 ]
  
  https://hal.inria.fr/hal-01191028

Publications of the year

Articles in International Peer-Reviewed Journals

• 14N. Cohen, F. Havet, D. Mazauric, I. Sau, R. Watrigant.
  
  Complexity dichotomies for the Minimum F -Overlay problem, in: Journal of Discrete Algorithms, September 2018, vol. 52-53, pp. 133-142. [ DOI : 10.1016/j.jda.2018.11.010 ]
  
  https://hal.inria.fr/hal-01947563
• 15A. Lhéritier, F. Cazals.
  
  A Sequential Non-Parametric Multivariate Two-Sample Test, in: IEEE Transactions on Information Theory, May 2018, vol. 64, n^o 5, pp. 3361-3370.
  
  https://hal.inria.fr/hal-01968190
• 16S. Magadan, L. Jouneau, M. Puelma Touzel, S. Marillet, W. Chara, A. Six, E. Quillet, T. Mora, A. Walczak, F. Cazals, O. Sunyer, S. Fillatreau, P. Boudinot.
  
  Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination, in: Frontiers in Immunology, September 2018, vol. 9.
  
  https://hal.inria.fr/hal-01968155

International Conferences with Proceedings

• 17J. Bensmail, D. Mazauric, F. Mc Inerney, N. Nisse, S. Pérennes.
  
  Localiser une cible dans un graphe, in: ALGOTEL 2018 - 20èmes Rencontres Francophones sur les Aspects Algorithmiques des Télécommunications, Roscoff, France, May 2018.
  
  https://hal.inria.fr/hal-01774827
• 18J. Bensmail, D. Mazauric, F. Mc Inerney, N. Nisse, S. Pérennes.
  
  Sequential Metric Dimension, in: 16th Workshop on Approximation and Online Algorithms (WAOA 2018), Helsinki, Finland, August 2018.
  
  https://hal.inria.fr/hal-01883712
• 19J.-C. Bermond, A. Chaintreau, G. Ducoffe, D. Mazauric.
  
  How long does it take for all users in a social network to choose their communities?, in: 9th International Conference on Fun with Algorithms (FUN 2018), La Maddalena, Italy, 2018.
  
  https://hal.inria.fr/hal-01780627
• 20F. Cazals, D. Mazauric, R. Tetley, R. Watrigant.
  
  Comparaison de deux clusterings par couplage entre clusters de clusters, in: ALGOTEL 2018 - 20èmes Rencontres Francophones sur les Aspects Algorithmiques des Télécommunications, Roscoff, France, May 2018.
  
  https://hal.inria.fr/hal-01774440

Internal Reports

• 21J. Bensmail, D. Mazauric, F. Mc Inerney, N. Nisse, S. Perennes.
  
  Sequential Metric Dimension, Inria, 2018.
  
  https://hal.archives-ouvertes.fr/hal-01717629
• 22A. Chevallier, F. Cazals.
  
  Wang-Landau Algorithm: an adapted random walk to boost convergence, Inria Sophia Antipolis, France, November 2018.
  
  https://hal.archives-ouvertes.fr/hal-01919860
• 23A. Chevallier, S. Pion, F. Cazals.
  
  Hamiltonian Monte Carlo with boundary reflections, and application to polytope volume calculations, Inria Sophia Antipolis, France, November 2018, n^o RR-9222.
  
  https://hal.archives-ouvertes.fr/hal-01919855

Other Publications

• 24J.-C. Bermond, D. Mazauric, V. Misra, P. Nain.
  
  Distributed Link Scheduling in Wireless Networks, January 2019, working paper or preprint.
  
  https://hal.inria.fr/hal-01977266
• 25F. Cazals, R. Tetley.
  
  Multiscale analysis of structurally conserved motifs, July 2018, working paper or preprint.
  
  https://hal.inria.fr/hal-01968176
• 26R. Tetley, F. Cazals.
  
  Characterizing molecular flexibility by combining lRMSD measures, July 2018, working paper or preprint.
  
  https://hal.inria.fr/hal-01968175
• 27R. Tetley, F. Cazals.
  
  Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins, July 2018, working paper or preprint.
  
  https://hal.inria.fr/hal-01968177

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• 29F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, A. Sali, M. Rout.
  
  The molecular architecture of the nuclear pore complex, in: Nature, 2007, vol. 450, n^o 7170, pp. 695–701.
• 30F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.
  
  Integrating Diverse Data for Structure Determination of Macromolecular Assemblies, in: Ann. Rev. Biochem., 2008, vol. 77, pp. 11.1–11.35.
• 31O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
  
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• 33M. L. Connolly.
  
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• 39H. Gohlke, G. Klebe.
  
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• 40J. Janin, S. Wodak, M. Levitt, B. Maigret.
  
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• 41J. Kleinberg, K. Ligett.
  
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• 42V. K. Krivov, M. Karplus.
  
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• 43E. Meerbach, C. Schutte, I. Horenko, B. Schmidt.
  
  Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution, in: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics 87, O. Kuhn, L. Wudste (editors), Springer, 2007.
• 44I. Mihalek, O. Lichtarge.
  
  On Itinerant Water Molecules and Detectability of Protein-Protein Interfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, n^o 2, pp. 584–595.
• 45J. Mintseris, B. Pierce, K. Wiehe, R. Anderson, R. Chen, Z. Weng.
  
  Integrating statistical pair potentials into protein complex prediction, in: Proteins, 2007, vol. 69, pp. 511–520.
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  Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
• 47E. Plaku, H. Stamati, C. Clementi, L. Kavraki.
  
  Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, in: Proteins: Structure, Function, and Bioinformatics, 2007, vol. 67, n^o 4, pp. 897–907.
• 48D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
  
  Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, n^o 31, pp. 11287-11292.
• 49D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber.
  
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• 51G. Rylance, R. Johnston, Y. Matsunaga, C.-B. Li, A. Baba, T. Komatsuzaki.
  
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  Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, n^o 1, pp. 1–3.
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