Table of contents

Books

Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor
F. Cazals, and P. Kornprobst (Editors)
Springer, 2013
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Preprints

Simpler protein domain identification using spectral clustering
F. Cazals, and J. Herrmann, and E. Sarti
Submitted
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Modeling the dynamics of proteins: techniques from geometry, kinematics, and statistics
T. O'Donnell, and F. Cazals
Submitted

Subspace-Embedded Spherical Clusters: a novel cluster model for compact clusters of arbitrary dimension
F. Cazals, and L. Goldenberg, and S. Suren
Submitted

Conflict coloring problems: (theory, complexity, algorithm), and application to multi-resolution modeling in structural bioinformatics
F. Cazals, and F. Havet, and D. Mazauric, and V.H. Nguyen
Submitted
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Computer Science

Geometric constraints within tripeptides and the existence of tripeptide reconstructions
T. O'Donnell, and V. Agashe, and F. Cazals
J. Comp. Chem., 44 (13), 2023
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Efficient computation of the the volume of a polytope in high-dimensions using Piecewise Deterministic Markov Processes
A. Chevallier, and F. Cazals, and P. Fearnhead
AISTATS, 2022
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Improved polytope volume calculations based on Hamiltonian Monte Carlo with boundary reflections and sweet arithmetics
A. Chevallier, and S. Pion, and F. Cazals
J. of Computational Geometry, 13 (1), 2022
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Fr\'echet mean and $p$-mean on the unit circle: decidability, algorithm, and applications to clustering on the flat torus
F. Cazals, and B. Delmas, and T. O'Donnell
Symposium on Experimental Algorithms, 2021
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Wang-Landau algorithm: an adapted random walk to boost convergence
A. Chevallier, and F. Cazals
J. of Computational Physics, 410 (1), 2020
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Low-Complexity Nonparametric Bayesian Online Prediction with Universal Guarantees
A. Lh\'eritier, and F. Cazals
NeurIPS, 2019

Comparing two clusterings using matchings between clusters of clusters
F. Cazals, and D. Mazauric, and R. Tetley, and R. Watrigant
ACM J. of Experimental Algorithms, 24 (1), 2019
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A Sequential Non-Parametric Multivariate Two-Sample Test
A. Lh\'eritier, and F. Cazals
IEEE Transactions on Information Theory, 64 (5), 2018

Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces
F. Cazals, and A. Lh\'eritier
IEEE/ACM International Conference on Data Science and Advanced Analytics, 2015
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Greedy Geometric Algorithms for Collections of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining
F. Cazals, and T. Dreyfus, and S. Sachdeva, and N. Shah
Computer Graphics Forum, 33 (6), 2014
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Connectivity Inference in Mass Spectrometry based Structure Determination
D. Agarwal, and J. Araujo, and C. Caillouet, and F. Cazals, and D. Coudert, and S. P{\'e}rennes
European Symposium on Algorithms (Springer LNCS 8125), 2013
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Reconstructing 3D compact sets
F. Cazals, and D. Cohen-Steiner
Computational Geometry Theory and Applications, 45 (1-2), 2011
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Computing the Volume of Union of Balls: a Certified Algorithm
F. Cazals, and H. Kanhere, and S. Loriot
ACM Transactions on Mathematical Software, 38 (1), 2011
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Shape Matching by Localized Calculations of Quasi-isometric Subsets,with Applications to the Comparison of Protein Binding Patches
F. Cazals, and N. Malod-Dognin
International Conference on Pattern Recognition in Bioinformatics, 2011
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Multi-scale Geometric Modeling of Ambiguous Shapes with Toleranced Balls and Compoundly Weighted $\alpha$-shapes
F. Cazals, and T. Dreyfus
Symposium on Geometry Processing, 2010
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Design of the CGAL Spherical Kernel and application to arrangements of circles on a sphere
P. Castro, and F. Cazals, and S. Loriot, and M. Teillaud
Computational Geometry: Theory and Applications, 42 (6-7), 2009
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Computing the exact arrangement of circles on a sphere, with applications in structural biology
F. Cazals, and S. Loriot
Computational Geometry: Theory and Applications, 42 (6-7), 2009
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A note on the problem of reporting maximal cliques
F. Cazals, and C. Karande
Theoretical Computer Science, 407 (1--3), 2008
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Robust construction of the three-dimensional flow complex
F. Cazals, and A. Parameswaran, and S. Pion
ACM Symposium on Computational Geometry, 2008
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Algorithm 889: Jet fitting 3---A Generic C++ Package for Estimating the Differential Properties on Sampled Surfaces via Polynomial Fitting
F. Cazals, and M. Pouget
ACM Transactions on Mathematical Software, 35 (3), 2008
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Computing the exact arrangement of circles on a sphere, with applications in structural biology
F. Cazals, and S. Loriot
ACM Symposium on Computational Geometry, Video/Multimedia track, 2007
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Ridges and umbilics of polynomial parametric surfaces
F. Cazals, and J.-C. Faug{\`e}re, and M. Pouget, and F. Rouillier
in Computational Methods for Algebraic Spline Surfaces II (Editors: B. Juettler, and R. Piene), Springer, 2006
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The implicit structure of ridges of a smooth parametric surface
F. Cazals, and J.-C. Faug{\`e}re, and M. Pouget, and F. Rouillier
Computer Aided Geometric Design, 23 (7), 2006
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Delaunay Triangulation Based Surface Reconstruction
F. Cazals, and J. Giesen
in Effective Computational Geometry for curves and surfaces (Editors: J.-D. Boissonnat, and M. Teillaud), Springer-Verlag, Mathematics and Visualization, 2006
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The conformal alpha shapes filtration
F. Cazals, and J. Giesen, and M. Pauly, and A. Zomorodian
The Visual Computer, 22 (8), 2006
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Conformal Alpha Shapes
F. Cazals, and J. Giesen, and M. Pauly, and A. Zomorodian
Symposium on Point Based Graphics, 2005

An algorithm for reporting maximal $c$-cliques
F. Cazals, and C. Karande
Theoretical Computer Science, 349 (3), 2005
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Differential topology and geometry of smooth embedded surfaces: selected topics
F. Cazals, and M. Pouget
Int. J. of Computational Geometry and Applications, 15 (5), 2005
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Estimating Differential Quantities using Polynomial fitting of Osculating Jets
F. Cazals, and M. Pouget
Computer Aided Geometric Design, 22 (2), 2005
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Accurate Interactive Specular Reflections on Curved Objects
P. Estalella, and I. Martin, and G. Drettakis, and D. Tost, and O. Devillers, and F. Cazals
Vision, Modeling, and Visualization, 2005

On the angular defect of triangulations and the pointwise approximation of curvatures
V. Borrelli, and F. Cazals, and J-M. Morvan
Computer Aided Geometric Design, 20 (6), 2003
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Randomized Jumplists: A Jump-and-Walk Dictionary Data Structure
H. Bronnimann, and F. Cazals, and M. Durand
STACS, 2003
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Molecular shape analysis based upon the Morse-Smale complex and the Connolly function
F. Cazals, and F. Chazal, and T. Lewiner
ACM Symposium on Computational Geometry, 2003
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Estimating Differential Quantities using Polynomial fitting of Osculating Jets
F. Cazals, and M. Pouget
Symp. on Geometry Processing, 2003
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Smooth Surface Reconstruction via Natural Neighbour Interpolation of Distance Functions
J.-D. Boissonnat, and F. Cazals
Computational Geometry Theory and Applications, 22 (1), 2002
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Non-intrusive Debugging and Incremental Visualization with the Geometric Stethoscope
F. Cazals
J. of Graphics Tools, 7 (2), 2002
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Coarse-to-fine surface simplification with geometric guarantees
J.-D. Boissonnat, and F. Cazals
Euromcs, 2001
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Natural Coordinates of Points on a Surface
J.-D. Boissonnat, and F. Cazals
Computational Geometry Theory and Applications, 19 (2), 2001
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Smooth surface reconstruction via natural neighbour interpolation of distance functions
J.-D. Boissonnat, and F. Cazals
ACM Symposium on Computational Geometry, 2000
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Data structures and basic algorithms
F. Cazals
in Mesh Generation. Application to finite elements (Editors: P. Frey, and P.-L. George), Oxford, 2000

Programming with CGAL: The Example of Triangulations
J.-D. Boissonnat, and F. Cazals, and F. Da, and O. Devillers, and S. Pion, and F. Rebufat, and M. Teillaud, and M. Yvinec
ACM Symposium on Computational Geometry, 1999
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Effective nearest neighbors searching on the hyper-cube, with applications to molecular clustering
F. Cazals
ACM Symposium on Computational Geometry, 1998
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Combinatorial properties of one-dimensional arrangements
F. Cazals
Experimental Mathematics, 6 (1), 1997
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Effect of tolerancing on the relative position of parts in an assembly
F. Cazals, and J-C. Latombe
IEEE International Conference on Robotics and Automation, 1997
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Bucket-like space partitioning data structures with applications to ray tracing
F. Cazals, and C. Puech
ACM Symposium on Computational Geometry, 1997
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Algorithms for computing the union and the intersection of toleranced polygons
F. Cazals, and G.D. Ramkumar
Artificial Intelligence for Engineering Design, Analysis and Manufacturing, 11 (4), 1997
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Assembly sequencing with toleranced parts
J-C. Latombe, and R. Wilson, and F. Cazals
Computer Aided Design, 29 (2), 1997
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Filtering, clustering and hierarchy construction: a new solution for ray-tracing complex scenes
F. Cazals, and G. Drettakis, and C. Puech
Euromcs, 1995
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Computational (Structural) Biology

A mini-review of clustering algorithms and their theoretical properties, with applications to molecular science
F. Cazals
Journal of Innovative Materials in Extreme Conditions, 5 (1), 2024. In honor of the 66th birthday of Christian Schoen.
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Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
H. Schweke, and Q. Xu, and G. Tauriello, and L. Pantolini, and T. Schwede, and F. Cazals, and A. Lhéritier, and J. Fernandez-Recio, and L. Rodríguez-Lumbreras, and O. Schueler-Furman, and J.K. Varga, and B. Jim\'enez-Garc\'ia, and M.F. R\'eau, and A. Bonvin, and C. Savojardo, and P-L. Martelli, and R. Casadio, and J. Tubiana, and H. Wolfson, and R. Oliva, and D. Barradas-Bautista, and T. Ricciardelli, and L. Cavallo, and C. Venclovas, and K. Olechnovic, and R. Guerois, and J. Andreani, and J. Martin, and X. Wang, and D. Kihara, and A. Marchand, and B. Correia, and X. Zou, and S. Dey, and R. Dunbrack, and E. Levy, and S. Wodak
Proteomics, 23 (17), 2023
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Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry
T. O'Donnell, and F. Cazals
J. Comp. Chem., 44 (11), 2023
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Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses
A. Sales-de-Queiroz, and G. Cruz, and A. Jean-Marie, and D. Mazauric, and J. Roux, and F. Cazals
PLOS One, 17 (11), 2022
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Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions
T. O'Donnell, and C.H. Robert, and F. Cazals
Proteins: structure, function, and bioinformatics, 90 (3), 2022
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Boosting the analysis of protein interfaces with Multiple Interface String Alignment: illustration on the spikes of coronaviruses
S. Bereux, and B. Delmas, and F. Cazals
Proteins: structure, function, and bioinformatics, 90 (3), 2022
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SARS-CoV-2 Through the Lens of Computational Biology:How bioinformatics is playing a key role in the study of the virus and its origins
Samuel Alizon, and Fr{\'e}d{\'e}ric Cazals, and St{\'e}phane Guindon, and Claire Lemaitre, and Tristan Mary-Huard, and Anna Niarakis, and Mika{\"e}l Salson, and Celine Scornavacca, and H{\'e}l{\`e}ne Touzet
Report 2021
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Studying dynamics without explicit dynamics: a structure-based study of the export mechanism by AcrB
M. Simsir, and I. Broutin, and I. Mus-Veteau, and F. Cazals
Proteins: structure, function, and bioinformatics, 89, 2021
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Characterizing molecular flexibility by combining lRMSD measures
F. Cazals, and R. Tetley
Proteins: structure, function, and bioinformatics, 87 (5), 2019
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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
C. Sorzano, and A. Jim{\'e}nez, and J. Mota, and J. Vilas, and D. Maluenda, and M. Mart{\'i}nez, and E. Ram{\'i}rez-Aportela, and T. Majtner, and J. Segura, and R. S{\'a}nchez-Garc{\'i}a, and Y. Rancel, and L. Ca{\~n}o, and P. Conesa, and R. Melero, and S. Jonic, and J. Vargas, and F. Cazals, and Z. Freyberg, and J. Krieger, and I. Bahar, and R. Marabini, and J. Carazo
Acta Crystallographica Section F, 75 (1), 2019
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Origin of public memory B cell clones in fish after antiviral vaccination
S. Magadan, and L. Jouneau, and M. Touzel, and S. Marillet, and W. Chaara, and A. Six, and E. Quillet, and T. Mora, and A. Walczak, and F. Cazals, and O. Sunyer, and S. Fillatreau, and P. Boudinot
Frontiers in immunology, 9 (NA), 2018
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Anti-interleukin-6 signalling therapy rebalances the disturbed cytokine production of B cells from patients with active rheumatoid arthritis
S. Fleischer, and S. Ries, and P. Shen, and A. Lh\'eritier, and F. Cazals, and G. Burmester, and T. D\"orner, and S. Fillatreau
European Journal of Immunology, 48 (1), 2017 -- DOI

Novel Structural Parameters of Ig--Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity
S. Marillet, and M-P. Lefranc, and P. Boudinot, and F. Cazals
Frontiers in immunology, 34 (8), 2017
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The Structural Bioinformatics Library: modeling in biomolecular science and beyond
F. Cazals, and T. Dreyfus
Bioinformatics, 7 (33), 2017
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Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation
S. Grudinin, and M. Kadukova, and A. Eisenbarth, and S. Marillet, and F. Cazals
J. of Computer-Aided Molecular Design, 9 (30), 2016
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Energy landscapes and persistent minima
J. Carr, and D. Mazauric, and F. Cazals, and D. Wales
The Journal of Chemical Physics, 144 (5), 2016
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Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes
A. Roth, and T. Dreyfus, and C.H. Robert, and F. Cazals
J. Comp. Chem., 37 (8), 2016
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High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions
S. Marillet, and P. Boudinot, and F. Cazals
Proteins: structure, function, and bioinformatics, 1 (84), 2015
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Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems
D. Agarwal, and C. Caillouet, and D. Coudert, and F. Cazals
Molecular and Cellular Proteomics, 14, 2015
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Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison
F. Cazals, and T. Dreyfus, and D. Mazauric, and A. Roth, and C.H. Robert
J. Comp. Chem., 36 (16), 2015
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Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection
R. Castro, and L. Journeau, and H.P. Pham, and O. Bouchez, and V. Giudicelli, and M-P. Lefranc, and E. Quillet, and A. Benmansour, and F. Cazals, and A. Six, and S. Fillatreau, and O. Sunyer, and P. Boudinot
PLOS Pathogens, 9 (1), 2013
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Modeling Macro-molecular Complexes : a Journey Across Scales
F. Cazals, and T. Dreyfus, and C.H. Robert
in Modeling in Computational Biology and Medicine: : A Multidisciplinary Endeavor (Editors: F. Cazals, and P. Kornprobst), Springer, 2013
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Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Sub-complexes
T. Dreyfus, and V. Doye, and F. Cazals
Proteins: structure, function, and bioinformatics, 81 (11), 2013
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Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models
T. Dreyfus, and V. Doye, and F. Cazals
Proteins: structure, function, and bioinformatics, 80 (9), 2012
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Characterizing the Morphology of Protein Binding Patches
N. Malod-Dognin, and A. Bansal, and F. Cazals
Proteins: structure, function, and bioinformatics, 80 (12), 2012
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On the Characterization and Selection of Diverse Conformational Ensembles
S. Loriot, and S. Sachdeva, and K. Bastard, and C. Prevost, and F. Cazals
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (2), 2011
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Revisiting the Voronoi description of Protein-Protein interfaces: Algorithms
F. Cazals
International Conference on Pattern Recognition in Bioinformatics, 2010
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Spectral Techniques to Explore Point Clouds in Euclidean Space, with Applications to Collective Coordinates in Structural Biology
F. Cazals, and F. Chazal, and J. Giesen
in Nonlinear Computational Geometry (Editors: Ioannis Emiris, and Frank Sottile, and Thorsten Theobald), Springer, 2010
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Modeling Macro-Molecular Interfaces with Intervor
S. Loriot, and F. Cazals
Bioinformatics, 26 (7), 2010
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ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
S. Loriot, and F. Cazals, and J. Bernauer
Bioinformatics, 26 (8), 2010
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Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition
B. Bouvier, and R. Grunberg, and M. Nilg{\`e}s, and F. Cazals
Proteins: structure, function, and bioinformatics, 76 (3), 2009
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A geometric knowledge-based biogeom-grained scoring potential for structure prediction evaluation
S. Loriot, and F. Cazals, and M. Levitt, and J. Bernauer
JOBIM, 2009
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Revisiting the Voronoi description of Protein-Protein interfaces
F. Cazals, and F. Proust, and R. Bahadur, and J. Janin
Protein Science, 15 (9), 2006
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$2D$-Structure Drawings of Similar Molecules
J.-D. Boissonnat, and F. Cazals, and J. Fl{\"o}totto
Graph Drawing: 8th international symposium, 2000
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Thesis

Computational Geometry and Topology: Concepts, Algorithms, Applications
F. Cazals
Habilitation from Univ. Nice Sophia Antipolis, 2006

Structures de donn\'ees hi\'erarchiques non recursives et probl\`emes de proximit\'e
F. Cazals
PhD thesis (Th\`ese de doctorat) from Univ. Paris VII, 1997

Outreach

L'intelligence artificielle au défi du design de protéines : des prouesses et limites d’AlphaFold
F. Cazals
TheConversation, (), 2022
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Misc

Multiscale analysis of structurally conserved motifs
F. Cazals, and R. Tetley
Preprint, NA (NA), 2020
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A generic framework for Wang-Landau type algorithms
A. Chevallier, and F. Cazals
Preprint, NA (NA), 2020
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Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins
R. Tetley, and J. Fedry, and P. Guardado-Calvo, and F. Rey, and F. Cazals
Preprint, NA (NA), 2019
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Optimal transportation problems with connectivity constraints
F. Cazals, and D. Mazauric
Inria Tech report 8991, 2016
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Stoichiometry Determination for Mass-spectrometry Data: the Interval Case
D. Agarwal, and F. Cazals, and N. Malod-Dognin
Inria Tech report 8101, 2014
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Towards Morse theory for point cloud data
F. Cazals, and C. Mueller, and C. Robert, and C.A. Roth
Inria Tech report 8331, 2013
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La morphologie des contacts entre bio-mol\'ecules
F. Cazals
Pour la Science, Juillet - Ao\^ut (), 2006

Topology driven algorithms for ridge extraction on meshes
F. Cazals, and M. Pouget
Inria Tech report 5526, 2005
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Combinatorics of Non-Crossing Configurations
F. Cazals
Studies in Automatic Combinatorics, Vol. 2, 1997
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Monomer-Dimer Tilings
F. Cazals
Studies in Automatic Combinatorics, Vol. 2, 1997
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Some integral geometry tools to estimate the complexity of 3d scenes
F. Cazals, and M. Sbert
Inria Tech report 3204, 1997
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