Table of contents

Books

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

Preprints

Optimal transportation problems with connectivity constraints
F. Cazals, and D. Mazauric
Submitted. Available as Inria tech report:
pdf

Clustering stability revealed by matchings between clusters of clusters
F. Cazals, and D. Mazauric, and R. Tetley
Submitted. Available as Inria tech report:
pdf

A Sequential Non-parametric Two-Sample Test
A. Lh\'eritier, and F. Cazals
Submitted. Available as Inria tech report:
pdf

Computer Science

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
pdf

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
pdf -- DOI

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
pdf

Reconstructing 3D compact sets
F. Cazals, and D. Cohen-Steiner
Computational Geometry Theory and Applications, 45 (1-2), 2011
pdf -- DOI

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
pdf -- DOI

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
pdf

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
pdf

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
pdf

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
pdf

A note on the problem of reporting maximal cliques
F. Cazals, and C. Karande
Theoretical Computer Science, 407 (1--3), 2008
pdf

Robust construction of the three-dimensional flow complex
F. Cazals, and A. Parameswaran, and S. Pion
ACM Symposium on Computational Geometry, 2008
pdf

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
pdf

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
pdf

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
pdf

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
pdf

Randomized Jumplists: A Jump-and-Walk Dictionary Data Structure
H. Bronnimann, and F. Cazals, and M. Durand
STACS, 2003
pdf

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
pdf

Estimating Differential Quantities using Polynomial fitting of Osculating Jets
F. Cazals, and M. Pouget
Symp. on Geometry Processing, 2003
pdf

Smooth Surface Reconstruction via Natural Neighbour Interpolation of Distance Functions
J.-D. Boissonnat, and F. Cazals
Computational Geometry Theory and Applications, 22 (1), 2002
pdf

Non-intrusive Debugging and Incremental Visualization with the Geometric Stethoscope
F. Cazals
J. of Graphics Tools, 7 (2), 2002
pdf

Coarse-to-fine surface simplification with geometric guarantees
J.-D. Boissonnat, and F. Cazals
Euromcs, 2001
pdf

Natural Coordinates of Points on a Surface
J.-D. Boissonnat, and F. Cazals
Computational Geometry Theory and Applications, 19 (2), 2001
pdf

Smooth surface reconstruction via natural neighbour interpolation of distance functions
J.-D. Boissonnat, and F. Cazals
ACM Symposium on Computational Geometry, 2000
pdf

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
pdf

Effective nearest neighbors searching on the hyper-cube, with applications to molecular clustering
F. Cazals
ACM Symposium on Computational Geometry, 1998
pdf

Combinatorial properties of one-dimensional arrangements
F. Cazals
Experimental Mathematics, 6 (1), 1997
pdf

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
pdf

Assembly sequencing with toleranced parts
J-C. Latombe, and R. Wilson, and F. Cazals
Computer Aided Design, 29 (2), 1997
pdf

Filtering, clustering and hierarchy construction: a new solution for ray-tracing complex scenes
F. Cazals, and G. Drettakis, and C. Puech
Euromcs, 1995
pdf

Computational (Structural) Biology

Dissecting Interfaces of Antibody - Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions
S. Marillet, and M-P. Lefranc, and P. Boudinot, and F. Cazals
Frontiers in immunology, NA (NA), 2017
pdf

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
pdf -- DOI

Energy landscapes and persistent minima
J. Carr, and D. Mazauric, and F. Cazals, and D. Wales
The Journal of Chemical Physics, 144 (5), 2016
pdf -- DOI

The Structural Bioinformatics Library: modeling in biomolecular science and beyond
F. Cazals, and T. Dreyfus
Bioinformatics, NA (NA), 2016
pdf -- DOI

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. of Computational Chemistry, 37 (8), 2016 -- DOI

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
pdf -- DOI

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
pdf -- DOI

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. of Computational Chemistry, 36 (16), 2015
pdf -- DOI

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
pdf -- DOI

Modeling Macro-molecular Complexes : a Journey Across Scales
F. Cazals, and T. Dreyfus, and C. Robert
in Modeling in Computational Biology and Medicine: : A Multidisciplinary Endeavor (Editors: F. Cazals, and P. Kornprobst), Springer, 2013
pdf -- DOI

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
pdf -- DOI

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
pdf -- DOI

Characterizing the Morphology of Protein Binding Patches
N. Malod-Dognin, and A. Bansal, and F. Cazals
Proteins: structure, function, and bioinformatics, 80 (12), 2012
pdf -- DOI

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
pdf -- DOI

Revisiting the Voronoi description of Protein-Protein interfaces: Algorithms
F. Cazals
International Conference on Pattern Recognition in Bioinformatics, 2010
pdf

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
pdf -- DOI

Modeling Macro-Molecular Interfaces with Intervor
S. Loriot, and F. Cazals
Bioinformatics, 26 (7), 2010
pdf -- DOI

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
pdf -- DOI

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
pdf -- DOI

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
pdf

Revisiting the Voronoi description of Protein-Protein interfaces
F. Cazals, and F. Proust, and R. Bahadur, and J. Janin
Protein Science, 15 (9), 2006
pdf -- DOI

$2D$-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

Misc

Stoichiometry Determination for Mass-spectrometry Data: the Interval Case
D. Agarwal, and F. Cazals, and N. Malod-Dognin
Inria Tech report 8101, 2014
pdf

Towards Morse theory for point cloud data
F. Cazals, and C. Mueller, and C. Robert, and C.A. Roth
Inria Tech report 8331, 2013
pdf

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
pdf

Combinatorics of Non-Crossing Configurations
F. Cazals
Studies in Automatic Combinatorics, Vol. 2, 1997
pdf

Monomer-Dimer Tilings
F. Cazals
Studies in Automatic Combinatorics, Vol. 2, 1997
pdf

Some integral geometry tools to estimate the complexity of 3d scenes
F. Cazals, and M. Sbert
Inria Tech report 3204, 1997
pdf