**Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor**

F. Cazals, and P. Kornprobst (Editors)

Springer, 2013

pdf -- DOI

**Optimal transportation problems with connectivity constraints**

F. Cazals, and D. Mazauric

Submitted. Available as Inria tech report:

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**Clustering stability revealed by matchings between clusters of clusters**

F. Cazals, and D. Mazauric, and R. Tetley

Submitted. Available as Inria tech report:

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**A Sequential Non-parametric Two-Sample Test**

A. Lh\'eritier, and F. Cazals

Submitted. Available as Inria tech report:

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**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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**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

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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

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

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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. 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

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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. 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

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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

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

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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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**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

**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

pdf

**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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