P.K. Agarwal. Range searching. In Handbook of Discrete and Computational Geometry, 809-837, eds J. Goodman and J. O'Rourke, CRC Press, Boca Raton, FL, 2004.

P.K. Agarwal, L. Arge, J. Erickson, and H. Yu. Efficient tradeoff schemes in data structures for querying moving objects. Proceedings of the 12th Annual European Symposium on Algorithms, 2004, to appear.
P.K. Agarwal, L. Arge, O. Procopiuc, and J. Vitter. A framework for index bulk loading and dynamization. Proceedings of the 28th Annual International Colloquium on Automata, Languages, and Programming, 2001.
P. K. Agarwal, M. de Berg, J. Gudmundsson, M. Hammar, and H.J. Haverkort. Box-trees and R-trees with near-optimal query time. Proceedings of the 17th Annual Symposium on Computational Geometry, 2001, 124-133.
P. K. Agarwal, M. de Berg, J. Gudmundsson, M. Hammar and H. J. Haverkort. Box-trees and R-trees with near-optimal query time. Discrete and Computational Geometry 28 (2002), 291-312.
P. K. Agarwal, A. Collins and J. Harer. HPRM: Hierarchical PRM. IEEE International Conference on Robotics and Automation, 2003.
P.K. Agarwal, H. Edelsbrunner, and Y. Wang. Computing the writhing number of a polygonal knot. Proceedings of the 13th ACM-SIAM Symposium on Discrete Algorithms, 2002, 791-799.

P.K. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang. Extreme elevation on a 2-manifold. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 357-365.
P.K. Agarwal, J. Gao, and L.J. Guibas. Kinetic medians and kd-Trees. Proceedings of the 10th Annual European Symposium on Algorithms, 2002.

P. Agarwal, L. Guibas, A. Nguyen, D. Russel, and L. Zhang. Collision detection for deforming necklaces. Computational Geometry: Theory and Applications, to appear.

P. K. Agarwal and S. Har-Peled. Maintaining approximate extent measures of moving points. Proceedings of the 12th ACM-SIAM Symposium on Discrete Algorithms, 2001, 148-157.
P.K. Agarwal, S. Har-Peled, N. Mustafa, and Y. Wang. Near-linear time approximation algorithms for curve simplification in two and three dimensions. Proceedings of the 10th Annual European Symposium on Algorithms, 2002.
P. K. Agarwal, S. Har-Peled, M. Sharir and Y. Wang. Hausdorff distance under translation for points, and balls. Proceedings of the 19th Annual Symposiun on Computational Geometry, 2003, 282-291.

P.K. Agarwal and N. H. Mustafa. k-means projective clustering. Proceedings of the 23rd Annual Symposium on Principles of Database Systems, 2004.

P.K. Agarwal, R. Poreddy, K. Varadarajan, and H. Yu. Practical methods for shape fitting and kinetic data structures using core sets. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 263-272.
P. K. Agarwal and C. M. Procopiuc. Advances in indexing moving objects. Bull. Data Engin. 25 (2002), 25-34.
P.K. Agarwal, C.M. Procopiuc, and K. Varadarajan. Approximation algorithms for k-line center. Proceedings of the 10th European Symposium on Algorithms, 2002.
P. K. Agarwal and C. M. Procopiuc. Approximation algorithms for projective clustering. Journal of Algorithms 46 (2003), 115-139.
P. K. Agarwal and M. Sharir. On the numbers of congruent simplices in a point set. Proceedings of the 17th Annual Symposium on Computational Geometry, 2001, 1-9.
P. K. Agarwal and M. Sharir. On the numbers of congruent simplices in a point set. Discrete and Computational Geometry 28 (2002), 123-150.

P.K. Agarwal and K. R. Varadarajan. A near-linear algorithm for Euclidean bipartite matching? Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 247-252.

P.K. Agarwal, Y. Wang, and H. Yu. A 2D Triangulation with near-quadratic topological changes. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 180-189.
M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu and J. C. Latombe. Stochastic conformational roadmaps for computing ensemble properties of molecular motion. Workshop on Algorithmic Foundations of Robotics (2002).
M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, and J.C. Latombe. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. Proceedings of RECOMB'02, 2002, 12-21.
M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, J. C. Latombe and C. Varma. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. Journal of Computational Biology 10 (2003), 257-281.
M.S. Apaydin, D.L. Brutlag, C. Guestrin, C. Varma, and J.C. Latombe. Stochastic roadmap simulation for the study of ligand-protein interactions. Proceedings of the European Conference on Computational Biology (ECCB'02), 2002.
M. S. Apaydin, C. Guestrin, C. Varma, D. L. Brutlag, and J. C. Latombe. Studying protein-ligand interactions with stochastic roadmap simulation, Bioinformatics 18 Suppl. 2 (2002), 18-26.
M.S. Apaydin, A.P. Singh, D.L. Brutlag, and J.C. Latombe. Capturing molecular energy landscapes with probabilistic conformational roadmaps. IEEE International Conference on Robotics and Automation, 2001.

Y.A. Ban, H. Edelsbrunner, and J. Rudolph. Interface surfaces for protein-protein complexes. Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, 2004, 205-212.

D. Bandyopadhyay and J. Snoeyink. Almost-Delaunay simplices: nearest neighbor relations for imprecise points. Proceedings of the ACM-SIAM Symposium on Discrete Algorithms, 2004, 403-412.

D. Bandyopadhyay and J. Snoeyink. Almost-Delaunay simplices: robust neighbor relations for imprecise 3D points using CGAL. 2nd CGAL Users Workshop, 2004, abstract..

D. Bandyopadhyay, A. Tropsha, and J. Snoeyink. Analyzing protein structure using almost-Delaunay tetrahedra. UNC-Chapel Hill Computer Science Technical Report TR03-043, 2003.
G. Barequet, D.Z. Chen, O. Daescu, M.T. Goodrich, and J. Snoeyink. Efficiently approximating polygonal paths in three and higher dimensions
Algorithmica 33 (2002), 150-167.
M. W. Bern, E. D. Demaine, D. Eppstein, E. Kuo, A. Mantler and J. Snoeyink. Un-unfoldable polyhedra with convex faces. Computational Geometry 24 (2003), 51-62.

S. Bespamyatnikh, Y.-E. Ban, and N. Mustafa. On a conjecture of Wiener indices in combinatorial chemistry. Algorithmica, Springer-Verlag, 2004. Available at OnlineFirst
S. Bililign. Energy transfer in Li(3p)+H_2 collisions. Journal of Physical Chemistry. A104 (2000), 9454-9458.
S. Bililign. Far-wing scattering studies in the reaction of Li(2p,3p)+H_2-LiH(v'',J'')+H.  Journal of Chemical Physics 114 (2001), 7052-7058.
S. Bililign and N. Vaval. DFT Studies of the Structure of Fe+Rn (R= Ar, Xe; n = 1 - 6) Clusters. Bulletin of American Physical Society 47 (2002), 17.
S. Bililign and N. Vaval. Density functional studies of the structure of transition metal -noble gas cluster ions. Proceedings of the Conference of the National Society of Black Physicists, 2002

A.A. Bokinsky. Interactive visualization of multiple spatial variables with data-driven spots ( Ph.D. dissertation, University of North Carolina Chapel Hill, 2003).

F.P. Brooks, Jr. Foreword in D. Luebke, M. Reddy, J. D. Cohen, A. Varshney, B. Watson, and R. Huebner, Level of Detail for 3D Graphics. San Francisco, CA: Morgan Kaufmann Publishers, 2003, ix.

D. L. Brutlag. Using robotics to fold proteins and dock ligands. European Conference on Computational Biology (2002).
S. Cabello, Y. Liu, A. Mantler and J. Snoeyink. Testing homotopy for paths in the plane. Proceedings of the 18th Annual ACM Symposium on Computational Geometry, 2002, 160-9.

S. Cabello, Y. Liu, A. Mantler, and J. Snoeyink. Testing homotopy for paths in the plane. Discrete and Computational Geometry, 31 (2004), 61-81.

W. Cardoen and R.J. Gdanitz. Increasing the stability of linear r 12-calculations on the multi-reference level of theory. Computat. Methods Science Technol., 9 (2004), to appear.

H. Carr. Topological manipulation of isosurfaces (Ph.D. dissertation, University of British Columbia, 2004).
H. Carr, T. Möller, and J. Snoeyink. Simplicial subdivisions and sampling artifacts. IEEE Vis'01, 2001, 99-108.

H. Carr and J. Snoeyink. Path seeds and flexible isosurfaces - using topology for exploratory visualization. IEEE/EG VisSym'03, 2003, 49-58, 285.
H. Carr, J. Snoeyink and U. Axen. Computing contour trees in all dimensions. Computational Geometry 24 (2003) 75-94.
C.W. Carter, Jr., B. LeFebvre, S.A. Cammer, A. Tropsha, and M. H. Edgell. Four-body potentials reveal protein-specific correlations to stability changes causd by hydrophobic core mutations. Journal of Molecular Biology 311 (2001), 625-638.
H.-L. Cheng, T. Dey, H. Edelsbrunner and J. Sullivan. Dynamic skin triangulation. Discrete and Computational Geometry 25 (2001), 525-568.
H.-L. Cheng and H. Edelsbrunner. Area and perimeter derivatives of a union of disks. Computer Science in Perspective, eds. R. Klein, H.-W. Six and L. Wegner, LNCS 2598, Springer-Verlag, 88-97.
H.-L. Cheng and H. Edelsbrunner. Area, perimeter, and derivatives of a skin curve. Computational Geometry (2003), to appear.
K. Cole-McLaughlin, H. Edelsbrunner, J. Harer, V. Natarajan and V. Pascucci. Loops in Reeb graphs of 2-manifolds. Proceedings of the 19th Annual Symposium on Computational Geometry, 2003, 344-350.
E. Demaine, S. Langerman, J. O'Rourke and J. Snoeyink. Interlocked open linkages with few joints. Proceedings of the 18th ACM Symposium on Computational Geometry, 2002, 189-198.

H. Edelsbrunner. Biological applications of computational topology. In Handbook of Discrete and Computational Geometry, 1395-1412, eds. J.E. Goodman and J. O’Rourke, CRC Press, Boca Raton, FL, 2004.

H. Edelsbrunner, P. Agarwal, and Y. Wang. Computing the writhing number of a polygonal knot. Discrete and Computational Geometry 32 (2004), 37-53.

H. Edelsbrunner, Y.-E. A. Ban, and J. Rudolph. Interface surfaces for protein-protein complexes. Proceedings of the 8th International Conference on Research in Computational Molecular Biology, 2004, 205-212.

H. Edelsbrunner, P.-T. Bremer, V. Pascucci, and B. Hamann. A multi-resolution data structure for two-dimensional Morse functions. Proceedings of the Annual IEEE Conference on Visualization, 2003, 139-146.

H. Edelsbrunner, P.-T. Bremer, V. Pascucci, and B. Hamann. A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics 10 (2004), 385-396.

H. Edelsbrunner, R. Bryant, P. Koehl, and M. Levitt. The area derivative of a space-filling diagram. Discrete and Computational Geometry, currently available online.
H. Edelsbrunner, and D. Guoy. An experimental study of sliver exudation. Proceedings of the 10th International Meshing Roundtable, 2001, 307-316.
H. Edelsbrunner, and D. Guoy. Sink-insertion for mesh improvement. International Journal of Foundations in Computer Science 13 (2002), 223-242.
H. Edelsbrunner and J. Harer. Jacobi sets of multiple Morse functions. In Foundations of Computational Mathematics, Minneapolis 2002, 37-57, eds. F. Cucker, R. DeVore, P. Oliver, E. Süli, Cambridge Univ. Press, England, 2004

H. Edelsbrunner, J. Harer, A. Mascarenhas, and V. Pascucci. Time-varying Reeb graphs. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 366-372.
H. Edelsbrunner, J. Harer, V. Natarajan and V. Pascucci. Morse-Smale complexes for piecewise linear 3-manifolds. Proceedings of the 19th Annual Symposium on Computational Geometry, 2003, 361-370.
H. Edelsbrunner, J. Harer and A. Zomorodian. Hierarchical Morse complexes for piecewise linear 2-manifolds. Proceedings of the 17th Annual Symposium. on Computational Geometry, 2001, 70-79.

H. Edelsbrunner, J. Harer and A. Zomorodian. Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds. Discrete and Computational Geometry 30 (2003), 87-107.
H. Edelsbrunner and P. Koehl. The weighted volume derivative of a space-filling diagram. Proceedings of the National Academy of Sciences 100 (2003), 2203-2208.

H. Edelsbrunner, D. Letscher, and A. Zomorodian. Computing linking numbers of a filtration. Homology, Homotopy, and Applications 5 (2003), 19-37.

H. Edelsbrunner and A. Ungor. Relaxed scheduling in dynamic skin triangulation. Japanese Conference on Discrete and Computational Geometry 2002, to appear.

H. Edelsbrunner and V. Natarajan. Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics, to appear
H. Edelsbrunner and A. Zomorodian. Computing linking numbers of a filtration. Proceedings of the 1st International Workshop on Algorithms in Bioinformatics, 2001, 112-127.

J. Gao, L. Guibas, and A. Nguyen. Deformable spanners and applications. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 190-199.

R. J. Gdanitz. Accurately solving the electronic Schrodinger equation using explicitly correlated (r12-) multi-reference methods. Recent Research Developments in Quantum Chemistry 3 (2002), 245-276.

L. Guibas. Modeling motion. In Handbook of Discrete and Computational, Geometry, 1117-1134, eds. J. Goodman and J. O’Rourke, Eds. CRC Press, Boca Raton, FL, 2004.

L.J. Guibas, A. Nguyen, D. Russel, and L. Zhang. Collision detection for deforming necklaces. Proceedings of the 18th ACM Symposium on Computational Geometry, 2002, 33-42.

L. Guibas and D. Russel. An empirical comparison of techniques for updating Delaunay triangulations. Proceedings of the 20th Annual Symposium on Computational Geometry, 2004, 170-179.

J. Huan, W. Wang, D. Bandyopadhyay, J. Snoeyink, J. Prins, and A. Tropsha. Mining protein-family-specific residue packing patterns from protein structure graphs. Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, 2004, 308-315.
M. Isenburg and J. Snoeyink. Spirale reversi: reverse decoding of the Edgebreaker encoding. Computational Geometry 20 (2001), 39-52.
M. Isenburg and J. Snoeyink. Coding polygon meshes as compressable ASCII. Proceedings of Web3D Symposium'02, 2002, 1-10.
M. Isenburg and S. Gumhold. Out-of-core compression for gigantic polygon meshes. Proceedings of SIGGRAPH ’03, 2003.
M. Isenburg and J. Snoeyink. Binary compression rates for {ASCII} formats. Proceedings of the Web3D Symposium ’03, 2003, 173-178.
M. Isenburg and J. Snoeyink. Compressing the property mapping of polygon meshes. Graphical Models 64 (2003), 114-127.

R. J. Gdanitz, W. Cardoen, T.L. Windus, and J. Simons. Very large-scale computations of the free energies of eight low-lying structures of arginine in the gas phase. Journal of Physical Chemistry A 108 (2004), 515-518.
L. Kettner, D. G. Kirkpatrick, A. Mantler, J. Snoeyink, B. Speckmann and F. Takeuchi. Tight degree bounds for pseudo-triangulations of points. Computational Geometry 25 (2003) 3-12.
L. Kettner, A. Mascarenhas, J. Rossignac and J. Snoeyink. A prototype system for visualizing time-dependent volume data. 17th European Workshop on Computational Geometry, 2001, 13-16.

R. Kolodny. Modeling and Comparing Protein Structures (Ph.D. dissertation, Stanford University, 2004).
R. Kolodny, P. Koehl, G. Guibas and M. Levitt. Small libraries of protein fragments model native protein structures accurately, Journal of Molecular Biology 323 (2002), 297-307.
R. Kolodny and M. Levitt. Protein decoy assembly using short fragments under geometric constraints. Biopolymers 68 (2003), 278-285.

B. Krishnamoorthy. Part I: Column basis reduction and integer programming. Part II: Using geometry and topology-based methods to evaluate and characterize protein structure ( Ph.D. dissertation, University of North Carolina Chapel Hill, 2004).

B. Krishnamoorthy and A. Tropsha. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 19 (2003) 1540-8.
S. Krishnan, N. Mustafa and S. Venkatasubramanian. Hardware-assisted computation of depth contours. Proceedings of the 13th ACM-SIAM Symposium on Discrete Algorithms, 2002, 558-567.

A. Leaver-Fay, Y. Liu, and J. Snoeyink. Faster placement of hydrogens in protein structures by dynamic programming. Proceedings of Algorithm Engineering and Experimentation, LNCS, Springer Verlag, 2004, to appear.

B. Lok, S. Naik, M. Whitton, and F. Brooks. Experiences in extemporaneous incorporation of real objects in immersive virtual environments. Beyond Glove and Wand Based Interaction Workshop, IEEE Virtual Reality 2004.

B. Lok, S. Naik, M. Whitton, and F.P. Brooks, Jr. Effects of handling real objects and self-avatar fidelity on cognitive task performance and sense of presence in virtual environments. Journal on Presence: Teleoperators and Virtual Environments 12 (2004), 615-628.

B. Lok, S. Naik, M.C. Whitton, and F.P. Brooks, Jr. Incorporating dynamic real objects into immersive virtual environments. ACM Transactions on Graphics 22, 701. Proceedings, ACM SIGGRAPH 2003.

L. L. Looger, M. A. Dwyer, J. J. Smith and H. W. Hellinga. Computational design of receptors and sensors with novel functions. Nature 423 (2003) 185.
L.L. Looger and H.W. Hellinga. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. Journal of Molecular Biology 307 (2001), 429-445.
I. Lotan, F. Schwarzer, D. Halperin, and J.C. Latombe. Efficient Maintenance and Self-Collision Testing for Kinematic Chains. Proceedings of the 18th ACM Symposium on Computational Geometry, 2002, 43-52.

I. Lotan, F. Schwarzer, D. Halperin, and J.C. Latombe. Algorithm and data structures for efficient energy maintenance during Monte Carlo simulation of proteins. Journal of Computational Biology, to appear.

I. Lotan, F. Schwarzer, and J.C. Latombe. Efficient energy maintenance for Monte Carlo simulation of proteins. Algorithms in Bioinformatics, eds. G. Benson and R. Page, LNCS 2812, Springer-Verlag, 354-373.

I. Lotan, H. van den Bedem, A.M. Deacon, and J.C. Latombe. Computing protein structures from electron density maps: the missing loop problem. Proceedings of the Workshop on the Algorithmic Foundations of Robotics, 2004, to appear.

M. Meehan, B. Insko, M. Whitton and F. P. Brooks Jr. Physiological measures of presence in stressful virtual environments. Proceedings of SIGGRAPH 2002.
M. Meehan, B. Insko, M. C. Whitton and F. P. Brooks. Physiological measures of presence in virtual environments. Proceedings of the 4th International Workshop on Presence, 2001, published as a CD.

N. Mustafa. Simplification, classification and estimation of geometric shapes (Ph.D. dissertation, Duke University, 2004).

V. Natarajan. Topological analysis of scalar functions for scientific data visualization (Ph.D. dissertation, Duke University, 2004).

K. Noonan, D. O’Brien, and J. Snoeyink. Probik: protein backbone motion by inverse kinematics. Proceedings of the 6th International Workshop on Algorithmic Foundations of Robotics, 2004, to appear.

D. O'Brien and J. Snoeyink. Computing four-body protein energy potentials with incremental 3D Delaunay triangulation. 2nd CGAL Users Workshop, 2004, abstract.
C.M. Procopiuc, P.K. Agarwal, and S. Har-Peled. STAR-tree: An efficent self-adjusting index for moving points. Proceedings of the 4th Workshop on Algorithm Engineering, 2002.
C.M. Procopiuc, M. Jones, P. K. Agarwal, and T.M. Murali. Classification using projective clustering. Proceedings of SIGMOD, 2002.
J.M. Roach and C.W. Carter, Jr. Local squaring equations. Acta Crystallographica A58, 2002, 215-220.
J. Roach and C. W. Carter, Jr. Local squaring functions for non-spherical templates. Acta Crystallographica A59 (2003), 273-280.
J. M. Roach, P. Retailleau, and C.W. Carter. Phase determination via Sayre-type equations with anomalous scattering. Acta Crystallographica A57, 2001, 341-350.
F. Schwarzer and I. Lotan. Approximation of protein structure for fast similarity measures. Proceedings of RECOMB'03 (2003).

F. Schwarzer and I. Lotan. Approximation of protein structure for fast similarity measures. Journal of Computational Biology, to appear.

D. B. Sherman, S. Zhang, J.B. Pitner, and A. Tropsha. Evaluation of the relative stability of liganded vs. ligand-free protein conformations using simplicial neighborhood analysis of protein packing (SNAPP) method. Proteins: Structure, Function, and Genetics, 2004, to appear.
R. Singh and M. Saha. Identifying structural motifs in proteins. Pacific Symposium on Biocomputing (2003).

A. Tropsha, C.W. Carter, Jr., S.A. Cammer, and I.I. Vaisman. Simplicial neighborhood analysis of protein packing (SNAPP): A computational geometry approach to studying proteins. In Methods in Enzymology 374 (2003), eds. C.W. Carter Jr., Robert M. Sweet, Elsevier, 509-544.
N. Vaval, S. Bililign and R. J. Gdanitz. Density functional studies on the structure and stability of iron rare gas clusters (Fe+Xn; X=Ar, Xe; n=1-6), Chemical Physics 290 (2003), 171-176.

A. Venkatnathan, A.B. Szilva, D. Walter, R.J. Gdanitz, and E.A. Carter. Size extensive modification of local multireference configuration interaction. Journal of Chemical Physics 120 (2004), 1693-1704.

M. Venkatraj, C. Bratschia, H. Huber, and R.J. Gdanitz. Monte Carlo simulations of vapor-liquid equilibria of neon using an accurate ab initio pair potential. Fluid Phase Equilibria 218 (2004), 285-289.

K. Wedderburn. Density functional theory studies of transition metal-ion benzene complexes (Master’s thesis, North Carolina A&T State University, 2004).
M.S. Wisz and H.W. Hellinga. An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins: Structure, Function, and Genetics 51 (2003), 360-377.

Y. Wang. Geometric and topological methods in protein structure analysis (Ph.D. dissertation, Duke University, 2004).

P. Zimmons. The influence of lighting quality on presence and task performance in virtual environments (Ph.D. dissertation, University of North Carolina Chapel Hill, 2004).