Alpha Shapes

• H. Edelsbrunner and A. Ungor. Relaxed scheduling in dynamic skin triangulation. In ``Japanese Conf. Comput. Geom., 2002'', J. Akiyama and M. Kano (eds.), Lecture Notes in Computer Science, Springer-Verlag, to appear. pdf-file
• H.-L. Cheng, T. K. Dey, H. Edelsbrunner and J. Sullivan. Dynamic skin triangulation. Discrete Comput. Geom. 25 (2001), 525-568. pdf-file
• H. Edelsbrunner. Deformable smooth surface design. Discrete Comput. Geom. 21 (1999), 87-115.
• H.-L. Cheng, H. Edelsbrunner and P. Fu. Shape space from deformation. Comput. Geom. Theory Appl. 19 (2001), 191-204. pdf-file
• S.-W. Cheng, H. Edelsbrunner, P. Fu and P. Lam. Design and analysis of planar shape deformation. Comput. Geom. Theory Appl. 19 (2001), 205-218. pdf-file
• H. Edelsbrunner, M. A. Facello and J. Liang. On the definition and the construction of pockets in macromolecules. Discrete Appl. Math. 88 (1998), 83-102. pdf-file
• N. Akkiraju and H. Edelsbrunner. Triangulating the surface of a molecule. Discrete Appl. Math. 71 (1996), 5-22.
• N. Akkiraju, H. Edelsbrunner, P. Fu and J. Qian. Viewing geometric protein structures from inside a CAVE. IEEE Comput. Graphics Appl. 16 (1996), 58-61.
• H. Edelsbrunner, P. Fu and J. Qian. Geometric modeling in CAVE. In ``Proc. ACM Sympos. Virtual Reality Softw. Techn., 1996'', Hong Kong, 35-41 and 193-194.
• N. Akkiraju, H. Edelsbrunner, M. Facello, P. Fu, E. P. Mucke and C. Varela. Alpha shapes: definition and software. In ``Proc. Internat. Comput. Geom. Software Workshop'', ed. N. Amenta, Rpt. GCG 80, Geometry Center, Minneapolis, Minnesota, 1995.
• H. Edelsbrunner. Smooth surfaces for multi-scale shape representation. In ``Proc. 15th Conf. Found. Software Techn. Theoret. Comput. Sci. 1995'', Bangalore, India, 391-412, 1995.
• H. Edelsbrunner. Algebraic decomposition of non-convex polyhedra. In ``Proc. 36th Ann. IEEE Sympos. Found. Comput. Sci. 1995'', 248-257.
• C. J. A. Delfinado and H. Edelsbrunner. An incremental algorithm for Betti numbers of simplicial complexes on the 3-sphere. Comput. Aided Geom. Design 12 (1995), 771-784. pdf-file
• H. Edelsbrunner. Weighted alpha shapes. Report UIUCDCS-R-92-1760, Dept. Comput. Sci., Univ. Illinois, Urbana, Illinois, 1992. pdf-file
• H. Edelsbrunner and E. P. Mucke. Three-dimensional alpha shapes. ACM Trans. Graphics 13 (1994), 43-72. pdf-file
• H. Edelsbrunner, D. G. Kirkpatrick and R. Seidel. On the shape of a set of points in the plane. IEEE Trans. Inform. Theory IT-29 (1983), 551-559.

Size and Variation

• D. Attali and H. Edelsbrunner. Inclusion-exclusion formulas from independent complexes. Discrete Comput. Geom. 37 (2007), 59-77. pdf-file
• H. Edelsbrunner and P. Koehl. The weighted volume derivative of a space-filling diagram. Proc. Natl. Acad. Sci. 100 (2003), 2203-2208. pdf-file
• R. Bryant, H. Edelsbrunner, P. Koehl and M. Levitt. The area derivative of a space-filling diagram. Discrete Comput. Geom. 32 (2004), 293-308. pdf-file
• H.-L. Cheng and H. Edelsbrunner. Area, perimeter, and derivatives of a skin curve. Comput. Geom. Theory Appl., to appear. pdf-file
• H.-L. Cheng and H. Edelsbrunner. Area and perimeter derivatives of a a union of disks. Computer Science in Perspective. Essays Dedicated to Thomas Ottmann, eds. R. Klein, H.-W. Six and L. Wegner, Lecture Notes Comput. Sci. 2598, Springer-Verlag, 88-97. pdf-file
• H. Edelsbrunner and E. A. Ramos. Inclusion-exclusion complexes for pseudodisk collections. Discrete Comput. Geom. 17 (1997), 287-306.
• H. Edelsbrunner. The union of balls and its dual shape. Discrete Comput. Geom. 13 (1995), 415-440. pdf-file

Biology Applications

• J. Headd, Y.-H. A. Ban, H. Edelsbrunner, M. Vaidya and J. Rudolph. Protein-protein interfaces: properties, preferences, and projections. Protein Research, to appear, 2007. pdf-file
• J. Sohn, J. Parks, G. Buhrman, P. Brown, H. Edelsbrunner, K. Kristjansdottir, A. Safi, W. Yang and J. Rudolph. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry 44 (2005), 16563-16573. pdf-file
• Y. Wang, P. K. Agarwal, P. Brown, H. Edelsbrunner and J. Rudolph. Coarse and reliable geometric alignment for protein docking. In ``Proc. Pacific Sympos. Biocomputing, 2005'', World Scientific, Singapore, 64-75. pdf-file
• V. Choi, P. K. Agarwal, H. Edelsbrunner and J. Rudolph. Local search heuristic for rigid protein docking. In ``Proc. 4th Intl. Workshop Alg. BioInformatics, 2004'', Springer-Verlag, Lecture Notes Comput. Sci. 3240, 218-229. pdf-file
• S. Bespamyatnikh, V. Choi, H. Edelsbrunner and J. Rudolph. Accurate protein docking by shape complementarity alone. Manuscript, Dept. Comput. Sci., Duke Univ., 2003. pdf-file
• Y.-H. A. Ban, H. Edelsbrunner and J. Rudolph. Interface surfaces for protein-protein complexes. In ``Proc. 8th Intl. Conf. Res. Comput. Mol. Bio., 2004'', San Diego, California, 205-212. pdf-file
• H. Edelsbrunner, J. Liang and C. Woodward. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Science 7 (1998), 1884-1897.
• J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudharkar and S. Subramaniam. Analytic shape computation of macromolecules II: inaccessible cavities in proteins. Proteins: Structure, Function, and Genetics 33 (1998), 18-29.
• J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudharkar and S. Subramaniam. Analytic shape computation of macromolecules I: molecular area and volume through alpha shape. Proteins: Structure, Function, and Genetics 33 (1998), 1-17.
• H. Edelsbrunner, M. A. Facello, P. Fu and J. Liang. Measuring proteins and voids in proteins. In ``Proc. 28th Ann. Hawaii Internat. Conf. System Sciences, 1995'', vol. V: Biotechnology Computing, 256-264.