Gene Expression

• M.-L. Dequeant, S. Ahnert, H. Edelsbrunner, T. M. A. Fink, E. F. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. R. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS ONE 3 (2008), e2856, doi:10.1371/journal.pone.0002856. pdf-file

Protein Interaction

• B. Wang, H. Edelsbrunner and D. Morozov. Computing elevation maxima by searching the Gauss sphere. In ``Proc. 13th Internat. Sympos. Experimental Alg., 2009'', Lecture Notes Comput. Sci. 5526, 281-292. pdf-file
• J. Headd, Y.-H. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya and J. Rudolph. Protein-protein interfaces: properties, preferences, and projections. Proteome Research 6 (2007), 2576-2586. pdf-file
• J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, 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
• P. K. Agarwal, H. Edelsbrunner, J. Harer and Y. Wang. Extreme elevation on a 2-manifold. Discrete Comput. Geom. 36 (2006), 553-572. 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. J. Assoc. Comput. Mach. 53 (2006), 361-378. pdf-file

Measuring Protein Structures

• Y.-H. Ban, J. Rudolph, P. Zhou and H. Edelsbrunner. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function, and Bioinformatics 62 (2006), 852-864. pdf-file
• J. Liang, H. Edelsbrunner 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. pdf-file
• 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. pdf-file
• 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. pdf-file
• 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. pdf-file
• H. Edelsbrunner and P. Fu. Measuring space filling diagrams and voids. Molecular Biophysic Report UIUC-BI-MB-94-01, Beckman Institute, Univ. Illinois at Urbana-Champaign, Illinois, 1994. pdf-file