Some Old Papers

These are old papers, retained for historical purposes. Up to date papers can be found from Google Scholar and DBLP.

• Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip data sets Bioinformatics, 2006 with S. Pyne and B. Futcher.
• Some Lower Bounds on Geometric Separability Problems (with E. Arkin, F. Hurtado, J. Mitchell, and C. Seara), International Journal of Computational Geometry and Applications, Vol. 16, No. 1, February 2006.
• Airplane Boarding, Disk Scheduling and Space-Time Geometry (with E. Bachmat, D. Berend, and L. Sapir), Algorithmic Applications in Management: First International Conference, AAIM 2005, Xian, China, June 22-25, 2005.
• Combinatorial Dominance and Heuristic Search (with D. Berend). submitted for publication.
• Attention and Communication: Decision Scenarios for Teleoperating Robots (with J. Nickerson) Proc. 38th IEEE Hawaii Int. Conf. System Sciences, Big Island Hawaii, January 3-6, 2005.
• Improved Bounds on Sorting with Length-Weighted Reversals (with M. Bender, D. Ge, S. He, H. Hu, R. Pinter and F. Swidan) 15th ACM-SIAM Symp. on Discrete Algorithms (SODA '04). New Orleans LA, January 2004.
• Alphabet Permutation for Differentially Encoding Text (with G. Landau and O. Levi). submitted for publication.
• Shift error detection in standardized exams (with P. Sumazin). Jounral of Discrete Algorithms, 2 (2004) 313-331
• A Model for Analyzing Black-Box Optimization (with V. Phan and P. Sumazin). WADS 2003. See also the Springer link.
• Sorting with Length-Weighted Reversals (with R. Pinter), Proc. 13th International Conference on Genome Informatics (GIW 2002), Universal Academic Press, 173-182, 2002.
• Microarray synthesis through multiple-use PCR primer design (with R. Fernandes) Proc. ISMB 2002 and Bioinformatics 2002 Jul;18 Suppl 1:S128-135
• Designing RNA Sequences: Natural and Artificial Selection (with B. Cohen) Proc. RECOMB 2002.
• Deconvolving Sequence Variation in Mixed DNA Populations (with A. Wildenburg and P. Sumazin) Proc. RECOMB 2002.
• Designing Better Phages Bioinformatics, 2001.
• Analysis techniques for microarray time-series data (with J. Zhi and V. Filkov), RECOMB 2001.
• Dealing With Errors in Interactive Sequencing by Hybridization (with V. Phan), Bioinformatics, 2001.
• Efficient Data Structures for Maintaining Set Partitions (with Michael Bender and Saurabh Sethia), Proc. SWAT 2000.
• A Case Study in Genome-Level Fragment Assembly (with Ting Chen), Bioinformatics, 2000.
• Filling a Penny Album (with Shiyong Lu), Chance, 13-2 (Spring 2000) 25-28.
• Identifying Gene Regulatory Networks from Experimental Data (with T. Chen and V. Filkov) Proc. RECOMB '99, Lyon France, April 1999.
• Optimizing Combinatorial Library Construction via Split Synthesis (with B. Cohen) Proc. RECOMB '99, Lyon France, April 1999. Also, to appear in the Journal of Combinatorial Chemistry
• Who is interested in algorithms and why?: lessons from the Stony Brook Algorithms Repository ACM SIGACT News, September 1999. Also Second Workshop on Algorithm Engineering, Saarbrucken, Germany, August 20-22, 1998.
• The Lazy Bureaucrat Scheduling Problem (with E. Arkin, M. Bender, and J. Mitchell). Workshop on Algorithms and Data Structures (WADS '99), Vancouver, B.C. August 1999.
• VType: Text Entry in an Immersive Virtual World (with F. Evans and A. Varshney) submitted to International Journal of Human-Computer Studies
• Matching for Run-Length Encoded Strings (with A. Apostolico and G. Landau). Journal of Complexity, 15 (1999) 4-16. Special issue for papers from Sequences '97, Positano Italy, June 11-13, 1997.
• Probe Trees for Touching Character Recognition (with G. Sazaklis, E. Arkin, and J. Mitchell) Proc. International Conference on Imaging Science, Systems and Technology, (CISST) Las Vegas, NV July 6-9, 1998, pp. 282-289.
• On the Maximum Scatter TSP (with E. Arkin, Y.-J. Chiang, J. Mitchell, and T. Yang). To appear in SIAM J. Computing Also, Proc. Eighth ACM-SIAM Symp. on Discrete Algorithms (SODA) pp. 211-220.
• Trie-Based Data Structures for Sequence Assembly (with T. Chen) Proc. Combinatorical Pattern Matching (CPM '97) Springer-Verlag LNCS v. 1264, pp. 206-223. Also, accidently accepted (but not submitted) to WADS '99.
• Efficiently Partitioning Arrays (with S. Khanna and M. Muthukrishnan). Proc. ICALP '97.
• Fabricating Arrays of Strings, (with R. Bradley), First Conf. Computational Biology (RECOMB '97), January 1997.
• Positional Sequencing by Hybridization (with S. Hannenhalli, W. Feldman, H. Lewis, and P. Pevzner). Computer Applications in the Biological Sciences (CABIOS), 12 (1996) 19-24.
• Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model (with R. Agarwala, S. Batzoglou, V. Dancik, S. Decatur, M. Farach, S. Hannenhalli, and S. Muthukrishnan). To appear in J. Computational Biology, RECOMB Special Issue. Also, Proc. Eighth ACM-SIAM Symp. on Discrete Algorithms (SODA) pp. 390-399 and Proc. First International Conf. on Computational Molecular Biology (RECOMB 97)
• Optimizing Triangle Strips for Fast Rendering, (with F. Evans and A. Varshney). Proc. IEEE Visualization '96, 319-326.
• Sorting with Fixed-Length Reversals, (with Ting Chen). Discrete Applied Mathematics, special issue on Computational Biology.
• On Minimum-Area Hulls, (with E. Arkin, M. Held, J. Mitchell, V. Sacristan, and T-C. Yang, Proc. European Symposium on Algorithms (ESA'96) 1996.
• Randomized Algorithms for Identifying Minimal Lottery Ticket Sets Journal of Undergraduate Research, 2-2 (1996) 88-97.
• Recognizing Polygonal Parts from Width Measurements, (with E. Arkin, M. Held, J. Mitchell), Computational Geometry: Theory and Applications.
• A Partial Digest Approach to Restriction Site Mapping, (with Gopalkrishnan Sundaram), Bulletin of Mathematical Biology, 56 (1994) 275-294.
• Unification Factoring for Efficient Execution of Logic Programs (with S. Dawson, C.R. Ramakrishnan, I.V. Ramakrishnan, K. Sagonas, T. Swift, and D.S. Warren). ACM Symposium on Principles of Programming Languages (POPL '95), San Francisco CA, January 23-25, 1995.
• Dialing for Documents: an Experiment in Information Theory, (with Harald Rau). Seventh ACM SIGGRAPH Symposium on User Interface Software and Technology (UIST '94), Marina Del Rey, California, November 2-4, 1994, 147-155.
• Reconstructing Strings from Substrings, (with Gopalkrishnan Sundaram), Journal of Computational Biology 2 (1995) 333-353. Also, Workshop on Data Structures and Algorithms (WADS '93), Springer-Verlag Lecture Notes in Computer Science, v. 709, 565-576.
• Algorithms for Square Roots of Graphs, (with Yaw-Ling Lin). SIAM J. Discrete Mathematics 8 (1995) pp. 99-118.
• Hamiltonian Triangulations for Fast Rendering, (with E. Arkin, M. Held, and J. Mitchell), The Visual Computer, to appear.
• Gracefully Labeling Prisms, (with Jen-Hsin Huang). ARS Combinatoria 38 (1994) 225-242.
• Point Probe Decision Trees for Geometric Concept Classes, (with E. Arkin, M. Goodrich, J.S.B. Mitchell, D. Mount, and C. Piatko), (two pages of FIGURES are separate), Workshop on Algorithms and Data Structures, August 1993, pp. 95-106.
• Frequencies of Large Distances in Integer Lattices (with Venugopal Reddy). Proc. Seventh International Conference on Graph Theory, Combinatorics, Algorithms, and Applications, Kalamazoo MI, in Graph Theory, Combinatorics, and Applications, ed. Y. Alavi and A. Schwenk, John Wiley and Sons, New York, v. 2, 981-989.
• Interactive Reconstruction via Probing Proceedings of the IEEE, 80 (1992) 1364-1383.
• Model-based probing strategies for convex polygons, in Comp. Geometry: Theory and Applications, 1992
• Probing convex polygons with half-planes, in Journal of Algorithms, 1991
• Reconstructing Sets from Interpoint Distances, (with Warren Smith and Paul Lemke). in Sixth ACM Symposium on Computational Geometry, June 1990, 332-339. Note: The long-standing problem of finding a strongly polynomial-time algorithm for the turnpike/partial digest problem remains open.
• Problems in geometric probing, in Algorithmica, 1989
• Geometric Probing, Ph.D. Thesis, University of Illinois, 1988.