PAPER 001 P. Agarwal and V. Bafna Detecting non-adjoining correlations within signals in DNA. PAPER 002 A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg From four-taxon trees to phylogenies: The case of mammalian evolution. PAPER 003 G. Benson An Algorithm for Finding Tandem Repeats of Unspecified Pattern PAPER 004 B. Berger, T.Leighton Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. PAPER 005 M. Bonet, M.Steel, T.Warnow, S.Yooseph Better Methods for Solving Parsimony and Compatiblity PAPER 006 C. C. Chen, J.P. Singh, R.B. Altman The Hierarchical Organization of Molecular Structure Computations PAPER 007 P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis On the Complexity of Protein Folding. PAPER 008 D. Fasulo, T. Jiang, R. M. Karp, N. Sharma Constructing Maps Using the Span and Inclusion Relations. PAPER 009 A. V. Finkelstein, A. Ya. Badretdinov How Fast a Protein Chain Can Fold to Its Most Stable Structure? PAPER 010 R. M. Fye, C.J. Benham A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA PAPER 011 I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules PAPER 012 R. A. Goldstein, J. M.Koshi, D. P.Mindell Beyond mutation matrices: Physical-Chemistry based evolutionary models. PAPER 013 W. N. Grundy Family-based Homology Detection via Pairwise Sequence Comparison. PAPER 014 I. Holmes and R. Durbin Dynamic Programmimg Alignment Accuracy. PAPER 015 T. Hwa, M. Lassig Optimal Detection of Sequence Similarity by Local Alignment. PAPER 016 R.M.Karp, R.Shamir Algorithms for Optical Mapping. PAPER 017 P. E. Kearney Ordinal Beats Additive PAPER 018 E. Koonin, R. Tatusov, M.Y. Galperin and M.N. Rozanov Genome analysis using clusters of orthologous groups (COGs) PAPER 019 J. K.Lee, V. Dancik, M. S. Waterman Estimation for restriction sites observed by optical mapping using reversible-jump markov chain monte carlo PAPER 020 H. Lenhof, K. Reinert, M. Vingron A Polyhedral Approach to RNA Sequence Structure Alignment. PAPER 021 A. M. Lesk Assessment of Ab Initio Protein Structure Prediction. PAPER 022 R. Liu, T. W. Blackwell and D. J. States A structure based similarity measure for nucleic acid sequence comparison. PAPER 023 B. Ma, M. Li, L. Zhang On Reconstructing Species Trees From Gene Trees In Term of Duplications PAPER 024 L. Parida, B. Mishra Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaions Problem PAPER 025 D. G.Politte, D. R. Maffitt, D. J.States Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms PAPER 026 M. Regnier A Unified Approach to Word Statistics PAPER 027 B. A.Reva, A. V.Finkelstein, J. Skolnick A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins PAPER 028 I. Rigoutsos,A. Floratos Motif Discovery in Biological Sequences Without Alignment or Enumeration PAPER 029 E. Rocke, M. Tompa An Algorithm for Finding Novel Gapped Motifs in DNA sequences PAPER 030 M. Sagot, E. W. Myers Identifying satellites in nucleic acid sequences PAPER 031 D. Sankoff, M. Blanchette Multiple genome rearrangement PAPER 032 F. Sun Modeling DNA shuffling PAPER 033 S. R. Sunyaev, I. V. Rodchenkov Analysis of the Position Dependent Amino Acid Probabilities and its Application to the Search for Remote Homologues. PAPER 034 A. Vologodskii Maxwell demon and topology simplification by type II topoisomerases. PAPER 035 W. L.Walker, D. S. Goodsell,E. M.Landaw The Theoretical Limits of DNA sequence discrimination of Polyamides PAPER 036 T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag Regression Analysis of Multiple Protein Structures PAPER 037 Y. Xu, D. Xu, E. C. Uberbacher A New Method for modeling and solving the protein fold recognition problem PAPER 038 Z. Zhang, P. Berman, W. Miller Alignments Without Low-Scoring Regions