ACCEPTED PAPERS

 

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 
 
 
 


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