


Experiments in computing sequences of reversals
A. Bergeron and F. Strasbourg

Improving the accuracy of evolutionary distances between genomes
L.S. Wang

On the practical solution of the reversal median problem
A. Caprara

Determination of the binding amino acids based on random peptide
array screening data
P.J. van der Veen, L.F.A. Wessels, J.W. Sloostra, R.H. Meloen,
M.J.T. Reinders, and J. Hellendoorn

Assessing the statistical significance of overrepresented oligonucleotides
A. Denise, M. Regnier, and M. Vandenbogaert

Comparing stochastic models
A. Jagota, R.B. Lyngso, and C.N.S. Pedersen

Computing linking numbers of a filtration
H. Edelsbrunner and A. Zomorodian

A simple hypergeometric approach for discovering putative transcription factor binding sites
Y. Barash, G. Bejerano, and N. Friedman

An improved model for statistical alignment
I. Miklos and Z. Toroczkai

Finding an optimal inversion median: experimental results
A. Siepel and B.M.E. Moret

Pattern matching and pattern discovery algorithms for protein topologies
J. Viksna and D. Gilbert

A chemicaldistancebased test for positive Darwinian selection
T. Pupko, R. Sharan, M. Hasegawa, R. Shamir, and D. Graur

Algorithms for finding gene clusters
S. Heber and J. Stoye

False positives in genomic map assembly and sequence validation
T. Anantharaman and B. Mishra

Finding the maximum compatible tree for a bounded number of trees withbounded degree is solvable in polynomial time
Ganeshkumar G. and T. Warnow

Boosting EM for radiation hybrid and genetic mapping
T. Schiex, P. Chabrier, M. Bouchez, and D. Milan

Placing probes along the genome using pairwise distance data
W. Casey, B. Mishra, and M. Wigler

Comparing assemblies using fragments and matepairs
D.H. Huson, A.L. Halpern, Z. Lai, E.W. Myers, K. Reinert,
and G.G. Sutton

MLMC trees and Hadamard conjugation
B. Chor, M. Hendy, and D. Penny

The performance of phylogenetic methods on trees of bounded diameter
L. Nakhleh, U. Roshan, K. St.John, J. Sun, and T. Warnow

(1+e)approximation of sorting by reversals and transpositions
N. Eriksen

Improving profileprofile alignments via log average scoring
N. von Oehsen and R. Zimmer

Side chainpositioning as an integer programming problem
O. Eriksson, Y. Zhou, and A. Elofsson
