PSB '99 Accepted papers

Gene Expression and Genetic Networks

* Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model
T. Akutsu, S. Miyano, and S. Kuhara

Modeling Gene Expression with Differential Equations
T. Chen, H. L. He, and G.M. Church

* Linear Modeling of mRNA Expression Levels During CNS Development and Injury
P. D'haeseleer, X. Wen, S. Fuhrman, and R. Somogyi

* Sensitivity of Biological Models to Errors in Parameter Estimates
R.S. Erb and G.S. Michaels

* Analysis of the Stabilizing Effect of ROM on the Genetic Network Controlling ColE1 Plasmid Replication
P.J.E. Goss and J. Peccoud

Simulation of Genetic Interaction for Drosophila Leg Formation
K. Kyoda and H. Kitano

Evolutionary Constraint Networks in Ligand-Binding Domains: An Information-Theoretic Approach
S.B. Nagl, J. Freeman, and T.F. Smith

* NetWork: An Interactive Interface to the Tools for Analysis of Genetic Network Structure and Dynamics
M.G. Samsonova and V.N. Serov

* Modeling Regulatory Networks with Weight Matrices
D.C. Weaver, C.T. Workman, G.D. Stormo

Data Mining and Knowledge Discovery in Molecular Databases

A Comparative Analysis of Computational Motif-Detection Methods
J. Hudak and M.A. McClure

* A Probabilistic Approach to a Consensus Multiple Alignment
B. Lazareva and D. Haussler

The Effects of Ordered-Series-of-Motifs Anchoring and Sub-Class Modeling on the Generation of HMMs Representing Highly Divergent Protein Sequences
M.A. McClure and J. Kowlaski

* Clustering and detection of 5' splice sites of mRNA by k weight-matrices model
K. Murakami and T. Takagi

* Use of Bonsai Decision Trees for the Identification of Potential MHC Class I Peptide Epitope Motifs
C.J. Savoie, N. Kamikawaji, T. Sasazuki, and S. Kuhara

* Application of Knowledge Discovery to Molecular Biology: Identifying Structural Regularities in Proteins
S. Su, D.J. Cook, and L.B. Holder

Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences
T. Tsunoda, M. Fukagawa, and T. Takagi

* Effective Query Filtering for Fast Homology Searching
H.E. Williams

Computer Modeling in Physiology: From Cell to Tissue

* Extension of Refractoriness in a Model of Cardiac Defibrillation
N.A. Trayanova, F. Aguel, K. Skouibine

Information Theoretic Approaches to Biology

MDL and the Statistical Mechanics of Protein Potentials
T.G. Dewey

* Using Information Theory to Discover Side Chain Rotamer Classes: Analysis of the Effects of Local Backbone Structure
J. S. Fetrow and G. Berg

Improving the Efficiency of a User-driven Learning System with Reconfigurable Hardware. Application to DNA Splicing.
E. Lemoine, D. Merceron, J. Sallantin, and E. Mephu-Nguifo

Optimizing Smith-Waterman Alignments
R. Olsen, T. Hwa, and M. Lassig

* Computing Minimum Description Length for Robust Linear Regression Model Selection
G. Qian

* Topology Selection in Unrooted Molecular Phylogenetic Tree By Minimum Model-Based Complexity Method
H. Tanaka, F. Ren, Okayama, and T. Gojobori

Molecules to Maps: Tools for Visualization & Interaction

* ProtAlign: A 3-Dimensional Protein Alignment Assessment Tool
D. Meads, M.C. Hansen, and A. Pang

* PROMUSE: A System for Multi-Media Data Presentation of Protein Structural Alignments
M.C. Hansen, E. Charp, S. Lodha, D. Meads, and A. Pang

Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology
G. Quinn, H-P Wang, D. Martinez, and P.E. Bourne

BioJAKE: A Tool for the Creation, Visualization and Manipulation of Metabolic Pathways
W. Salamonsen, K.Y.C. Mok, P. Kolatkar, and S. Subbiah

* Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS
M.F. Sanner, B.S. Duncan, C.J. Carrillo, and A.J. Olson

Computer-Aided Drug Design

* Thermodynamics and Kinetics of Ligand-protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing
D. Bouzida, S. Arthurs, A.B. Colson, S.T. Freer, D.K. Gehlhaar, V. Larson, B.A. Luty, P.A. Rejto, P.W. Rose, and G.M. Verkhivker

Empirical vs. "Rational" Methods of Discovering New Drugs
P. Gund

* Binary QSAR: A New Method for the Determination of Quantitative Structure Activity Relationships
P. Labute

Ligand-Receptor 3-D Similarity Studies Using Multiple 4-Point Pharmacophres
J.S. Mason and D.L. Cheney

Two-dimensional Reaction of Biological Molecules Studied by Weighted-Ensemble Brownian Dynamics
I.A. Shkel and S. Kim

Protein Structure Prediction

* Protein Evolution and Protein Folding: Non-Functional Conserved Residues and Their Probable Role
O.B. Ptitsyn

* A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence
R. Samudrala, Y. Xia, M. Levitt, and E. S. Huang

Disorder in Protein Structure and Function

* Similarity Between the Sequences of Taxol-Selected Peptides and the Disordered Loop of the Anti-Apoptotic Protein, BCL-2
D.J. Rodi and L. Makowski

Characterisation of Side-Chain Conformational Preferences in a Biologically Active But Unfolded Protein
S. I. Mathieson, C. J. Penkett, and L. J. Smith

The Locally Denatured State of Glutathione S-Transferase A1-1: Transition State Analysis of Ligand-dependent Formation of the C-Terminal Helix
B.S. Nieslanik, E.C. Dietze, W.M. Atkins, I. Le Trong, and E. Adman

* One Sequence, Four Folds: Transitions Between an Ensemble of Metastable Folds for the N-Terminal Domain of CD2
R.B. Sessions, M.J. Hayes, A.J. Murray, A.R. Clarke, and R.L. Brady

* The Hydrophilic, Protease-Sensitive Terminal Domain of Eucaryotic DNA Topoisomerase Has Essential Intracellular Functions
W.-L. Shaiu, T. Hu, and T.-S. Hsieh

* Recognition between Disordered Polypeptide Chains from Cleavage of an a/b Domain: Self- versus Non-Self Association
X.-M. Yang, R. Georgescu, J.-H. Li, W.-F. Yu, Haierhan, and M.L. Tasayco