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TABLE OF CONTENTS
Issue No. 01 - January-February (vol. 8)
ISSN: 1545-5963
Editorial
Regular Papers

A Fast Algorithm for Computing Geodesic Distances in Tree Space (Abstract)

Megan Owen , North Carolina State University, Raleigh
J. Scott Provan , University of North Carolina, Chapel Hill
pp. 2-13

A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments (Abstract)

Mohak Shah , McGill University, Montreal
Jacques Corbeil , Laval University, Quebec
pp. 14-26

Efficient Formulations for Exact Stochastic Simulation of Chemical Systems (Abstract)

Sean Mauch , California Institute of Technology, Pasadena
Mark Stalzer , California Institute of Technology, Pasadena
pp. 27-35

Estimating Haplotype Frequencies by Combining Data from Large DNA Pools with Database Information (Abstract)

Dario Gasbarra , University of Helsinki, Helsinki
Sangita Kulathinal , University of Helsinki, Helsinki and Indic Society for Education and Development, Nashik
Matti Pirinen , University of Helsinki, Helsinki
Mikko J. Sillanpää , University of Helsinki, Helsinki
pp. 36-44

$F^2$Dock: Fast Fourier Protein-Protein Docking (Abstract)

Chandrajit Bajaj , University of Texas at Austin, Austin
Rezaul Chowdhury , University of Texas at Austin, Austin
Vinay Siddavanahalli , Google Inc., Mountain View
pp. 45-58

Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description (Abstract)

Joachim Giard , Université catholique de Louvain, Belgium
Patrice Rondao Alface , Interuniversity Micro Electronics Centre (IMEC), Belgium
Jean-Luc Gala , Université catholique de Louvain, Belgium
Benoît Macq , Université catholique de Louvain, Belgium
pp. 59-68

Finding Significant Matches of Position Weight Matrices in Linear Time (Abstract)

Cinzia Pizzi , University of Padova, Padova
Pasi Rastas , University of Helsinki, Helsinki
Esko Ukkonen , University of Helsinki, Helsinki
pp. 69-79

Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors Using a Small Molecular Data Set (Abstract)

Răzvan Andonie , Central Washington University, Ellensburg and Transylvania University of Braşov, Romania
Levente Fabry-Asztalos , Central Washington University, Ellensburg
Christopher Badi' Abdul-Wahid , Central Washington University, Ellensburg
Sarah Abdul-Wahid , Central Washington University, Ellensburg
Grant I. Barker , Central Washington University, Ellensburg
Lukas C. Magill , Central Washington University, Ellensburg
pp. 80-93

Genetic Networks and Soft Computing (Abstract)

Sushmita Mitra , Indian Statistical Institute, Kolkata
Ranajit Das , Indian Statistical Institute, Kolkata
Yoichi Hayashi , Meiji University, Kawasaki
pp. 94-107

Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data (Abstract)

Wenxue Wang , University of California Santa Barbara, Santa Barbara
Bijoy K. Ghosh , Texas Tech University, Lubbock
Himadri B. Pakrasi , Washington University in Saint Louis, Saint Louis
pp. 108-121

Improving the Computational Efficiency of Recursive Cluster Elimination for Gene Selection (Abstract)

Lin-Kai Luo , Xiamen University, Xiamen
Deng-Feng Huang , Xiamen University, Xiamen
Ling-Jun Ye , Xiamen University, Xiamen
Qi-Feng Zhou , Xiamen University, Xiamen
Gui-Fang Shao , Xiamen University, Xiamen
Hong Peng , Xiamen University, Xiamen
pp. 122-129

Influence of Prior Knowledge in Constraint-Based Learning of Gene Regulatory Networks (Abstract)

Mehmet Tan , Middle East Technical University, Ankara and University of Calgary, Calgary
Mohammed Alshalalfa , University of Calgary, Calgary
Reda Alhajj , University of Calgary, Calgary and Global University, Beirut
Faruk Polat , Middle East Technical University, Ankara
pp. 130-142

Information-Theoretic Model of Evolution over Protein Communication Channel (Abstract)

Liuling Gong , University of Illinois at Chicago, Chicago
Nidhal Bouaynaya , University of Arkansas at Little Rock, Little Rock
Dan Schonfeld , University of Illinois at Chicago, Chicago
pp. 143-151

Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli (Abstract)

Delphine Ropers , INRIA Grenoble-Rhône-Alpes, Saint Ismier Cedex
Valentina Baldazzi , INRIA Grenoble-Rhône-Alpes, Saint Ismier Cedex
Hidde de Jong , INRIA Grenoble-Rhône-Alpes, Saint Ismier Cedex
pp. 166-181

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints (Abstract)

Rogier J.P. van Berlo , Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft
Dick de Ridder , Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft
Jean-Marc Daran , Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft
Pascale A.S. Daran-Lapujade , Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft
Bas Teusink , Vrijie Universiteit, Amsterdam and Kluyver Centre for Genomics of Industrial Fermentation, Delft
Marcel J.T. Reinders , Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft
pp. 206-216

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays (Abstract)

Leo Lahti , Helsinki University of Technology, TKK
Laura L. Elo , University of Turku, Turku
Tero Aittokallio , University of Turku, Turku
Samuel Kaski , Helsinki University of Technology, TKK
pp. 217-225

Topology Improves Phylogenetic Motif Functional Site Predictions (Abstract)

Dukka B. KC , University of North Carolina at Charlotte, Charlotte
Dennis R. Livesay , Univeristy of North Carolina at Charlotte, Charlotte
pp. 226-233

Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model (Abstract)

Md Tamjidul Hoque , Griffith University, Nathan
Madhu Chetty , Monash University, Churchill
Andrew Lewis , Griffith University, Nathan
Abdul Sattar , Griffith University, Nathan
pp. 234-245
Short Papers

A Weighted Principal Component Analysis and Its Application to Gene Expression Data (Abstract)

Joaquim F. Pinto da Costa , University of Porto, Porto
Hugo Alonso , University of Aveiro, Aveiro
Luís Roque , ISEP, Porto
pp. 246-252

Disturbance Analysis of Nonlinear Differential Equation Models of Genetic SUM Regulatory Networks (Abstract)

Ping Li , The University of Hong Kong, Hong Kong
James Lam , The University of Hong Kong, Hong Kong
pp. 253-259

Linear-Time Algorithms for the Multiple Gene Duplication Problems (Abstract)

Cheng-Wei Luo , National Taiwan University, Taipei
Ming-Chiang Chen , National Taiwan University, Taipei
Yi-Ching Chen , National Taiwan University, Taipei
Roger W.L. Yang , National Taiwan University, Taipei
Hsiao-Fei Liu , National Taiwan University, Taipei
Kun-Mao Chao , National Taiwan University, Taipei
pp. 260-265

Recursive Mahalanobis Separability Measure for Gene Subset Selection (Abstract)

K.Z. Mao , Nanyang Technological University, Singapore
Wenyin Tang , Nanyang Technological University, Singapore
pp. 266-272

Semi-Markov Models for Brownian Dynamics Permeation in Biological Ion Channels (Abstract)

Vikram Krishnamurthy , University of British Columbia, Vancouver
Kai Yiu Luk , University of British Columbia, Vancouver
pp. 273-281
Reviewers List

2010 TCBB Reviewers List (PDF)

pp. 282-284
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