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TABLE OF CONTENTS
Issue No. 03 - May/June (vol. 8)
ISSN: 1545-5963
REGULAR PAPERS

A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory (Abstract)

Alfredo Benso , Politecnico di Torino, Torino
Gianfranco Politano , Politecnico di Torino, Torino
Stefano Di Carlo , Politecnico di Torino, Torino
pp. 577-591

A Comprehensive Statistical Model for Cell Signaling (Abstract)

Donald Geman , The Johns Hopkins University, Baltimore
Laurent Younes , The Johns Hopkins University, Baltimore
Erdem Yörük , The Johns Hopkins University, Baltimore
Michael F. Ochs , The Johns Hopkins University, Baltimore
pp. 592-606

A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks (Abstract)

Yi Pan , Georgia State University, Atlanta
Min Li , Central South University, Changsha
Jianer Chen , Texas A & M University, College Station
Jianxin Wang , Central South University, ChangSha
pp. 607-620

A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data (Abstract)

Rui Jiang , Tsinghua University, Beijing
Tao Jiang , University of California, Riverside
Jianxing Feng , Tsinghua Univ., Beijing
pp. 621-634

A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks (Abstract)

Leo van Iersel , University of Canterbury, Christchurch
Katharina T. Huber , University of East Anglia, Norwich
Steven Kelk , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
Radosław Suchecki , University of East Anglia, Norwich
pp. 635-649

A Theoretical Analysis of the Prodrug Delivery System for Treating Antibiotic-Resistant Bacteria (Abstract)

James T. Murphy , Dublin City University, Dublin
Ray Walshe , Dublin City University, Dublin
Marc Devocelle , Royal College of Surgeons in Ireland, Dublin
pp. 650-658

Cancer Classification from Gene Expression Data by NPPC Ensemble (Abstract)

Anirban Mukherjee , Indian Institute of Technology, Kharagpur
Pranab K. Dutta , Indian Institute of Technology, Kharagpur
Sanghamitra Sengupta , University of Calcutta, Kolkata
Santanu Ghorai , MCKV Institute of Engineering, Howrah and Indian Institute of Technology, Kharagpur
pp. 659-671

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers (Abstract)

Cristin Print , University of Auckland, Auckland
Seiya Imoto , University of Tokyo, Tokyo
Hiromitsu Araki , Cell Innovator, Inc
Masao Nagasaki , University of Tokyo, Tokyo
Satoru Miyano , University of Tokyo, Tokyo
D. Stephen Charnock-Jones , University of Cambridge, Cambridge
Yoshinori Tamada , University of Tokyo, Tokyo
pp. 683-697

FEAST: Sensitive Local Alignment with Multiple Rates of Evolution (Abstract)

Daniel G. Brown , University of Waterloo, Waterloo
Alexander K. Hudek , University of Waterloo, Waterloo
pp. 698-709

Identifiability of Two-Tree Mixtures for Group-Based Models (Abstract)

John A. Rhodes , University of Alaska, Fairbanks
Seth Sullivant , North Carolina State University, Raleigh
Elizabeth S. Allman , University of Alaska, Fairbanks
Sonja Petrović , University of Illinois at Chicago, Chicago
pp. 710-722

Incorporating Nonlinear Relationships in Microarray Missing Value Imputation (Abstract)

Tianwei Yu , Emory University, Atlanta
Wei Sun , University of North Carolina, Chapel Hill
Hesen Peng , Emory University, Atlanta
pp. 723-731

Manipulating the Steady State of Metabolic Pathways (Abstract)

Bin Song , University of Florida-Gainesville, FL
Sanjay Ranka , University of Florida-Gainesville, FL
Tamer Kahveci , University of Florida-Gainesville, FL
İ. Esra Büyüktahtakin , University of Arizona-Tucson, AZ
pp. 732-747

Multitask Learning for Protein Subcellular Location Prediction (Abstract)

Hannah Hong Xue , Hong Kong University of Science and Technology, Clearwater Bay, Kowloon
Sinno Jialin Pan , Hong Kong University of Science and Technology, Clearwater Bay, Kowloon
Qiang Yang , Hong Kong University of Science and Technology, Clearwater Bay, Kowloon
Qian Xu , Hong Kong University of Science and Technology, Clearwater Bay, Kowloon
pp. 748-759

Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms (Abstract)

Rubén Armañanzas , Universidad Politécnica de Madrid, Madrid
Concha Bielza , Universidad Politécnica de Madrid, Madrid
Pedro Larrañaga , Universidad Politécnica de Madrid, Madrid
Iñaki Inza , University of the Basque Country, San Sebastián
Miguel García-Torres , Pablo de Olavide University, Seville
Yvan Saeys , Ghent University, Ghent
Yves van de Peer , Ghent University, Ghent
pp. 760-774

Prediction of Protein Functions with Gene Ontology and Interspecies Protein Homology Data (Abstract)

Bud Mishra , New York University, New York
Antonina Mitrofanova , New York University, New York
Vladimir Pavlovic , Rutgers University, Piscataway
pp. 775-784

3D Shape Reconstruction of Loop Objects in X-Ray Protein Crystallography (Abstract)

Tilo Strutz , Deutsche Telekom AG, Hochschule fuer Telekommunikation Leipzig, Leipzig
pp. 797-807

TCLUST: A Fast Method for Clustering Genome-Scale Expression Data (Abstract)

Vineet Bafna , University of California, San Diego, La Jolla
Chunlei Wu , The Genomics Institute of the Novartis Research Foundation, La Jolla
Banu Dost , University of California, San Diego, La Jolla
Andrew Su , The Genomics Institute of the Novartis Research Foundation, La Jolla
pp. 808-818

TRIAL: A Tool for Finding Distant Structural Similarities (Abstract)

Christopher Jermaine , University of Florida, Gainesville
Bin Song , University of Florida, Gainesville
Jayendra Gnanaskandan Venkateswaran , University of Florida, Gainesville
Tamer Kahveci , University of Florida, Gainesville
pp. 819-831

True Path Rule Hierarchical Ensembles for Genome-Wide Gene Function Prediction (Abstract)

Giorgio Valentini , Università degli Studi di Milano, Milano
pp. 832-847
SHORT PAPERS

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem (Abstract)

Mukul S. Bansal , Tel-Aviv University, Tel Aviv
Ron Shamir , Tel-Aviv University, Tel Aviv
pp. 848-850

Identifying Relevant Data for a Biological Database: Handcrafted Rules versus Machine Learning (Abstract)

Keith Noto , University of California at San Diego, La Jolla
Milton H. Saier, Jr. , University of California at San Diego, La Jolla
Sanmay Das , Rensselaer Polytechnic Institute, Troy
Aditya Kumar Sehgal , Parity Computing, La Jolla
Charles Elkan , University of California at San Diego, La Jolla
pp. 851-857

Toward Better Understanding of Protein Secondary Structure: Extracting Prediction Rules (Abstract)

Jacek M. Zurada , BioInformatics Research Center, Singapore
Minh N. Nguyen , BioInformatics Institute, Singapore
Jagath C. Rajapakse , BioInformatics Research Center, Singapore
pp. 858-864
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