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TABLE OF CONTENTS
Issue No. 02 - March/April (vol. 8)
ISSN: 1545-5963
EDITORIAL

EIC Editorial (HTML)

pp. 289-291
SPECIAL SECTION ON BIBM

A Framework for Semisupervised Feature Generation and Its Applications in Biomedical Literature Mining (Abstract)

Zhihao Yang , Dalian University of Technology, Dalian
Hongfei Lin , Dalian University of Technology, Dalian
Xiaohua Hu , Drexel University, Philadelphia
Yanpeng Li , Dalian University of Technology, Dalian and Drexel University, Philadelphia
pp. 294-307

On Position-Specific Scoring Matrix for Protein Function Prediction (Abstract)

Xiaotong Lin , The University of Kansas, Lawrence
Jong Cheol Jeong , University of Kansas, Lawrence
Xue-Wen Chen , The University of Kansas, Lawrence
pp. 308-315

Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification (Abstract)

Sangyoon Oh , Ajou University, Suwon
Min Su Lee , Seoul National University, Seoul
Byoung-Tak Zhang , Seoul National University, Seoul
pp. 316-325

Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks (Abstract)

Zina M. Ibrahim , University of Windsor, Ontario
Alioune Ngom , University of Windsor, Ontario
Ahmed Y. Tawfik , French University in Egypt, Cairo
pp. 326-334

A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems (Abstract)

Amit Sabnis , Georgia State University, Atlanta
Robert W. Harrison , Georgia State University, Atlanta
pp. 335-341
REGULAR PAPERS

A Genetic Optimization Approach for Isolating Translational Efficiency Bias (Abstract)

Dan E. Krane , Wright State University, Dayton
Travis E.W. Doom , Wright State University, Dayton
Michael L. Raymer , Wright State University, Dayton
Douglas W. Raiford , Southern Methodist University, Dallas
pp. 342-352

A Markov-Blanket-Based Model for Gene Regulatory Network Inference (Abstract)

Madhu Chetty , Monash University, Churchill
Ramesh Ram , Monash University, Churchill
pp. 353-367

A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data (Abstract)

Weichuan Yu , Hong Kong University of Science and Technology, Hong Kong
Zengyou He , Hong Kong University of Science and Technology, Hong Kong
Can Yang , Hong Kong University of Science and Technology, Hong Kong
pp. 368-380

Accurate Construction of Consensus Genetic Maps via Integer Linear Programming (Abstract)

Timothy J. Close , University of California, Riverside, Riverside
Yonghui Wu , Google Inc., Mountain View
Stefano Lonardi , University of California, Riverside, Riverside
pp. 381-394

Bayesian Models and Algorithms for Protein β-Sheet Prediction (Abstract)

Hakan Erdogan , Sabanci University, Istanbul
Zafer Aydin , Georgia Institute of Technology, Atlanta
Yucel Altunbasak , Georgia Institute of Technology, Atlanta
pp. 395-409

Comparison of Galled Trees (Abstract)

Francesc Rosselló , University of the Balearic Islands, Palma de Mallorca
Gabriel Valiente , Technical University of Catalonia, Barcelona
Mercè Llabrés , University of the Balearic Islands, Palma de Mallorca
Gabriel Cardona , University of the Balearic Islands, Palma de Mallorca
pp. 410-427

Data Mining on DNA Sequences of Hepatitis B Virus (Abstract)

Stephen K.W. Tsui , The Chinese University of Hong Kong, Hong Kong
Kwong-Sak Leung , The Chinese University of Hong Kong, Hong Kong
Joseph Jao-Yiu Sung , The Chinese University of Hong Kong, Hong Kong
Eddie Y.T. Ng , The Chinese University of Hong Kong, Hong Kong
Henry L.Y. Chan , The Chinese University of Hong Kong, Hong Kong
Pete Chi-Hang Tse , The Chinese University of Hong Kong, Hong Kong
Tony S.K. Mok , The Chinese University of Hong Kong, Hong Kong
Jin-Feng Wang , The Chinese University of Hong Kong, Hong Kong
Kin Hong Lee , The Chinese University of Hong Kong, Hong Kong
pp. 428-440

Discriminative Motif Finding for Predicting Protein Subcellular Localization (Abstract)

Ziv Bar-Joseph , Carnegie Mellon University, Pittsburgh
Tien-ho Lin , Carnegie Mellon University, Pittsburgh
Robert F. Murphy , Carnegie Mellon University, Pittsburgh
pp. 441-451

ICGA-PSO-ELM Approach for Accurate Multiclass Cancer Classification Resulting in Reduced Gene Sets in Which Genes Encoding Secreted Proteins Are Highly Represented (Abstract)

Suresh Sundaram , Indian Institute of Technology, New Delhi, India
Michael Zimmermann , Iowa State University, Ames, IA
Saras Saraswathi , Iowa State University, Ames, IA
Marit Nilsen-Hamilton , Iowa state University, Ames, IA
Narasimhan Sundararajan , Nanyang Technological University, Singapore
pp. 452-463

Microarray Time Course Experiments: Finding Profiles (Abstract)

Concepción Arenas , University of Barcelona, Barcelona
Itziar Irigoien , University of the Basque Country, Donostia
Sergi Vives , University of Barcelona, Barcelona
pp. 464-475

Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning (Abstract)

Shuigeng Zhou , Fudan university, Shanghai
Qiwen Dong , Fudan university, Shanghai
pp. 476-486

On the Characterization and Selection of Diverse Conformational Ensembles with Applications to Flexible Docking (Abstract)

Karine Bastard , Université de Nantes, CNRS, France
Sébastien Loriot , INRIA Sophia-Antipolis, France
Chantal Prévost , CNRS, France
Frédéric Cazals , INRIA Sophia-Antipolis, France
Sushant Sachdeva , Princeton University, USA
pp. 487-498

Semantics and Ambiguity of Stochastic RNA Family Models (Abstract)

Robert Giegerich , Bielefeld University, Bielefeld
Christian Höner zu Siederdissen , University of Vienna, Vienna
pp. 499-516

Simultaneous Identification of Duplications and Lateral Gene Transfers (Abstract)

Michael Hallett , McGill University, Montreal
Ali Tofigh , KTH Royal Institute of Technology, Stockholm
Jens Lagergren , KTH Royal Institute of Technology, Stockholm
pp. 517-535

Visual Exploration across Biomedical Databases (Abstract)

Huimin Guo , University of Maryland, College Park
Michael D. Lieberman , University of Maryland, College Park
Sima Taheri , University of Maryland, College Park
Inbal Yahav , University of Maryland, College Park
Fatemeh Mirrashed , University of Maryland, College Park
Ben Shneiderman , University of Maryland, College Park
Aleks Aris , University of Maryland, College Park
pp. 536-550
SHORT PAPERS

An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss (Abstract)

Mathieu Blanchette , McGill University, Montreal
Paz Carmi , Ben-Gurion University of the Negev, Beer-Sheva
Norbert Zeh , Dalhousie University, Halifax
Glenn Hickey , McGill University, Montreal
Anil Maheshwari , Carleton University, Ottawa
pp. 551-556

Encoding Molecular Motions in Voxel Maps (Abstract)

Monique Erard , IPBS-CNRS, Toulouse, France
Sophie Barbe , LISBP, Toulouse, France
Juan Cortés , LAAS-CNRS, Toulouse, France
Thierry Siméon , LAAS-CNRS, Toulouse, France
pp. 557-563

Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis (Abstract)

J. Rocha , University of the Balearic Islands, Palma
pp. 564-569

Inferring Contagion in Regulatory Networks (Abstract)

Mari Cleide Sogayar , University of São Paulo, São Paulo, Brazil
Rui Yamaguchi , University of Tokyo, Japan
Carlos Eduardo Ferreira , University of São Paulo, São Paulo, Brazil
Satoru Miyano , University of Tokyo, Japan
Teppei Shimamura , University of Tokyo, Japan
João Ricardo Sato , Universidade Federal do ABC, São Paulo, Brazil
Marcos Angelo Almeida Demasi , University of São Paulo, São Paulo, Brazil
André Fujita , RIKEN, Japan
pp. 570-576
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