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TABLE OF CONTENTS
Issue No. 05 - September/October (vol. 8)
ISSN: 1545-5963
Regular Papers

A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements (Abstract)

Lipi Acharya , University of New Orleans, New Orleans
Hui Zhang , Novartis Pharmaceutical Corporation, East Hanover
Dongxiao Zhu , University of New Orleans, New Orleans, Children's Hospital, New Orleans, and Tulane University Cancer Center, New Orleans
pp. 1153-1169

A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention (Abstract)

Robert Shoemaker , University of California, San Diego, San Diego
Wei Wang , University of California, San Diego, San Diego
Rui Chang , University of California, San Diego, San Diego
pp. 1170-1182

A Preprocessing Procedure for Haplotype Inference by Pure Parsimony (Abstract)

Borja Calvo , University of the Basque Country, Donostia
Jose A. Lozano , University of the Basque Country, Donostia
Ekhine Irurozki , University of the Basque Country, Donostia
pp. 1183-1195

An Efficient Algorithm for Approximating Geodesic Distances in Tree Space (Abstract)

Francesco Rubino , IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab, Bari
Gaetano Scioscia , IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab, Bari
Pietro Leo , IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab, Bari
Simone Battagliero , IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab, Bari
Giuseppe Puglia , IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab, Bari
Saverio Vicario , Consiglio Nazionale delle Ricerche-Istituto di Tecnologie Biomediche-Sede di Bari, Bari
pp. 1196-1207

Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data (Abstract)

Jacquelyn S. Fetrow , Wake Forest University, Winston-Salem
David J. John , Wake Forest University, Winston-Salem
James L. Norris , Wake Forest University, Winston-Salem
pp. 1208-1222

Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling (Abstract)

Tatiana Baumuratova , University of Luxembourg, Luxembourg
Carito Guziolowski , University Hospital, Heidelberg
Ovidiu Radulescu , Universie de Montpelier 2
Anne Siegel , University of Rennes 1, Rennes
Sylvain Blachon , Max-Planck Institute, Potsdam
Gautier Stoll , Institut Curie, Paris
pp. 1223-1234

Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach (Abstract)

Sitanshu Sekhar Sahu , National Institute of Technology, Rourkela
Ganapati Panda , Indian Institute of Technology, Bhubaneswar
pp. 1235-1246

Fast Flexible Modeling of RNA Structure Using Internal Coordinates (Abstract)

Samuel Coulbourn Flores , Stanford University, Stanford
Peter Eastman , Stanford University, Stanford
Michael A. Sherman , Stanford University, Stanford
Russ Biagio Altman , Stanford University, Stanford
Christopher M. Bruns , Stanford University, Stanford
pp. 1247-1257

Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees (Abstract)

Biing-Feng Wang , National Tsing Hua University, Hsinchu
Chien-Hsin Lin , National Tsing Hua University, Hsinchu
pp. 1258-1272

Metasample-Based Sparse Representation for Tumor Classification (Abstract)

Lei Zhang , The Hong Kong Polytechnic University, Hong Kong
Simon C.K. Shiu , The Hong Kong Polytechnic University, Hong Kong
To-Yee Ng , The Hong Kong Polytechnic University, Hong Kong
Chun-Hou Zheng , Qufu Normal University, Rizhao and The Hong Kong Polytechnic University, Hong Kong
De-Shuang Huang , Tongi University, Shanghai
pp. 1273-1282

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome (Abstract)

Qian Peng , University of California, San Diego, La Jolla
Andrew D. Smith , University of Southern California, Los Angeles
pp. 1283-1295

Parameterized Algorithmics for Finding Connected Motifs in Biological Networks (Abstract)

Rolf Niedermeier , Friedrich-Schiller-Universität Jena, Jena
Michael R. Fellows , Charles Darwin University, Darwin
René van Bevern , Friedrich-Schiller-Universität Jena, Jena
Christian Komusiewicz , Friedrich-Schiller-Universität Jena, Jena
Nadja Betzler , Friedrich-Schiller-Universität Jena, Jena
pp. 1296-1308

Probabilistic Models for Semisupervised Discriminative Motif Discovery in DNA Sequences (Abstract)

Seungjin Choi , Pohang University of Science and Technology, Pohang
Jong Kyoung Kim , Pohang University of Science and Technology, Pohang
pp. 1309-1317

SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems (Abstract)

João Meidanis , Scylla Bioinformatics and University of Campinas, Campinas
Pedro Feijão , University of Campinas, Campinas
pp. 1318-1329

SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison (Abstract)

Gerhard Klebe , Philipps University, Marburg
Eyke Hüllermeier , Philipps University, Marburg
Marco Mernberger , Philipps University, Marburg
pp. 1330-1343

SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks (Abstract)

Aalt D.J. van Dijk , Applied Bioinformatics - Plant Research International, Wageningen
Roeland C.H.J. van Ham , Applied Bioinformatics - Plant Research International, Wageningen
Dries Van Dyck , Hasselt University, Diepenbeek and Transnational University of Limburg
Peter Boyen , Hasselt University, Diepenbeek and Transnational University of Limburg
Frank Neven , Hasselt University, Diepenbeek and Transnational University of Limburg
pp. 1344-1357

Some Mathematical Refinements Concerning Error Minimization in the Genetic Code (Abstract)

Wouter M. Koolen , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
Peter T.S. van der Gulik , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
Leen Stougie , Centrum voor Wiskunde en Informatica (CWI) and Vrije Universiteit, Amsterdam
Harry Buhrman , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
Steven M. Kelk , Centrum voor Wiskunde en Informatica (CWI), Amsterdam
pp. 1358-1372

Using Kernel Alignment to Select Features of Molecular Descriptors in a QSAR Study (Abstract)

Forbes J. Burkowski , University of Waterloo, Waterloo
William W.L. Wong , University of Toronto, Toronto
pp. 1373-1384
Short Papers

A Mathematical Model for the Validation of Gene Selection Methods (Abstract)

Alessandro Beghini , Università degli Studi di Milano, Milano
Marco Muselli , Consiglio Nazionale delle Ricerche, Genova
Francesca Ruffino , Università degli Studi di Milano, Milano
Marco Frasca , Università degli Studi di Milano, Milano
Giorgio Valentini , Università degli Studi di Milano, Milano
Alberto Bertoni , Università degli Studi di Milano, Milano
pp. 1385-1392

A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks (Abstract)

Maxim Teslenko , Royal Institute of Technology, Stockholm
Elena Dubrova , Royal Institute of Technology, Stockholm
pp. 1393-1399

Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)-Motif Model (Abstract)

Lusheng Wang , City University of Hong Kong, Hong Kong
Zhi-Zhong Chen , Tokyo Denki University, Hatomaya, Saitama
pp. 1400-1410

Probabilistic Mixture Regression Models for Alignment of LC-MS Data (Abstract)

Getachew K. Befekadu , Georgetown University Medical Center, Washington DC
Habtom W. Ressom , Georgetown University Medical Center, Washington DC
Tsung-Heng Tsai , Virginia Polytechnic Institute and State University, Arlington
Mahlet G. Tadesse , Georgetown University, Washington DC
pp. 1417-1424

Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability (Abstract)

Antonella Isacchi , Nerviano Medical Sciences, Nerviano
Paolo Magni , Università degli Studi di Pavia, Pavia
Angela Simeone , (BIOTEC), Technische Universität Dresden
Sandra Healy , National University of Ireland, Galway
Roberta Bosotti , Nerviano Medical Sciences, Nerviano
pp. 1425-1430

The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery (Abstract)

Ehud Aharoni , IBM Research Laboratory, Haifa
Hani Neuvirth , IBM Research Laboratory, Haifa
Saharon Rosset , Tel Aviv University, Tel Aviv
pp. 1431-1437
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