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TABLE OF CONTENTS
Issue No. 02 - April-June (vol. 6)
ISSN: 1545-5963
REGULAR PAPERS

Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views (Abstract)

B. Hamann , Dept. of Comput. Sci., Univ. of California, Davis, CA, USA
M.D. Biggin , Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
D.W. Knowles , Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
J. Malik , Comput. Sci. Div., Univ. of California, Berkeley, CA, USA
H. Hagen , Dept. of Comput. Sci., Univ. of Kaiserslautern, Kaiserslautern, Germany
C.L. Luengo Hendriks , Centre for Image Anal., Uppsala Univ., Uppsala, Sweden
S.V.E. Keranen , Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
C.C. Fowlkes , Dept. of Comput. Sci., Univ. of California, Irvine, CA, USA
A.H. DePace , Med. Sch., Dept. of Syst. Biol., Harvard Univ., Boston, MA, USA
O. Rubel , Dept. of Comput. Sci., Univ. of Kaiserslautern, Kaiserslautern, Germany
G.H. Weber , Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
pp. 1
EDITORIAL
SPECIAL SECTION ON BIOINFORMATICS RESEARCH AND APPLICATIONS (ISBRA)

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats (Abstract)

Todd J. Treangen , Institut Pasteur, CNRS and UPMC University, France
Guillaume Achaz , UPMC University, CNRS, MNHN, IRD, UMR, Paris
Mark A. Ragan , University of Queensland and ARC Centre of Excellence, Brisbane
Xavier Messeguer , Technical University of Catalonia, Barcelona
Eduardo P.C. Rocha , Institut Pasteur, CNRS and UPMC University, France
Aaron E. Darling , University of California-Davis, Davis
pp. 180-189

A Framework for Multiple Kernel Support Vector Regression and Its Applications to siRNA Efficacy Prediction (Abstract)

Shibin Qiu , Pathwork Diagnostics, Inc., Sunnyvale
Terran Lane , University of New Mexico, Albuquerque
pp. 190-199

Network-Based Inference of Cancer Progression from Microarray Data (Abstract)

Stanley Shackney , Drexel University, Pittsburgh
Yongjin Park , Carnegie Mellon University, Pittsburgh
Russell Schwartz , Carnegie Mellon University, Pittsburgh
pp. 200-212

Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution (Abstract)

David Sankoff , University of Ottawa, Ottawa
Zaky Adam , University of Ottawa, Ottawa
Vicky Choi , Virginia Tech, Blacksburg
Qian Zhu , University of Ottawa, Ottawa
pp. 213-220

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches (Abstract)

André Wehe , Iowa State University, Ames
Oliver Eulenstein , Iowa State University, Ames
Mukul S. Bansal , Iowa State University, Ames
pp. 221-231
REGULAR PAPERS

Designing Patterns and Profiles for Faster HMM Search (Abstract)

Yanni Sun , Washington University, St. Louis
Jeremy Buhler , Washington University, St. Louis
pp. 232-243

Semantics of Multimodal Network Models (Abstract)

Lenwood S. Heath , Virginia Tech, Blacksburg
Allan A. Sioson , Ateneo de Naga University, Naga City
pp. 271-280

Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence (Abstract)

Ana Arribas-Gil , Universidad Carlos III de Madrid, Spain
Jean-Louis Plouhinec , Institut de Transgénose, CNRS-IEM, France
Dirk Metzler , Johann Wolfgang Goethe-Universität, Germany
pp. 281-295

Multimodal Networks: Structure and Operations (Abstract)

Lenwood S. Heath , Virginia Tech, Blacksburg
Allan A. Sioson , Ateneo de Naga University, Naga City
pp. 321-332

Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics (Abstract)

Ying Xu , University of Georgia, Athens
Hongwei Wu , University of Georgia, Athens
Victor Olman , University of Georgia, Athens
Fenglou Mao , University of Georgia, Athens
pp. 344-352
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