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TABLE OF CONTENTS
Issue No. 03 - July-September (vol. 6)
ISSN: 1545-5963
EDITORIAL
PAPERS

A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences (Abstract)

Chengpeng Bi , Children's Mercy Hospitals and Clinics and University of Missouri, Kansas City
pp. 370-386

A Unified Approach for Reconstructing Ancient Gene Clusters (Abstract)

Roland Wittler , Bielefeld University, Bielefeld
Jens Stoye , Bielefeld University, Bielefeld
pp. 387-400

An Approximation Algorithm for the Minimum Breakpoint Linearization Problem (Abstract)

Yun Cui , Nanyang Technological University, Singapore
Xin Chen , Nanyang Technological University, Singapore
pp. 401-409

An Extended Kalman Filtering Approach to Modeling Nonlinear Dynamic Gene Regulatory Networks via Short Gene Expression Time Series (Abstract)

Jinling Liang , Southeast University, Nanjing
Yurong Liu , Yangzhou University, Yangzhou
Veronica Vinciotti , Brunel University, Uxbridge, UK
Zidong Wang , Brunel University, Uxbridge, UK
Xiaohui Liu , Brunel University, Uxbridge, UK
pp. 410-419

Computing the Distribution of a Tree Metric (Abstract)

David Bryant , University of Auckland, Auckland
Mike Steel , University of Canterbury, Christchurch
pp. 420-426

Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction (Abstract)

Marcel J.T. Reinders , Delft University of Technology, Delft
Marc Hulsman , Delft University of Technology, Delft
Dick de Ridder , Delft University of Technology, Delft
pp. 427-437

Improved Approximation Algorithms for Reconstructing the History of Tandem Repeats (Abstract)

Zhi-Zhong Chen , Tokyo Denki University, Hatoyama
Lusheng Wang , City University of Hong Kong, Hong Kong
pp. 438-453

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics (Abstract)

Mercè Llabrés , University of the Balearic Islands, Palma de Mallorca
Francesc Rosselló , University of the Balearic Islands, Palma de Mallorca
Gabriel Valiente , Technical University of Catalonia, Barcelona
Gabriel Cardona , University of the Balearic Islands, Palma de Mallorca
pp. 454-469

Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study (Abstract)

Yiannis N. Kaznessis , University of Minnesota, Minneapolis
Prodromos Daoutidis , University of Minnesota, Minneapolis
Vassilios Sotiropoulos , University of Minnesota, Minneapolis
pp. 470-482

On Subset Seeds for Protein Alignment (Abstract)

Ewa Szczurek , Max Planck Institute for Molecular Genetics, Berlin
Eugenia Furletova , Institute of Mathematical Problems in Biology, Pushchino, Moscow
Laurent Noé , LIFL/CNRS/INRIA, France
Gregory Kucherov , LIFL/CNRS/INRIA, France
Slawomir Lasota , Warsaw University, Poland
Mikhail Roytberg , Institute of Mathematical Problems in Biology, Pushchino, Moscow
Anna Gambin , Warsaw University, Poland
pp. 483-494

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic (Abstract)

Guohua Jin , Rice University, Houston
Sagi Snir , University of Haifa, Haifa
Luay Nakhleh , Rice University, Houston
Tamir Tuller , Tel Aviv University, Tel Aviv
pp. 495-505

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints (Abstract)

Naren Ramakrishnan , Virginia Tech, Blacksburg
Chris Bailey-Kellogg , Dartmouth College, Hanover
John Thomas , Dartmouth College, Hanover
pp. 506-516

RNA Search with Decision Trees and Partial Covariance Models (Abstract)

Jennifer A. Smith , Boise State University, Boise
pp. 517-527
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