Wednesday, 17 August 2011

IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 8, No. 5, 2011


A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements
Dongxiao Zhu, Lipi Acharya, Hui Zhang

A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention
Rui Chang, Robert Shoemaker, Wei Wang

A Preprocessing Procedure for Haplotype Inference by Pure Parsimony
Ekhine Irurozki, Borja Calvo, Jose A. Lozano

An Efficient Algorithm for Approximating Geodesic Distances in Tree Space
Simone Battagliero, Giuseppe Puglia, Saverio Vicario, Francesco Rubino, Gaetano Scioscia, Pietro Leo

Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data
David J. John, Jacquelyn S. Fetrow, James L. Norris

Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling
Carito Guziolowski, Sylvain Blachon, Tatiana Baumuratova, Gautier Stoll, Ovidiu Radulescu, Anne Siegel

Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach
Sitanshu Sekhar Sahu, Ganapati Panda

Fast Flexible Modeling of RNA Structure Using Internal Coordinates
Samuel Coulbourn Flores, Michael A. Sherman, Christopher M. Bruns, Peter Eastman, Russ Biagio Altman

Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees
Biing-Feng Wang, Chien-Hsin Lin

Metasample-Based Sparse Representation for Tumor Classification
Chun-Hou Zheng, Lei Zhang, To-Yee Ng, Simon C.K. Shiu, De-Shuang Huang

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome
Qian Peng, Andrew D. Smith

Parameterized Algorithmics for Finding Connected Motifs in Biological Networks
Nadja Betzler, Rene van Bevern, Michael R. Fellows, Christian Komusiewicz, Rolf Niedermeier

Probabilistic Models for Semisupervised Discriminative Motif Discovery in DNA Sequences
Jong Kyoung Kim, Seungjin Choi

SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems
Pedro Feijao, Joao Meidanis

SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison
Marco Mernberger, Gerhard Klebe, Eyke Hullermeier

SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks
Peter Boyen, Dries Van Dyck, Frank Neven, Roeland C.H.J. van Ham, Aalt D.J. van Dijk

Some Mathematical Refinements Concerning Error Minimization in the Genetic Code
Harry Buhrman, Peter T.S. van der Gulik, Steven M. Kelk, Wouter M. Koolen, Leen Stougie

Using Kernel Alignment to Select Features of Molecular Descriptors in a QSAR Study
William W.L. Wong, Forbes J. Burkowski


A Mathematical Model for the Validation of Gene Selection Methods
Marco Muselli, Alberto Bertoni, Marco Frasca, Alessandro Beghini, Francesca Ruffino, Giorgio Valentini

A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks
Elena Dubrova, Maxim Teslenko

Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)-Motif Model
Zhi-Zhong Chen, Lusheng Wang

On the Distribution of the Number of Cycles in the Breakpoint Graph of a Random Signed Permutation
Simona Grusea

Probabilistic Mixture Regression Models for Alignment of LC-MS Data
Getachew K. Befekadu, Mahlet G. Tadesse, Tsung-Heng Tsai, Habtom W. Ressom

Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability
Paolo Magni, Angela Simeone, Sandra Healy, Antonella Isacchi, Roberta Bosotti

The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery
Ehud Aharoni, Hani Neuvirth, Saharon Rosset

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