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

REGULAR PAPERS

A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements
Dongxiao Zhu, Lipi Acharya, Hui Zhang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.102

A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention
Rui Chang, Robert Shoemaker, Wei Wang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.18

A Preprocessing Procedure for Haplotype Inference by Pure Parsimony
Ekhine Irurozki, Borja Calvo, Jose A. Lozano
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.125

An Efficient Algorithm for Approximating Geodesic Distances in Tree Space
Simone Battagliero, Giuseppe Puglia, Saverio Vicario, Francesco Rubino, Gaetano Scioscia, Pietro Leo
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.121

Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data
David J. John, Jacquelyn S. Fetrow, James L. Norris
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.95

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
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.71

Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach
Sitanshu Sekhar Sahu, Ganapati Panda
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.109

Fast Flexible Modeling of RNA Structure Using Internal Coordinates
Samuel Coulbourn Flores, Michael A. Sherman, Christopher M. Bruns, Peter Eastman, Russ Biagio Altman
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.104

Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees
Biing-Feng Wang, Chien-Hsin Lin
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.127

Metasample-Based Sparse Representation for Tumor Classification
Chun-Hou Zheng, Lei Zhang, To-Yee Ng, Simon C.K. Shiu, De-Shuang Huang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.20

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome
Qian Peng, Andrew D. Smith
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.107

Parameterized Algorithmics for Finding Connected Motifs in Biological Networks
Nadja Betzler, Rene van Bevern, Michael R. Fellows, Christian Komusiewicz, Rolf Niedermeier
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.19

Probabilistic Models for Semisupervised Discriminative Motif Discovery in DNA Sequences
Jong Kyoung Kim, Seungjin Choi
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.84

SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems
Pedro Feijao, Joao Meidanis
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.34

SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison
Marco Mernberger, Gerhard Klebe, Eyke Hullermeier
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.35

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
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.17

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
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.40

Using Kernel Alignment to Select Features of Molecular Descriptors in a QSAR Study
William W.L. Wong, Forbes J. Burkowski
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.31

SHORT PAPERS

A Mathematical Model for the Validation of Gene Selection Methods
Marco Muselli, Alberto Bertoni, Marco Frasca, Alessandro Beghini, Francesca Ruffino, Giorgio Valentini
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.83

A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks
Elena Dubrova, Maxim Teslenko
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.20

Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)-Motif Model
Zhi-Zhong Chen, Lusheng Wang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.21

On the Distribution of the Number of Cycles in the Breakpoint Graph of a Random Signed Permutation
Simona Grusea
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.123

Probabilistic Mixture Regression Models for Alignment of LC-MS Data
Getachew K. Befekadu, Mahlet G. Tadesse, Tsung-Heng Tsai, Habtom W. Ressom
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.88

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
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.82

The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery
Ehud Aharoni, Hani Neuvirth, Saharon Rosset
http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.105