IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 6

Volume 6, Number 1, January 2009

• Dan Gusfield:
  Final, Five-Year End, Editorial. 1-2
  
• Marie-France Sagot:
  New EIC Editorial. 3
  
• Daniel H. Huson, Vincent Moulton, Mike A. Steel:
  Special Section: Phylogenetics. 4-6
  
• Kevin Liu, Serita M. Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy Warnow:
  Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy. 7-21
  
• Bui Quang Minh, Fabio Pardi, Steffen Klaere, Arndt von Haeseler:
  Budgeted Phylogenetic Diversity on Circular Split Systems. 22-29
  
• Simone Linz, Charles Semple:
  Hybridization in Nonbinary Trees. 30-45
  
• Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
  Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric. 46-61
  
• Stephen J. Willson:
  Robustness of Topological Supertree Methods for Reconciling Dense Incompatible Data. 62-75
  
• Elizabeth S. Allman, John A. Rhodes:
  The Identifiability of Covarion Models in Phylogenetics. 76-88
  
• Frederick A. Matsen III:
  Fourier Transform Inequalities for Phylogenetic Trees. 89-95
  
• Dan Gusfield:
  Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics. 96
  
• Stefan Grünewald, Vincent Moulton:
  Maximum Parsimony for Tree Mixtures. 97-102
  
• Daniel H. Huson:
  Drawing Rooted Phylogenetic Networks. 103-109
  
• Magnus Bordewich, Olivier Gascuel, Katharina T. Huber, Vincent Moulton:
  Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference. 110-117
  
• Taoyang Wu, Vincent Moulton, Mike A. Steel:
  Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony. 118-125
  
• Elchanan Mossel, Sébastien Roch, Mike A. Steel:
  Shrinkage Effect in Ancestral Maximum Likelihood. 126-133
  
• Jianmin Ma, Minh Ngoc Nguyen, Jagath C. Rajapakse:
  Gene Classification Using Codon Usage and Support Vector Machines. 134-143
  
• Ranjan Maitra:
  Initializing Partition-Optimization Algorithms. 144-157
  
• Sridharakumar Narasimhan, Raghunathan Rengaswamy, Rajanikanth Vadigepalli:
  Structural Properties of Gene Regulatory Networks: Definitions and Connections. 158-170
  

Volume 6, Number 2, April 2009

• Marie-France Sagot:
  EIC Editorial. 177
  
• Ion I. Mandoiu, Yi Pan, Raj Sunderraman, Alexander Zelikovsky:
  Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 178-179
  
• Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha:
  A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. 180-189
  
• Shibin Qiu, Terran Lane:
  A Framework for Multiple Kernel Support Vector Regression and Its Applications to siRNA Efficacy Prediction. 190-199
  
• Yongjin Park, Stanley Shackney, Russell Schwartz:
  Network-Based Inference of Cancer Progression from Microarray Data. 200-212
  
• Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff:
  Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution. 213-220
  
• Mukul S. Bansal, Oliver Eulenstein, André Wehe:
  The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches. 221-231
  
• Yanni Sun, Jeremy Buhler:
  Designing Patterns and Profiles for Faster HMM Search. 232-243
  
• Jahangheer S. Shaik, Mohammed Yeasin:
  Fuzzy-Adaptive-Subspace-Iteration-Based Two-Way Clustering of Microarray Data. 244-259
  
• Matthieu Vignes, Florence Forbes:
  Gene Clustering via Integrated Markov Models Combining Individual and Pairwise Features. 260-270
  
• Lenwood S. Heath, Allan A. Sioson:
  Semantics of Multimodal Network Models. 271-280
  
• Ana Arribas-Gil, Dirk Metzler, Jean-Louis Plouhinec:
  Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence. 281-295
  
• Gunther H. Weber, Oliver Rübel, Min-Yu Huang, Angela H. DePace, Charless C. Fowlkes, Soile V. E. Keränen, Cris L. Luengo Hendriks, Hans Hagen, David W. Knowles, Jitendra Malik, Mark D. Biggin, Bernd Hamann:
  Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views. 296-309
  
• Edward R. Dougherty, Marcel Brun, Jeffrey M. Trent, Michael L. Bittner:
  Conditioning-Based Modeling of Contextual Genomic Regulation. 310-320
  
• Lenwood S. Heath, Allan A. Sioson:
  Multimodal Networks: Structure and Operations. 321-332
  
• Naoto Yukinawa, Shigeyuki Oba, Kikuya Kato, Shin Ishii:
  Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles. 333-343
  
• Victor Olman, Fenglou Mao, Hongwei Wu, Ying Xu:
  Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics. 344-352
  
• Topon Kumar Paul, Hitoshi Iba:
  Prediction of Cancer Class with Majority Voting Genetic Programming Classifier Using Gene Expression Data. 353-367
  

Volume 6, Number 3, July 2009

• Marie-France Sagot:
  EIC Editorial: Introducing New Associate Editors. 369
  
• Chengpeng Bi:
  A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences. 370-386
  
• Jens Stoye, Roland Wittler:
  A Unified Approach for Reconstructing Ancient Gene Clusters. 387-400
  
• Xin Chen, Yun Cui:
  An Approximation Algorithm for the Minimum Breakpoint Linearization Problem. 401-409
  
• Zidong Wang, Xiaohui Liu, Yurong Liu, Jinling Liang, Veronica Vinciotti:
  An Extended Kalman Filtering Approach to Modeling Nonlinear Dynamic Gene Regulatory Networks via Short Gene Expression Time Series. 410-419
  
• David Bryant, Mike A. Steel:
  Computing the Distribution of a Tree Metric. 420-426
  
• Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder:
  Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction. 427-437
  
• Zhi-Zhong Chen, Lusheng Wang:
  Improved Approximation Algorithms for Reconstructing the History of Tandem Repeats. 438-453
  
• Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
  Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics. 454-469
  
• Vassilios Sotiropoulos, Marie-Nathalie Contou-Carrere, Prodromos Daoutidis, Yiannis N. Kaznessis:
  Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study. 470-482
  
• Mikhail A. Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, Ewa Szczurek, Gregory Kucherov:
  On Subset Seeds for Protein Alignment. 483-494
  
• Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
  Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. 495-505
  
• John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg:
  Protein Design by Sampling an Undirected Graphical Model of Residue Constraints. 506-516
  
• Jennifer A. Smith:
  RNA Search with Decision Trees and Partial Covariance Models. 517-527
  

Volume 6, Number 4, October 2009

• Jie Chen, Yu-Ping Wang:
  A Statistical Change Point Model Approach for the Detection of DNA Copy Number Variations in Array CGH Data. 529-541
  
• Amol Prakash, Martin Tompa:
  Assessing the Discordance of Multiple Sequence Alignments. 542-551
  
• Gabriel Cardona, Francesc Rosselló, Gabriel Valiente:
  Comparison of Tree-Child Phylogenetic Networks. 552-569
  
• Changjin Hong, Ahmed H. Tewfik:
  Heuristic Reusable Dynamic Programming: Efficient Updates of Local Sequence Alignment. 570-582
  
• Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, Luonan Chen:
  Evaluating Protein Similarity from Coarse Structures. 583-593
  
• Miquel Salicru, Sergi Vives, Tian Zheng:
  Inferential Clustering Approach for Microarray Experiments with Replicated Measurements. 594-604
  
• Satoshi Niijima, Yasushi Okuno:
  Laplacian Linear Discriminant Analysis Approach to Unsupervised Feature Selection. 605-614
  
• Carl Edward Rasmussen, Bernard J. de la Cruz, Zoubin Ghahramani, David L. Wild:
  Modeling and Visualizing Uncertainty in Gene Expression Clusters Using Dirichlet Process Mixtures. 615-628
  
• Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
  On Nakhleh's Metric for Reduced Phylogenetic Networks. 629-638
  
• Pradeep Chowriappa, Sumeet Dua, Jinko Kanno, Hilary W. Thompson:
  Protein Structure Classification Based on Conserved Hydrophobic Residues. 639-651
  
• Hiroaki Uehara, Masakazu Jimbo:
  A Positive Detecting Code and Its Decoding Algorithm for DNA Library Screening. 652-666
  
• Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout:
  Constructing Level-2 Phylogenetic Networks from Triplets. 667-681
  
• Saad Mneimneh:
  On the Approximation of Optimal Structures for RNA-RNA Interaction. 682-688
  
• Luis A. Diago, Ernesto Moreno:
  Evaluation of Geometric Complementarity between Molecular Surfaces Using Compactly Supported Radial Basis Functions. 689-694
  
• Ana M. González, Francisco Azuaje, Jose L. Ramirez, Jose F. da Silveira, José R. Dorronsoro:
  Machine Learning Techniques for the Automated Classification of Adhesin-Like Proteins in the Human Protozoan Parasite Trypanosoma cruzi. 695-702
  

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