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ORCIDIEEE/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 J. 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 IV:
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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