Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

Volume 5, Issue 4

481 -- 0Dan Gusfield. EIC Editorial
482 -- 483Raffaele Giancarlo, Sridhar Hannenhalli. Guest Editors Introduction to the Special Section on Algorithms in Bioinformatics
484 -- 491Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka. Improving Strand Pairing Prediction through Exploring Folding Cooperativity
492 -- 502Loredana M. Genovese, Filippo Geraci, Marco Pellegrini. SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate andLow Coverage
503 -- 513Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson. Seeded Tree Alignment
514 -- 524Mukul S. Bansal, Oliver Eulenstein. An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
525 -- 533Xueyi Wang, Jack Snoeyink. Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment
534 -- 545Peggy Yao, Ankur Dhanik, Nathan Marz, Ryan Propper, Charles Kou, Guanfeng Liu, Henry van den Bedem, Jean-Claude Latombe, Inbal Halperin-Landsberg, Russ B. Altman. Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops
546 -- 556Eagu Kim, John D. Kececioglu. Learning Scoring Schemes for Sequence Alignment from Partial Examples
557 -- 567Alexander Schliep, Roland Krause. Efficient Algorithms for the Computational Design of Optimal Tiling Arrays
568 -- 582Zeyun Yu, Chandrajit L. Bajaj. Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes
583 -- 593Yann Christinat, Bernd Wachmann, Lei Zhang. Gene Expression Data Analysis Using a Novel Approach to Biclustering Combining Discrete and Continuous Data
594 -- 617Vincent Lacroix, Ludovic Cottret, Patricia Thébault, Marie-France Sagot. An Introduction to Metabolic Networks and Their Structural Analysis
618 -- 629Ravi Vijaya Satya, Amar Mukherjee. The Undirected Incomplete Perfect Phylogeny Problem
630 -- 638Cedric Gondro, Brian P. Kinghorn. Optimization of cDNA Microarray Experimental Designs Using an Evolutionary Algorithm

Volume 5, Issue 3

321 -- 322Ion I. Mandoiu, Yi Pan, Alexander Zelikovsky. Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications
323 -- 331Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz. Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
332 -- 347Matthias Bernt, Daniel Merkle, Martin Middendorf. Solving the Preserving Reversal Median Problem
348 -- 356Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier. Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution
357 -- 367Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio. Reconstruction of 3D Structures From Protein Contact Maps
368 -- 384George Lee, Carlos Rodriguez, Anant Madabhushi. Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies
385 -- 400Hyuk Cho, Inderjit S. Dhillon. Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
401 -- 415Peng Wei, Wei Pan. Incorporating Gene Functions into Regression Analysis of DNA-Protein Binding Data and Gene Expression Data to Construct Transcriptional Networks
416 -- 422Man-Wai Mak, Jian Guo, Sun-Yuan Kung. PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM
423 -- 431Laura Elo, Sanna Filen, Riitta Lahesmaa, Tero Aittokallio. Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies
432 -- 447Douglas Stott Parker Jr., Ruey-Lung Hsiao, Yi Xing, Alissa M. Resch, Christopher J. Lee. Solving the Problem of Trans-Genomic Query with Alignment Tables
448 -- 460Zaher Dawy, Michel Sarkis, Joachim Hagenauer, Jakob C. Mueller. Fine-Scale Genetic Mapping Using Independent Component Analysis
461 -- 471Michael D. Hendy, Sagi Snir. Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets
472 -- 479Philippe Gambette, Daniel H. Huson. Improved Layout of Phylogenetic Networks

Volume 5, Issue 2

161 -- 171Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru. Consensus Genetic Maps as Median Orders from Inconsistent Sources
172 -- 182Anupam Gupta, Ziv Bar-Joseph. Extracting Dynamics from Static Cancer Expression Data
183 -- 197John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg. Graphical Models of Residue Coupling in Protein Families
198 -- 207Jesus P. Mena-Chalco, Helaine Carrer, Yossi Zana, Roberto M. Cesar. Identification of Protein Coding Regions Using the Modified Gabor-Wavelet Transform
208 -- 222Hidde de Jong, Michel Page. Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks
223 -- 234Avital Sadot, Jasmin Fisher, Dan Barak, Yishai Admanit, Michael J. Stern, E. Jane Albert Hubbard, David Harel. Toward Verified Biological Models
235 -- 244Andreas Spillner, Binh T. Nguyen, Vincent Moulton. Computing Phylogenetic Diversity for Split Systems
245 -- 251Giuseppe Lancia, R. Ravi, Romeo Rizzi. Haplotyping for Disease Association: A Combinatorial Approach
252 -- 261Alexander Gusev, Ion I. Mandoiu, Bogdan Pasaniuc. Highly Scalable Genotype Phasing by Entropy Minimization
262 -- 274Wentao Zhao, Erchin Serpedin, Edward R. Dougherty. Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria
275 -- 280Magnus Bordewich, Charles Semple. Nature Reserve Selection Problem: A Tight Approximation Algorithm
281 -- 290Yong-Hsian Hsieh, Chih-Chiang Yu, Biing-Feng Wang. Optimal Algorithms for the Interval Location Problem with Range Constraints on Length and Average
291 -- 300Susanna L. Lamers, Marco Salemi, Michael S. McGrath, Gary B. Fogel. Prediction of R5, X4, and R5X4 HIV-1 Coreceptor Usage with Evolved Neural Networks
301 -- 312Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie. Shorelines of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems
313 -- 318Dumitru Brinza, Alexander Zelikovsky. 2SNP: Scalable Phasing Method for Trios and Unrelated Individuals

Volume 5, Issue 1

1 -- 14Clare Bates Congdon, Joseph C. Aman, Gerardo M. Nava, H. Rex Gaskins, Carolyn J. Mattingly. An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach
15 -- 24Riccardo Boscolo, James C. Liao, Vwani P. Roychowdhury. An Information Theoretic Exploratory Method for Learning Patterns of Conditional Gene Coexpression from Microarray Data
25 -- 41Kay C. Wiese, Alain Deschênes, Andrew Hendriks. RnaPredict-An Evolutionary Algorithm for RNA Secondary Structure Prediction
42 -- 55Diego Rother, Guillermo Sapiro, Vijay Pande. Statistical Characterization of Protein Ensembles
56 -- 66Yun Cui, Lusheng Wang, Daming Zhu, Xiaowen Liu. A (1.5 + epsilon)-Approximation Algorithm for Unsigned Translocation Distance
67 -- 79Tuan Zea Tan, Geok See Ng, Chai Quek. A Novel Biologically and Psychologically Inspired Fuzzy Decision Support System: Hierarchical Complementary Learning
80 -- 90Federica Ciocchetta, Corrado Priami, Paola Quaglia. An Automatic Translation of SBML into Beta-Binders
91 -- 100Sebastian Böcker, Veli Mäkinen. Combinatorial Approaches for Mass Spectra Recalibration
101 -- 109Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe er. Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele
110 -- 119Francis Y. L. Chin, Henry C. M. Leung. DNA Motif Representation with Nucleotide Dependency
120 -- 135Zong-Xian Yin, Jung-Hsien Chiang. Novel Algorithm for Coexpression Detection in Time-Varying Microarray Data Sets
136 -- 145Adrien Goëffon, Jean-Michel Richer, Jin-Kao Hao. Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem