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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 5
Volume 5, Number 1, January 2008
- Clare Bates Congdon, Joseph C. Aman, Gerardo M. Nava
, H. Rex Gaskins
An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach. 1-14 - Riccardo Boscolo, James C. Liao
An Information Theoretic Exploratory Method for Learning Patterns of Conditional Gene Coexpression from Microarray Data. 15-24 - Kay C. Wiese, Alain Deschênes, Andrew Hendriks:
RnaPredict-An Evolutionary Algorithm for RNA Secondary Structure Prediction. 25-41 - Diego Rother, Guillermo Sapiro, Vijay Pande:
Statistical Characterization of Protein Ensembles. 42-55 - Yun Cui, Lusheng Wang
A (1.5 + epsilon)-Approximation Algorithm for Unsigned Translocation Distance. 56-66 - Tuan Zea Tan, Geok See Ng, Chai Quek
A Novel Biologically and Psychologically Inspired Fuzzy Decision Support System: Hierarchical Complementary Learning. 67-79 - Federica Ciocchetta, Corrado Priami, Paola Quaglia
An Automatic Translation of SBML into Beta-Binders. 80-90 - Sebastian Böcker
Combinatorial Approaches for Mass Spectra Recalibration. 91-100 - Tamar Barzuza, Jacques S. Beckmann
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele. 101-109 - Francis Y. L. Chin, Henry C. M. Leung:
DNA Motif Representation with Nucleotide Dependency. 110-119 - Zong-Xian Yin, Jung-Hsien Chiang
Novel Algorithm for Coexpression Detection in Time-Varying Microarray Data Sets. 120-135 - Adrien Goëffon, Jean-Michel Richer, Jin-Kao Hao
Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem. 136-145
Volume 5, Number 2, April 2008
- Benjamin G. Jackson, Patrick S. Schnable
Consensus Genetic Maps as Median Orders from Inconsistent Sources. 161-171 - Anupam Gupta, Ziv Bar-Joseph
Extracting Dynamics from Static Cancer Expression Data. 172-182 - John Thomas, Naren Ramakrishnan
Graphical Models of Residue Coupling in Protein Families. 183-197 - Jesús P. Mena-Chalco, Helaine Carrer, Yossi Zana, Roberto M. Cesar
Identification of Protein Coding Regions Using the Modified Gabor-Wavelet Transform. 198-207 - Hidde de Jong
Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks. 208-222 - Avital Sadot, Jasmin Fisher
Toward Verified Biological Models. 223-234 - Andreas Spillner, Binh T. Nguyen, Vincent Moulton
Computing Phylogenetic Diversity for Split Systems. 235-244 - Giuseppe Lancia
Haplotyping for Disease Association: A Combinatorial Approach. 245-251 - Alexander Gusev, Ion I. Mandoiu
Highly Scalable Genotype Phasing by Entropy Minimization. 252-261 - Wentao Zhao, Erchin Serpedin, Edward R. Dougherty:
Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria. 262-274 - Magnus Bordewich
Nature Reserve Selection Problem: A Tight Approximation Algorithm. 275-280 - Yong-Hsian Hsieh, Chih-Chiang Yu, Biing-Feng Wang:
Optimal Algorithms for the Interval Location Problem with Range Constraints on Length and Average. 281-290 - Susanna L. Lamers, Marco Salemi, Michael S. McGrath, Gary B. Fogel:
Prediction of R5, X4, and R5X4 HIV-1 Coreceptor Usage with Evolved Neural Networks. 291-300 - Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie:
Shorelines of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems. 301-312 - Dumitru Brinza, Alexander Zelikovsky
2SNP: Scalable Phasing Method for Trios and Unrelated Individuals. 313-318
Volume 5, Number 3, July 2008
- Ion I. Mandoiu
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 321-322 - Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference. 323-331 - Matthias Bernt
Solving the Preserving Reversal Median Problem. 332-347 - Marília D. V. Braga, Marie-France Sagot, Céline Scornavacca, Eric Tannier:
Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution. 348-356 - Marco Vassura, Luciano Margara
Reconstruction of 3D Structures From Protein Contact Maps. 357-367 - George Lee, Carlos Rodriguez, Anant Madabhushi
Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies. 368-384 - Hyuk Cho, Inderjit S. Dhillon:
Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering. 385-400 - Peng Wei
Incorporating Gene Functions into Regression Analysis of DNA-Protein Binding Data and Gene Expression Data to Construct Transcriptional Networks. 401-415 - Man-Wai Mak
PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM. 416-422 - Laura Elo
Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies. 423-431 - Douglas Stott Parker Jr., Ruey-Lung Hsiao, Yi Xing, Alissa M. Resch, Christopher J. Lee:
Solving the Problem of Trans-Genomic Query with Alignment Tables. 432-447 - Zaher Dawy, Michel Sarkis, Joachim Hagenauer, Jakob C. Mueller:
Fine-Scale Genetic Mapping Using Independent Component Analysis. 448-460 - Michael D. Hendy, Sagi Snir:
Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets. 461-471 - Philippe Gambette
Improved Layout of Phylogenetic Networks. 472-479
Volume 5, Number 4, October 2008
- Dan Gusfield:
EIC Editorial. 481 - Raffaele Giancarlo, Sridhar Hannenhalli:
Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics. 482-483 - Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
Improving Strand Pairing Prediction through Exploring Folding Cooperativity. 484-491 - Loredana M. Genovese, Filippo Geraci
SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage. 492-502 - Antoni Lozano
Seeded Tree Alignment. 503-513 - Mukul S. Bansal
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. 514-524 - Xueyi Wang, Jack Snoeyink
Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment. 525-533 - Peggy Yao, Ankur Dhanik, Nathan Marz, Ryan Propper, Charles Kou, Guanfeng Liu, Henry van den Bedem
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. 534-545 - Eagu Kim, John D. Kececioglu:
Learning Scoring Schemes for Sequence Alignment from Partial Examples. 546-556 - Alexander Schliep
Efficient Algorithms for the Computational Design of Optimal Tiling Arrays. 557-567 - Zeyun Yu, Chandrajit L. Bajaj:
Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes. 568-582 - Yann Christinat, Bernd Wachmann, Lei Zhang:
Gene Expression Data Analysis Using a Novel Approach to Biclustering Combining Discrete and Continuous Data. 583-593 - Vincent Lacroix, Ludovic Cottret
An Introduction to Metabolic Networks and Their Structural Analysis. 594-617 - Ravi Vijaya Satya, Amar Mukherjee:
The Undirected Incomplete Perfect Phylogeny Problem. 618-629 - Cedric Gondro
Optimization of cDNA Microarray Experimental Designs Using an Evolutionary Algorithm. 630-638
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