Volume 5,
Number 1,
January 2008
- Clare 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.
1-14
- Riccardo Boscolo, James C. Liao, Vwani P. Roychowdhury:
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, Daming Zhu, Xiaowen Liu:
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, Veli Mäkinen:
Combinatorial Approaches for Mass Spectra Recalibration.
91-100
- Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er:
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, Srinivas Aluru:
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, Chris Bailey-Kellogg:
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, Michel Page:
Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks.
208-222
- Avital Sadot, Jasmin Fisher, Dan Barak, Yishai Admanit, Michael J. Stern, E. Jane Albert Hubbard, David Harel:
Toward Verified Biological Models.
223-234
- Andreas Spillner, Binh T. Nguyen, Vincent Moulton:
Computing Phylogenetic Diversity for Split Systems.
235-244
- Giuseppe Lancia, R. Ravi, Romeo Rizzi:
Haplotyping for Disease Association: A Combinatorial Approach.
245-251
- Alexander Gusev, Ion I. Mandoiu, Bogdan Pasaniuc:
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, Charles Semple:
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, Yi Pan, Alexander Zelikovsky:
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, Daniel Merkle, Martin Middendorf:
Solving the Preserving Reversal Median Problem.
332-347
- Marília 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.
348-356
- Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio:
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, Wei Pan:
Incorporating Gene Functions into Regression Analysis of DNA-Protein Binding Data and Gene Expression Data to Construct Transcriptional Networks.
401-415
- Man-Wai Mak, Jian Guo, Sun-Yuan Kung:
PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM.
416-422
- Laura Elo, Sanna Filen, Riitta Lahesmaa, Tero Aittokallio:
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, Daniel H. Huson:
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, Marco Pellegrini:
SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate andLow Coverage.
492-502
- Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson:
Seeded Tree Alignment.
503-513
- Mukul S. Bansal, Oliver Eulenstein:
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, Jean-Claude Latombe, Inbal Halperin-Landsberg, Russ B. Altman:
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, Roland Krause:
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, Patricia Thébault, Marie-France Sagot:
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, Brian P. Kinghorn:
Optimization of cDNA Microarray Experimental Designs Using an Evolutionary Algorithm.
630-638
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