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, 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
  
• Jesus 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