Volume 8, Number 1, January 2011

• 
  Marie-France Sagot: EIC Editorial. 1
• 
  Megan Owen, J. Scott Provan: A Fast Algorithm for Computing Geodesic Distances in Tree Space. 2-13
• 
  Mohak Shah, Jacques Corbeil: A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments. 14-26
• 
  Sean Mauch, Mark A. Stalzer: Efficient Formulations for Exact Stochastic Simulation of Chemical Systems. 27-35
• 
  Dario Gasbarra, Sangita Kulathinal, Matti Pirinen, Mikko J. Sillanpää: Estimating Haplotype Frequencies by Combining Data from Large DNA Pools with Database Information. 36-44
• 
  Chandrajit L. Bajaj, Rezaul Alam Chowdhury, Vinay Siddahanavalli: F²Dock: Fast Fourier Protein-Protein Docking. 45-58
• 
  Joachim Giard, Patrice Rondao-Alface, Jean-Luc Gala, Benoit M. Macq: Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description. 59-68
• 
  Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: Finding Significant Matches of Position Weight Matrices in Linear Time. 69-79
• 
  Razvan Andonie, Levente Fabry-Asztalos, Christopher B. Abdul-Wahid, Sarah Abdul-Wahid, Grant I. Barker, Lukas Magill: Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors Using a Small Molecular Data Set. 80-93
• 
  Sushmita Mitra, Ranajit Das, Yoichi Hayashi: Genetic Networks and Soft Computing. 94-107
• 
  Wenxue Wang, Bijoy K. Ghosh, Himadri B. Pakrasi: Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data. 108-121
• 
  Linkai Luo, Dengfeng Huang, Ling-Jun Ye, Qifeng Zhou, Guifang Shao, Hong Peng: Improving the Computational Efficiency of Recursive Cluster Elimination for Gene Selection. 122-129
• 
  Mehmet Tan, Mohammed Al-Shalalfa, Reda Alhajj, Faruk Polat: Influence of Prior Knowledge in Constraint-Based Learning of Gene Regulatory Networks. 130-142
• 
  Liuling Gong, Nidhal Bouaynaya, Dan Schonfeld: Information-Theoretic Model of Evolution over Protein Communication Channel. 143-151
• 
  Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahara: Learning Genetic Regulatory Network Connectivity from Time Series Data. 152-165
• 
  Delphine Ropers, Valentina Baldazzi, Hidde de Jong: Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli. 166-181
• 
  Yufeng Wu: New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations. 182-193
• 
  Ankit Agrawal, Xiaoqiu Huang: Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices. 194-205
• 
  Rogier J. P. van Berlo, Dick de Ridder, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Bas Teusink, Marcel J. T. Reinders: Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints. 206-216
• 
  Leo Lahti, Laura Elo, Tero Aittokallio, Samuel Kaski: Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. 217-225
• 
  Dukka B. Kc, Dennis R. Livesay: Topology Improves Phylogenetic Motif Functional Site Predictions. 226-233
• 
  Tamjidul Hoque, Madhu Chetty, Andrew Lewis, Abdul Sattar: Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model. 234-245
• 
  Joaquim F. Pinto da Costa, Hugo Alonso, Luis Roque: A Weighted Principal Component Analysis and Its Application to Gene Expression Data. 246-252
• 
  Ping Li, James Lam: Disturbance Analysis of Nonlinear Differential Equation Models of Genetic SUM Regulatory Networks. 253-259
• 
  Cheng-Wei Luo, Ming-Chiang Chen, Yi-Ching Chen, Roger W. L. Yang, Hsiao-Fei Liu, Kun-Mao Chao: Linear-Time Algorithms for the Multiple Gene Duplication Problems. 260-265
• 
  Kezhi Mao, Wenyin Tang: Recursive Mahalanobis Separability Measure for Gene Subset Selection. 266-272
• 
  Vikram Krishnamurthy, Kai Yiu Luk: Semi-Markov Models for Brownian Dynamics Permeation in Biological Ion Channels. 273-281

Volume 8, Number 2, March 2011

• 
  Marie-France Sagot: EIC Editorial. 289-291
• 
  Fang-Xiang Wu, Jun Huan: Guest Editorial: Special Focus on Bioinformatics and Systems Biology. 292-293
• 
  Yanpeng Li, Xiaohua Hu, Hongfei Lin, Zhiahi Yang: A Framework for Semisupervised Feature Generation and Its Applications in Biomedical Literature Mining. 294-307
• 
  Jong Cheol Jeong, Xiaotong Lin, Xue-wen Chen: On Position-Specific Scoring Matrix for Protein Function Prediction. 308-315
• 
  Sangyoon Oh, Min Su Lee, Byoung-Tak Zhang: Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification. 316-325
• 
  Zina M. Ibrahim, Alioune Ngom, Ahmed Y. Tawfik: Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks. 326-334
• 
  Amit Sabnis, Robert W. Harrison: A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems. 335-341
• 
  Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer: A Genetic Optimization Approach for Isolating Translational Efficiency Bias. 342-352
• 
  Ramesh Ram, Madhu Chetty: A Markov-Blanket-Based Model for Gene Regulatory Network Inference. 353-367
• 
  Zengyou He, Can Yang, Weichuan Yu: A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data. 368-380
• 
  Yonghui Wu, Timothy J. Close, Stefano Lonardi: Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. 381-394
• 
  Zafer Aydin, Yucel Altunbasak, Hakan Erdogan: Bayesian Models and Algorithms for Protein β-Sheet Prediction. 395-409
• 
  Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente: Comparison of Galled Trees. 410-427
• 
  Kwong-Sak Leung, Kin-Hong Lee, Jin Feng Wang, Eddie Y. T. Ng, Henry L. Y. Chan, Stephen Kwok-Wing Tsui, Tony Shu Kam Mok, Pete Chi-Hang Tse, Joseph J. Y. Sung: Data Mining on DNA Sequences of Hepatitis B Virus. 428-440
• 
  Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph: Discriminative Motif Finding for Predicting Protein Subcellular Localization. 441-451
• 
  Saras Saraswathi, Suresh Sundaram, Narasimhan Sundararajan, Michael Zimmermann, Marit Nilsen-Hamilton: ICGA-PSO-ELM Approach for Accurate Multiclass Cancer Classification Resulting in Reduced Gene Sets in Which Genes Encoding Secreted Proteins Are Highly Represented. 452-463
• 
  Itziar Irigoien, Sergi Vives, Concepcion Arenas: Microarray Time Course Experiments: Finding Profiles. 464-475
• 
  Qiwen Dong, Shuigeng Zhou: Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning. 476-486
• 
  Sébastien Loriot, Sushant Sachdeva, Karine Bastard, Chantal Prévost, Frédéric Cazals: On the Characterization and Selection of Diverse Conformational Ensembles with Applications to Flexible Docking. 487-498
• 
  Robert Giegerich, Christian Höner zu Siederdissen: Semantics and Ambiguity of Stochastic RNA Family Models. 499-516
• 
  Ali Tofigh, Michael T. Hallett, Jens Lagergren: Simultaneous Identification of Duplications and Lateral Gene Transfers. 517-535
• 
  Michael D. Lieberman, Sima Taheri, Huimin Guo, Fatemeh Mirrashed, Inbal Yahav, Aleks Aris, Ben Shneiderman: Visual Exploration across Biomedical Databases. 536-550
• 
  Glenn Hickey, Mathieu Blanchette, Paz Carmi, Anil Maheshwari, Norbert Zeh: An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss. 551-556
• 
  Juan Cortés, Sophie Barbe, Monique Erard, Thierry Siméon: Encoding Molecular Motions in Voxel Maps. 557-563
• 
  J. Rocha: Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis. 564-569
• 
  André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano: Inferring Contagion in Regulatory Networks. 570-576

Volume 8, Number 3, May 2011

• 
  Alfredo Benso, Stefano Di Carlo, Gianfranco Politano: A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory. 577-591
• 
  Erdem Yörük, Michael F. Ochs, Donald Geman, Laurent Younes: A Comprehensive Statistical Model for Cell Signaling. 592-606
• 
  Jianxin Wang, Min Li, Jianer Chen, Yi Pan: A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks. 607-620
• 
  Jianxing Feng, Rui Jiang, Tao Jiang: A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data. 621-634
• 
  Katharina T. Huber, Leo van Iersel, Steven Kelk, Radoslaw Suchecki: A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. 635-649
• 
  James T. Murphy, Ray Walshe, Marc Devocelle: A Theoretical Analysis of the Prodrug Delivery System for Treating Antibiotic-Resistant Bacteria. 650-658
• 
  Santanu Ghorai, Anirban Mukherjee, Sanghamitra Sengupta, Pranab K. Dutta: Cancer Classification from Gene Expression Data by NPPC Ensemble. 659-671
• 
  Gregor Goessler: Component-Based Modeling and Reachability Analysis of Genetic Networks. 672-682
• 
  Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano: Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. 683-697
• 
  Alexander K. Hudek, Daniel Gregory Brown: FEAST: Sensitive Local Alignment with Multiple Rates of Evolution. 698-709
• 
  Elizabeth S. Allman, Sonia Petrovic, John A. Rhodes, Seth Sullivant: Identifiability of Two-Tree Mixtures for Group-Based Models. 710-722
• 
  Tianwei Yu, Hesen Peng, Wei Sun: Incorporating Nonlinear Relationships in Microarray Missing Value Imputation. 723-731
• 
  Bin Song, I. Esra Büyüktahtakin, Sanjay Ranka, Tamer Kahveci: Manipulating the Steady State of Metabolic Pathways. 732-747
• 
  Qian Xu, Sinno Jialin Pan, Hannah Hong Xue, Qiang Yang: Multitask Learning for Protein Subcellular Location Prediction. 748-759
• 
  Rubén Armañanzas, Yvan Saeys, Iñaki Inza, Miguel García-Torres, Concha Bielza, Yves Van de Peer, Pedro Larrañaga: Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms. 760-774
• 
  Antonina Mitrofanova, Vladimir Pavlovic, Bud Mishra: Prediction of Protein Functions with Gene Ontology and Interspecies Protein Homology Data. 775-784
• 
  Stephen J. Willson: Regular Networks Can be Uniquely Constructed from Their Trees. 785-796
• 
  Tilo Strutz: 3D Shape Reconstruction of Loop Objects in X-Ray Protein Crystallography. 797-807
• 
  Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna: TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. 808-818
• 
  Jayendra Venkateswaran, Bin Song, Tamer Kahveci, Chris Jermaine: TRIAL: A Tool for Finding Distant Structural Similarities. 819-831
• 
  Giorgio Valentini: True Path Rule Hierarchical Ensembles for Genome-Wide Gene Function Prediction. 832-847
• 
  Mukul S. Bansal, Ron Shamir: A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. 848-850
• 
  Aditya Kumar Sehgal, Sanmay Das, Keith Noto, Milton H. Saier Jr., Charles Elkan: Identifying Relevant Data for a Biological Database: Handcrafted Rules versus Machine Learning. 851-857
• 
  Minh Ngoc Nguyen, Jacek M. Zurada, Jagath C. Rajapakse: Toward Better Understanding of Protein Secondary Structure: Extracting Prediction Rules. 858-864

Volume 8, Number 4, July 2011

• 
  Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky: Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 865-866
• 
  Yosi Shibberu, Allen Holder: A Spectral Approach to Protein Structure Alignment. 867-875
• 
  Nicola Ferraro, Luigi Palopoli, Simona Panni, Simona E. Rombo: Asymmetric Comparison and Querying of Biological Networks. 876-889
• 
  John Wiedenhoeft, Roland Krause, Oliver Eulenstein: The Plexus Model for the Inference of Ancestral Multidomain Proteins. 890-901
• 
  Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret: Uncovering Hidden Phylogenetic Consensus in Large Data Sets. 902-911
• 
  Rob Gysel, Dan Gusfield: Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem. 912-917
• 
  Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz: A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure. 918-928
• 
  Sanghamitra Bandyopadhyay, Malay Bhattacharyya: A Biologically Inspired Measure for Coexpression Analysis. 929-942
• 
  Nuno Tenazinha, Susana Vinga: A Survey on Methods for Modeling and Analyzing Integrated Biological Networks. 943-958
• 
  Chao-Wen Huang, Wun-Shiun Lee, Sun-Yuan Hsieh: An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences. 959-975
• 
  Sebastian Böcker, Birte Kehr, Florian Rasche: Determination of Glycan Structure from Tandem Mass Spectra. 976-986
• 
  Samuel S. Y. Wong, Weimin Luo, Keith C. C. Chan: EvoMD: An Algorithm for Evolutionary Molecular Design. 987-1003
• 
  Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi: Image-Based Surface Matching Algorithm Oriented to Structural Biology. 1004-1016
• 
  Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio: Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations? 1017-1028
• 
  Katharina T. Huber, Andreas Spillner, Radoslaw Suchecki, Vincent Moulton: Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds. 1029-1040
• 
  Xin Zhao, Leo Wang-Kit Cheung: Multiclass Kernel-Imbedded Gaussian Processes for Microarray Data Analysis. 1041-1053
• 
  Peng Zhang, Houqiang Li, Honghui Wang, Stephen T. C. Wong, Xiaobo Zhou: Peak Tree: A New Tool for Multiscale Hierarchical Representation and Peak Detection of Mass Spectrometry Data. 1054-1066
• 
  Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar: Predicting MHC-II Binding Affinity Using Multiple Instance Regression. 1067-1079
• 
  Feng Yang, Kezhi Mao: Robust Feature Selection for Microarray Data Based on Multicriterion Fusion. 1080-1092
• 
  Peter Tiño, Hongya Zhao, Hong Yan: Searching for Coexpressed Genes in Three-Color cDNA Microarray Data Using a Probabilistic Model-Based Hough Transform. 1093-1107
• 
  Li-San Wang, James Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy Warnow: The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. 1108-1119
• 
  Bashir Sadjad, Zsolt Zsoldos: Toward a Robust Search Method for the Protein-Drug Docking Problem. 1120-1133
• 
  Yang Chen, Jinglu Hu: Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic. 1134-1140
• 
  Sylvain Guillemot, Jesper Jansson, Wing-Kin Sung: Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets. 1141-1147
• 
  Tim Peters, David W. Bulger, To-ha Loi, Jean Yee Hwa Yang, David Ma: Two-Step Cross-Entropy Feature Selection for Microarrays - Power Through Complementarity. 1148-1151

Volume 8, Number 5, September 2011

• 
  Dongxiao Zhu, Lipi R. Acharya, Hui Zhang: A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements. 1153-1169
• 
  Rui Chang, Robert Shoemaker, Wei Wang: A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention. 1170-1182
• 
  Ekhine Irurozki, Borja Calvo, José Antonio Lozano: A Preprocessing Procedure for Haplotype Inference by Pure Parsimony. 1183-1195
• 
  Simone Battagliero, Giuseppe Puglia, Saverio Vicario, Francesco Rubino, Gaetano Scioscia, Pietro Leo: An Efficient Algorithm for Approximating Geodesic Distances in Tree Space. 1196-1207
• 
  David J. John, Jacquelyn S. Fetrow, James L. Norris: Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data. 1208-1222
• 
  Carito Guziolowski, Sylvain Blachon, Tatiana Baumuratova, Gautier Stoll, Ovidiu Radulescu, Anne Siegel: Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. 1223-1234
• 
  Sitanshu Sekhar Sahu, Ganapati Panda: Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach. 1235-1246
• 
  Samuel Coulbourn Flores, Michael A. Sherman, Christopher M. Bruns, Peter Eastman, Russ B. Altman: Fast Flexible Modeling of RNA Structure Using Internal Coordinates. 1247-1257
• 
  Biing-Feng Wang, Chien-Hsin Lin: Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees. 1258-1272
• 
  Chun-Hou Zheng, Lei Zhang, To-Yee Ng, Chi Keung Shiu, De-Shuang Huang: Metasample-Based Sparse Representation for Tumor Classification. 1273-1282
• 
  Qian Peng, Andrew D. Smith: Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome. 1283-1295
• 
  Nadja Betzler, René van Bevern, Michael R. Fellows, Christian Komusiewicz, Rolf Niedermeier: Parameterized Algorithmics for Finding Connected Motifs in Biological Networks. 1296-1308
• 
  Jong Kyoung Kim, Seungjin Choi: Probabilistic Models for Semisupervised Discriminative Motif Discovery in DNA Sequences. 1309-1317
• 
  Pedro Feijão, João Meidanis: SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems. 1318-1329
• 
  Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier: SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison. 1330-1343
• 
  Peter Boyen, Dries Van Dyck, Frank Neven, Roeland C. H. J. van Ham, Aalt D. J. van Dijk: SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks. 1344-1357
• 
  Harry Buhrman, Peter T. S. van der Gulik, Steven Kelk, Wouter M. Koolen, Leen Stougie: Some Mathematical Refinements Concerning Error Minimization in the Genetic Code. 1358-1372
• 
  William W. L. Wong, Forbes J. Burkowski: Using Kernel Alignment to Select Features of Molecular Descriptors in a QSAR Study. 1373-1384
• 
  Marco Muselli, Alberto Bertoni, Marco Frasca, Alessandro Beghini, Francesca Ruffino, Giorgio Valentini: A Mathematical Model for the Validation of Gene Selection Methods. 1385-1392
• 
  Elena Dubrova, Maxim Teslenko: A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks. 1393-1399
• 
  Zhi-Zhong Chen, Lusheng Wang: Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L, d)-Motif Model. 1400-1410
• 
  Simona Grusea: On the Distribution of the Number of Cycles in the Breakpoint Graph of a Random Signed Permutation. 1411-1416
• 
  Getachew K. Befekadu, Mahlet G. Tadesse, Tsung-Heng Tsai, Habtom W. Ressom: Probabilistic Mixture Regression Models for Alignment of LC-MS Data. 1417-1424
• 
  Paolo Magni, Angela Simeone, Sandra Healy, Antonella Isacchi, Roberta Bosotti: Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability. 1425-1430
• 
  Ehud Aharoni, Hani Neuvirth, Saharon Rosset: The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery. 1431-1437

Volume 8, Number 6, November 2011

• 
  Apostolos Axenopoulos, Petros Daras, Georgios Papadopoulos, Elias Houstis: A Shape Descriptor for Fast Complementarity Matching in Molecular Docking. 1441-1457
• 
  Wenqi Zhao, Guoliang Xu, Chandrajit L. Bajaj: An Algebraic Spline Model of Molecular Surfaces for Energetic Computations. 1458-1467
• 
  Markus E. Nebel, Anika Scheid: Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model. 1468-1482
• 
  Liang Zhao, Limsoon Wong, Jinyan Li: Antibody-Specified B-Cell Epitope Prediction in Line with the Principle of Context-Awareness. 1483-1494
• 
  Murat Can Cobanoglu, Yücel Saygin, Osman Ugur Sezerman: Classification of GPCRs Using Family Specific Motifs. 1495-1508
• 
  Qi Li, Chandra Kambhamettu: Contour Extraction of Drosophila Embryos. 1509-1521
• 
  Jung Hun Oh, Jean Gao: Fast Kernel Discriminant Analysis for Classification of Liver Cancer Mass Spectra. 1522-1534
• 
  Qingfeng Chen, Yi-Ping Phoebe Chen: Function Annotation for Pseudoknot Using Structure Similarity. 1535-1544
• 
  Georgios Chalkidis, Masao Nagasaki, Satoru Miyano: High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. 1545-1556
• 
  Helong Li, Sam Kwong, Lihua Yang, Daren Huang, Dongping Xiao: Hilbert-Huang Transform for Analysis of Heart Rate Variability in Cardiac Health. 1557-1567
• 
  Jinhua Sheng, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang: Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis. 1568-1579
• 
  Carla C. M. Chen, Holger Schwender, Jonthan Keith, Robin Nunkesser, Kerrie L. Mengersen, Paula E. Macrossan: Methods for Identifying SNP Interactions: A Review on Variations of Logic Regression, Random Forest and Bayesian Logistic Regression. 1580-1591
• 
  Chun-Hou Zheng, Lei Zhang, Vincent To-Yee Ng, Chi Keung Shiu, De-Shuang Huang: Molecular Pattern Discovery Based on Penalized Matrix Decomposition. 1592-1603
• 
  Xavier Le Faucheur, Eli Hershkovitz, Rina Tannenbaum, Allen Tannenbaum: Nonparametric Clustering for Studying RNA Conformations. 1604-1619
• 
  Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote: On Lattice Protein Structure Prediction Revisited. 1620-1632
• 
  Hong-Dong Li, Yi-Zeng Liang, Qing-Song Xu, Dong-Sheng Cao, Bin-Bin Tan, Bai-Chuan Deng, Chen-Chen Lin: Recipe for Uncovering Predictive Genes Using Support Vector Machines Based on Model Population Analysis. 1633-1641
• 
  Christoph Hafemeister, Roland Krause, Alexander Schliep: Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential. 1642-1652
• 
  Thomas Fober, Gerghei Glinca, Gerhard Klebe, Eyke Hüllermeier: Superposition and Alignment of Labeled Point Clouds. 1653-1666
• 
  Tamir Tuller, Elchanan Mossel: Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. 1667-1670
• 
  Bing-Yu Sun, Zhi-Hua Zhu, Jiuyong Li, Bin Linghu: Combined Feature Selection and Cancer Prognosis Using Support Vector Machine Regression. 1671-1677
• 
  Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig: CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. 1678-1684
• 
  Louxin Zhang: From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events. 1685-1691
• 
  Michael R. Fellows, Tzvika Hartman, Danny Hermelin, Gad M. Landau, Frances A. Rosamond, Liat Rozenberg: Haplotype Inference Constrained by Plausible Haplotype Data. 1692-1699
• 
  Jérôme Ambroise, Joachim Giard, Jean-Luc Gala, Benoit M. Macq: Identification of Relevant Properties for Epitopes Detection Using a Regression Model. 1700-1707
• 
  Qingguo Wang, Yi Shang, Dong Xu: Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy. 1708-1715
• 
  Aleksandar Poleksic: Optimizing a Widely Used Protein Structure Alignment Measure in Expected Polynomial Time. 1716-1720
• 
  Thiago de Souza Rodrigues, Fernanda Caldas Cardoso, Santuza Maria Ribeiro Teixeira, Sergio Costa Oliveira, Antônio de Pádua Braga: Protein Classification with Extended-Sequence Coding by Sliding Window. 1721-1726

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