Table of Contents

• Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic ProteinsM. Michael Gromiha, Liang-Tsung Huang, Lien Fu Lai. 1-12 [doi]
• A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)Chetan Kumar, Nishith Kumar, Sarani Rangarajan, Narayanaswamy Balakrishnan, Kanagaraj Sekar. 13-27 [doi]
• Predicting SUMOylation SitesDenis C. Bauer, Fabian A. Buske, Mikael Bodén. 28-40 [doi]
• DFS Based Partial Pathways in GA for Protein Structure PredictionTamjidul Hoque, Madhu Chetty, Andrew Lewis, Abdul Sattar. 41-53 [doi]
• Evaluation of the Stability of Folding Nucleus upon MutationMathieu Lonquety, Zoé Lacroix, Jacques Chomilier. 54-65 [doi]
• Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical ApproachYuki Kato, Tatsuya Akutsu, Hiroyuki Seki. 66-77 [doi]
• Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer TypesQi-Peng Li, Shao-Wu Zhang, Quan Pan. 78-86 [doi]
• Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular SurfacesSatoshi Koizumi, Keisuke Imada, Tomonobu Ozaki, Takenao Ohkawa. 87-97 [doi]
• A Clustering Based Hybrid System for Mass Spectrometry Data AnalysisPengyi Yang, Zili Zhang. 98-109 [doi]
• A Modified Markov Clustering Approach for Protein Sequence ClusteringLehel Medvés, László Szilágyi, Sándor M. Szilágyi. 110-120 [doi]
• Feature Selection and Classification for Small Gene SetsGregor Stiglic, Juan J. Rodriguez, Peter Kokol. 121-131 [doi]
• Pseudoknot Identification through Learning TAGRNASahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar. 132-143 [doi]
• Support Vector Based T-Score for Gene RankingPiyushkumar A. Mundra, Jagath C. Rajapakse. 144-153 [doi]
• Prediction of Transcription Factor Families Using DNA Sequence FeaturesAshish Anand, Gary B. Fogel, Ganesan Pugalenthi, Ponnuthurai N. Suganthan. 154-164 [doi]
• g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector MachinesXiaonan Ji, James Bailey, Kotagiri Ramamohanarao. 165-177 [doi]
• Domain-Domain Interaction Identification with a Feature Selection ApproachXing-Ming Zhao, Luonan Chen. 178-186 [doi]
• Dividing Protein Interaction Networks by Growing Orthologous ArticulationsPavol Jancura, Jaap Heringa, Elena Marchiori. 187-200 [doi]
• Constraint Minimization for Efficient Modeling of Gene Regulatory NetworkRamesh Ram, Madhu Chetty, Dieter Bulach. 201-213 [doi]
• Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain ModelsIti Chaturvedi, Jagath C. Rajapakse. 214-224 [doi]
• TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic TreesTingting Zhou, Keith C. C. Chan, Zhenghua Wang. 225-236 [doi]
• Generating Synthetic Gene Regulatory NetworksRamesh Ram, Madhu Chetty. 237-249 [doi]
• Gene Selection for Microarray Data by a LDA-Based Genetic AlgorithmEdmundo Bonilla Huerta, Béatrice Duval, Jin-Kao Hao. 250-261 [doi]
• Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection ProblemLili Wang, Alioune Ngom, Luis Rueda. 262-275 [doi]
• On Finding and Interpreting Patterns in Gene Expression Data from Time Course ExperimentsYvonne E. Pittelkow, Susan R. Wilson. 276-287 [doi]
• Microarray Design Using the Hilbert-Schmidt Independence CriterionJustin Bedo. 288-298 [doi]
• Identifying Non-random Patterns from Gene Expression ProfilesRadhakrishnan Nagarajan, Meenakshi Upreti, Mariofanna G. Milanova. 299-310 [doi]
• A Study on the Importance of Differential Prioritization in Feature Selection Using Toy DatasetsChia Huey Ooi, Shyh Wei Teng, Madhu Chetty. 311-322 [doi]
• Weighted Top Score Pair Method for Gene Selection and ClassificationHuaien Luo, Yuliansa Sudibyo, Lance D. Miller, Karuturi R. Krishna Murthy. 323-333 [doi]
• Identifying Conserved Discriminative MotifsJyotsna Kasturi, Raj Acharya, Ross Hardison. 334-348 [doi]
• Exploratory Data Analysis for Investigating GC-MS BiomarkersKenneth McGarry, Kim Bartlett, Morteza Pourfarzam. 349-358 [doi]
• Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting ProteinsKaren T. Girão, Fátima C. E. Oliveira, Kaio M. Farias, Italo M. C. Maia, Samara C. Silva, Carla R. F. Gadelha, Laura D. G. Carneiro, Ana C. L. Pacheco, Michel T. Kamimura, Michely C. Diniz, Maria C. Silva, Diana M. Oliveira. 359-372 [doi]
• Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-genomic Knowledge DiscoveryMuhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence S. Dooley, Ross L. Coppel. 373-387 [doi]
• Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component AnalysisXiaoxu Han, Joseph Scazzero. 388-399 [doi]
• Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to CancerGeoff Macintyre, James Bailey, Daniel Gustafsson, Alex Boussioutas, Izhak Haviv, Adam Kowalczyk. 400-411 [doi]
• Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression DataCem Meydan, Alper Küçükural, Deniz Yörükoglu, Osman Ugur Sezerman. 412-423 [doi]
• Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance StudyAlexandros Stamatakis, Michael Ott. 424-435 [doi]
• Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANAJan Schröder, Lars Wienbrandt, Gerd Pfeiffer, Manfred Schimmler. 436-447 [doi]
• GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA SequencesChen Chen, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig. 448-459 [doi]
• Accelerating BLASTP on the Cell Broadband EngineHuiliang Zhang, Bertil Schmidt, Wolfgang Müller-Wittig. 460-470 [doi]