| Protein: Structure, Function, and Interaction / Part I： |
| Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai |
| A Method to Find Sequentially Separated Motifsin Biological Sequences (SSMBS) / Chetan Kumar ; Nishith Kumar ; Sarani Rangarajan ; Narayanaswamy Balakrishnan ; Kanagaraj Sekar |
| Predicting SUMOylation Sites / Denis C. Bauer ; Fabian A. Buske ; Mikael Boden |
| DFS Based Partial Pathways in GA for Protein Structure Prediction / Md Tamjidul Hoque ; Madhu Chetty ; Andrew Lewis ; Abdul Sattar |
| Evaluation of the Stability of Folding Nucleus upon Mutation / Mathieu Lonquety ; Zoe Lacroix ; Jacques Chomilier |
| Prediction of Protein Beta-Sheets: Dynamic Programming Versus Grammatical Approach / Yuki Kato ; Tatsuya Akutsu ; Hiroyuki Seki |
| Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types / QiPeng Li ; Shao Wu Zhang ; Quan Pan |
| Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces / Satoshi Koizumi ; Keisuke Imada ; Tomonobu Ozaki ; Takenao Ohkawa |
| Learning, Classification, and Clustering / Part II： |
| A Clustering Based Hybrid System for Mass Spectrometry Data Analysis / Pengyi Yang ; Zili Zhang |
| A Modified Markov Clustering Approach for Protein Sequence Clustering / Lehel Medves ; Laszlo Szilagyi ; Sandor M. Szilagyi |
| Feature Selection and Classification for Small Gene Sets / Gregor Stiglic ; Juan J. Rodriguez ; Peter Kokol |
| Pseudoknot Identification through Learning TAG[subscript RNA] / Sahar Al Seesi ; Sanguthevar Rajasekaran ; Reda Ammar |
| Support Vector Based T-Score for Gene Ranking / Piyushkumar A. Mundra ; Jagath C. Rajapakse |
| Prediction of Transcription Factor Families Using DNA Sequence Features / Ashish Anand ; Gary B. Fogel ; Ganesan Pugalenthi ; P.N. Suganthan |
| g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines / Xiaonan Ji ; James Bailey ; Kotagiri Ramamohanarao |
| Bio-Molecular Networks and Pathways Analysis / Part III： |
| Domain-Domain Interaction Identification with a Feature Selection Approach / Xing-Ming Zhao ; Luonan Chen |
| Dividing Protein Interaction Networks by Growing Orthologous Articulations / Pavol Jancura ; Jaap Heringa ; Elena Marchiori |
| Constraint Minimization for Efficient Modeling of Gene Regulatory Network / Ramesh Ram ; Dieter Bulach |
| Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models / Iti Chaturvedi |
| TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees / Tingting Zhou ; Keith C.C. Chan ; Zhenghua Wang |
| Generating Synthetic Gene Regulatory Networks |
| Microarray and Gene Expression Analysis / Part IV： |
| Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm / Edmundo Bonilla Huerta ; Beatrice Duval ; Jin-Kao Hao |
| Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem / Lili Wang ; Alioune Ngom ; Luis Rueda |
| On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments / Yvonne E. Pittelkow ; Susan R. Wilson |
| Microarray Design Using the Hilbert-Schmidt Independence Criterion / Justin Bedo |
| Identifying Non-random Patterns from Gene Expression Profiles / Radhakrishnan Nagarajan ; Meenakshi Upreti ; Mariofanna Milanova |
| A Study on the Importance of Differential Prioritization in Feature Selection Using Toy Datasets / Chia Huey Ooi ; Shyh Wei Teng |
| Weighted Top Score Pair Method for Gene Selection and Classification / Huaien Luo ; Yuliansa Sudibyo ; Lance D. Miller ; R. Krishna Murthy Karuturi |
| Data Mining and Knowledge Discovery / Part V： |
| Identifying Conserved Discriminative Motifs / Jyotsna Kasturi ; Raj Acharya ; Ross Hardison |
| Exploratory Data Analysis for Investigating GC-MS Biomarkers / Ken McGarry ; Kim Bartlett ; Morteza Pourfarzam |
| Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins / Karen T. Girao ; Fatima 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 |
| Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-Genomic Knowledge Discovery / Muhammad Shoaib B. Sehgal ; Iqbal Gondal ; Laurence S. Dooley ; Ross Coppel |
| Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis / Xiaoxu Han ; Joseph Scazzero |
| Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer / Geoff Macintyre ; Daniel Gustafsson ; Alex Boussioutas ; Izhak Haviv ; Adam Kowalczyk |
| Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data / Cem Meydan ; Alper Kucukural ; Deniz Yorukoglu ; O. Ugur Sezerman |
| Applications of High Performance Computing / Part VI： |
| Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study / Alexandros Stamatakis ; Michael Ott |
| Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA / Jan Schroder ; Lars Wienbrandt ; Gerd Pfeiffer ; Manfred Schimmler |
| GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences / Chen Chen ; Bertil Schmidt ; Liu Weiguo ; Wolfgang Muller-Wittig |
| Accelerating BLASTP on the Cell Broadband Engine / Huiliang Zhang |
| Author Index |
| Protein: Structure, Function, and Interaction / Part I： |
| Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai |
| A Method to Find Sequentially Separated Motifsin Biological Sequences (SSMBS) / Chetan Kumar ; Nishith Kumar ; Sarani Rangarajan ; Narayanaswamy Balakrishnan ; Kanagaraj Sekar |
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