PRIB 2008: Melbourne, Australia

Madhu Chetty, Alioune Ngom, Shandar Ahmad (Eds.): Pattern Recognition in Bioinformatics, Third IAPR International Conference, PRIB 2008, Melbourne, Australia, October 15-17, 2008. Proceedings. Lecture Notes in Computer Science 5265 Springer 2008, ISBN 978-3-540-88434-7

Protein: Structure, Function, and Interaction

M. Michael Gromiha, Liang-Tsung Huang, Lien Fu Lai:
Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins. 1-12
Chetan Kumar, Nishith Kumar, Sarani Rangarajan, Narayanaswamy Balakrishnan, Kanagaraj Sekar:
A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS). 13-27
Denis C. Bauer, Fabian A. Buske, Mikael Bodén:
Predicting SUMOylation Sites. 28-40
Tamjidul Hoque, Madhu Chetty, Andrew Lewis, Abdul Sattar:
DFS Based Partial Pathways in GA for Protein Structure Prediction. 41-53
Mathieu Lonquety, Zoé Lacroix, Jacques Chomilier:
Evaluation of the Stability of Folding Nucleus upon Mutation. 54-65
Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki:
Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach. 66-77
Qi-Peng Li, Shao-Wu Zhang, Quan Pan:
Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types. 78-86
Satoshi Koizumi, Keisuke Imada, Tomonobu Ozaki, Takenao Ohkawa:
Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces. 87-97

Pengyi Yang, Zili Zhang:
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis. 98-109
Lehel Medvés, László Szilágyi, Sándor M. Szilágyi:
A Modified Markov Clustering Approach for Protein Sequence Clustering. 110-120
Gregor Stiglic, Juan J. Rodríguez Diez, Peter Kokol:
Feature Selection and Classification for Small Gene Sets. 121-131
Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar:
Pseudoknot Identification through Learning TAGRNA. 132-143
Piyushkumar A. Mundra, Jagath C. Rajapakse:
Support Vector Based T-Score for Gene Ranking. 144-153
Ashish Anand, Gary B. Fogel, Ganesan Pugalenthi, Ponnuthurai N. Suganthan:
Prediction of Transcription Factor Families Using DNA Sequence Features. 154-164
Xiaonan Ji, James Bailey, Kotagiri Ramamohanarao:
g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines. 165-177

Xing-Ming Zhao, Luonan Chen:
Domain-Domain Interaction Identification with a Feature Selection Approach. 178-186
Pavol Jancura, Jaap Heringa, Elena Marchiori:
Dividing Protein Interaction Networks by Growing Orthologous Articulations. 187-200
Ramesh Ram, Madhu Chetty, Dieter Bulach:
Constraint Minimization for Efficient Modeling of Gene Regulatory Network. 201-213
Iti Chaturvedi, Jagath C. Rajapakse:
Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models. 214-224
Tingting Zhou, Keith C. C. Chan, Zhenghua Wang:
TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees. 225-236
Ramesh Ram, Madhu Chetty:
Generating Synthetic Gene Regulatory Networks. 237-249

Edmundo Bonilla Huerta, Béatrice Duval, Jin-Kao Hao:
Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm. 250-261
Lili Wang, Alioune Ngom, Luis Rueda:
Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem. 262-275
Yvonne E. Pittelkow, Susan R. Wilson:
On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments. 276-287
Justin Bedo:
Microarray Design Using the Hilbert-Schmidt Independence Criterion. 288-298
Radhakrishnan Nagarajan, Meenakshi Upreti, Mariofanna G. Milanova:
Identifying Non-random Patterns from Gene Expression Profiles. 299-310
Chia Huey Ooi, Shyh Wei Teng, Madhu Chetty:
A Study on the Importance of Differential Prioritization in Feature Selection Using Toy Datasets. 311-322
Huaien Luo, Yuliansa Sudibyo, Lance D. Miller, Karuturi R. Krishna Murthy:
Weighted Top Score Pair Method for Gene Selection and Classification. 323-333

Jyotsna Kasturi, Raj Acharya, Ross Hardison:
Identifying Conserved Discriminative Motifs. 334-348
Kenneth McGarry, Kim Bartlett, Morteza Pourfarzam:
Exploratory Data Analysis for Investigating GC-MS Biomarkers. 349-358
Karen 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 Carolina L. Pacheco, Michel T. Kamimura, Michely C. Diniz, Maria C. Silva, Diana M. Oliveira:
Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins. 359-372
Muhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence S. Dooley, Ross L. Coppel:
Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-genomic Knowledge Discovery. 373-387
Xiaoxu Han, Joseph Scazzero:
Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis. 388-399
Geoff MacIntyre, James Bailey, Daniel Gustafsson, Alex Boussioutas, Izhak Haviv, Adam Kowalczyk:
Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer. 400-411
Cem Meydan, Alper Küçükural, Deniz Yörükoglu, Osman Ugur Sezerman:
Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data. 412-423

Alexandros Stamatakis, Michael Ott:
Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study. 424-435
Jan Schröder, Lars Wienbrandt, Gerd Pfeiffer, Manfred Schimmler:
Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA. 436-447
Chen Chen, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig:
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. 448-459
Huiliang Zhang, Bertil Schmidt, Wolfgang Müller-Wittig:
Accelerating BLASTP on the Cell Broadband Engine. 460-470

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