Advances in Computational Biology

Advances in Computational Biology Arabnia, Hamid R. ISBN-13: 9781441959126

Table of Contents Part I: Bioinformatics Databases, Data Mining, and Pattern Discovery. A Classification Method Based on Similarity Measures of Generalized Fuzzy Numbers in Building Expert System for Postoperative Patients by Pasi Luukka. Efficient Support Vector Machine Method for Survival Prediction with SEER Data by Zhenqiu Liu, Dechang Chen, Guoliang Tian, Man-Lai Tang, Ming Tan, and Li Sheng. Searching Maximal Degenerate Motifs Guided by a Compact Suffix Tree by Hongshan Jiang, Ying Zhao, Wenguang Chen, Weimin Zheng. Exploring Motif Composition of Eukaryotic Promoter Regions by Nikola Stojanovic, Abanish Singh. Large-Scale Analysis of Phylogenetic Search Behavior by Hyun Jung Park, Seung-Jin Sul, and Tiffani L. Williams. Silicosection and Elucidation of the Plant Circadian Clock Using Bayesian Classifiers and New Genemining Algorithm by Sandra Smieszek, Rainer Richter, Bartlomiej Przychodzen, Jaroslaw Maciejewski. ChemBrowser: A Flexible Framework for Mining Chemical Documents by Xian Wu, Li Zhang, Ying Chen, James Rhodes, Thomas D Griffin, Stephen K Boyer, Alfredo Alba, Keke Cai.-Experimental Study of Modified Voting Algorithm for Planted (l,d)-Motif Problem by Hazem M Bahig, Mostafa M Abbas, and Ashraf Bhery. Prediction of Severe Sepsis Using SVM Model by Shu-Li Wang, Fan Wu, Bo-Hang, Wang. Online Multi-Divisive Hierarchical Clustering for On-body Sensor Data by Ibrahim Musa Ishag Musa, Anour F.A. Dafa-Alla, Gyeong Min Yi, Dong Gyu Lee, Myeong-Chan Cho, Jang-Whan Bae, and Keun Ho Ryu. On Quality Assurance and Assessment of Biological Datasets and Related Statistics by Maria Vardaki and Haralambos Papageorgiou. Pattern Recognition Informed Feedback for Nanopore Detector Cheminformatics by A. Murat Eren, Iftekhar Amin, Amanda Alba, Eric Morales, Alexander Stoyanov, Stephen Winters-Hilt. A MLP Neural Network for ECG Noise Removal Based on Kalman Filter by Sara Moein. Discovery of Structural Motifs Using Protein Structural Alphabets and 1D Motif-finding Methods by Shih-Yen Ku, Yuh-Jyh Hu. Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies by Yuichi Kodama, Eli Kaminuma, Satoshi Saruhashi, Kazuho Ikeo, Hideaki Sugawara, Yoshio Tateno and Yasukazu Nakamura. Part II: Microarray, Gene Expression Analysis, and Gene Regulatory Networks. Comparison of Microarray Pre-Processing Methods by Kabita Shakya, Heather J. Ruskin, Grainne Kerr, Martin Crane, Jeremie Becker. A Robust Ensemble Classification Method for Microarray Data Analysis by Zhongwei Zhang, Jiuyong Li, Hong Hu, Hong Zhou. k-NN for the Classification of Human Cancer Samples using the Gene Expression Profiles by Manuel Martin-Merino. The Application of Regular Expression Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear by Christopher M. Frenz & Dorothy A. Frenz. Functionally Informative Tag SNP Prioritization Using a Pareto-Optimal Approach by Phil Hyoun Lee, Jae-Yoon Jung, and Hagit Shatkay. KMeans-Greedy Search Hybrid Algorithm for Biclustering Gene Expression Data by Shyama Das and Sumam Mary Idicula. Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of E.Coli by A. meyer-Baese, F. Theis and M. Emmett. FM-GA and CM-GA for Gene Microarray Analysis by Lily R. Liang, Rommel A. Benites Palomino, Zhao Lu, Vinay Mandal, Deepak Kumar. Part III: Protein Classification and Structure Prediction, and Computational Structural Biology. Novel Features for Automated Cell Phenotype Image Classification by Loris Nanni, Sheryl Brahnam, Alessandra Lumini. A Relational Fuzzy C-Means Algorithm for Detecting Protein Spots in Two-Dimensional Gel Images by Shaheera Rashwan, Talaat Faheem, Amany Sarhan, Bayumy A.B.Youssef. Assigning Probabilities to Mascot Peptide Identification Using Logistic Regression by Jinhong Shi and Fang-Xiang Wu. Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies by Yunfeng Shan and Robin Gras. Building a Parallel between Structural and Topological Properties by Omar Gaci and Stefan Balev. GNCPro: Navigate Human Genes and Relationships through Net-Walking by Guozhen Gordon Liu, Elvena Fong, Xiao Zeng. Small-scale modeling approach and circuit wiring of the unfolded protein response in mammalian cells by Rodica Curtu and Danilo Diedrichs. Random-walk Mechanism in the Genetic Recombination by Youhei Fujitani, Junji Kawai, Ichizo Kobayashi. Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation by Anna Marabotti and Angelo Facchiano. Temporal Anomaly Detection: an Artificial Immune Approach Based on T-cell Activation, Clonal Size Regulation and Homeostasis by Mario J. Antunes and Manuel E. Correia. An integrated methodology for mining promiscuous proteins: A case study of an integrative bioinformatics approach for Hepatitis C Virus non- structural 5a protein by Mahmoud M. El Hefnawi, Aliaa A. Youssif , Atef Z. Ghalwash, Wessam H. El Behaidy. Enhanced prediction of conformational flexibility and phosphorylation in proteins by Karthikeyan Swaminathan, Rafal Adamczak, Aleksey Porollo and Jaroslaw Meller.

Why are MD simulated protein folding times wrong? By Dmitry Nerukh. Automatic TEM image analysis of membranes for 2D crystal detection by Argyro Karathanou, Nicolas Coudray, Gilles Hermann, Jean-Luc Buessler and Jean-Philippe Urban. High Performance Computing Approaches For 3D Reconstruction Of Complex Biological Specimens by M. Laura Da Silva, Javier Roca-piera, Jose-jesus Fernandez. Protein Identification using Receptor Arrays and Mass Spectrometry by Timothy R. Langlois, Richard W. Vachet, Ramgopal R. Mettu. Part IV: Comparative Sequence, Genome Analysis, Genome Assembly, and Genome Scale Computational Methods. Assessing Consistency Between Versions of Genotype Calling Algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 Using HapMap Samples by Huixiao Hong, Lei Xu, Weida Tong. An Overview of the BioExtract Server - a Distributed, Web Based System for Genomic Analysis by Carol Lushbough and Volker Brendel. A Deterministic DNA Database Search by A. Kheniche, A.Salhi, A.Harrison, J.M.Dowden. Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes by Padmanabhan Mahadevan and Donald Seto. Analysis of Gene Translation Using a Communications Theory Approach by Mohammad Al Bataineh, Lun Huang, Maria Alonso, Nick Menhart, and Guillermo E. Atkin. A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome by Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis. Sequence Analysis and Homology Modeling Gallus gallus Glutathione S-transferase (Q08392) by Patchikolla Satheesh, Allam Appa Rao, G.R Sridhar, Kudipudi Srinivas, Chandra Sekhar Akula. Toward Optimizing the Cache Performance of Suffix Trees for Sequence Analysis Algorithms by Chih Lee and Chun-Hsi Huang. Towards a Visualization of DNA Sequences by David Cox, Alan Tharp. A practical approach for computing the active site of the ribonucleoside hydrolase of E. coli encoded by rich by Anthony Farone, Mary Farone, Paul Kline, Terrance Quinn and Zachariah Sinkala. Part V: Drug Design, Drug Screening, and Related Topics. Addressing the Docking Problem: Finding Similar 3-D Protein Envelopes for Computer-aided Drug Design by Eric Paquet and Herna Lydia Viktor. Simultaneous Pathogen Detection and Antibiotic Resistance Characterization Using SNP-based Multiplexed Oligonucleotide Ligation-PCR (MOL-PCR) by Jian Song, Po-E Li, Jason Gans, Momchilo Vuyisich, Alina Deshpande, Murray Wolinsky & P. Scott White. Specification and Verification of Pharmacokinetic Models by YoungMin Kwon and Eunhee Kim. Dehydron Analysis: Quantifying the Effect of Hydrophobic Groups on the Strength and Stability of Hydrogen Bonds by Christopher M. Fraser, Ariel Fernandez, L. Ridgway Scott. Docking to large allosteric binding sites on protein surfaces by Ursula D. Ramirez, Faina Myachina, Linda Stith, & Eileen K. Jaffe. Modeling of ATP-Sensitive Inward Rectifier Potassium Channel 11 and Inhibition Mechanism of the Natural Ligand Ellagic Acid Using Molecular Docking Studies by Alex Mathew J, Nixon Raj N, Sugappriya M, Sangeetha Priyadarshini M. SPG1036 GPU Acceleration of Dock6's Amber Scoring Computation by Hailong Yang, Bo Li, Yongjian Wang. Part VI: Computational Methods and Diagnostic Tools in Biomedical. Discriminative Distance Functions and the Patient Neighborhood Graph for Clinical Decision Support by Alexey Tsymbal, Martin Huber, Shaohua Kevin Zhou. A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology by Ben Compani, Trent Su, Ivan Chang, Jianlin Cheng, Kandarp H. Shah, Thomas Whisenant, Yimeng Dou, Adriel Bergmann, Raymond Cheong, Barbara Wold, Lee Bardwell, Andre Levchenko, Pierre Baldi, Eric Mjolsness. Registration of In Vivo Fluorescence Endomicroscopy Images based on Feature Detection by Feng Zhao, Lee Sing Cheong, Feng Lin, Kemao Qian, Hock Soon Seah, and Sun-Yuan Kung. Kinetic models for cancer imaging by Volker J Schmid. Using Web and Social Media for Influenza Surveillance by Courtney D Corley, Diane J Cook, Armin R Mikler and Karan P Singh. CodeSlinger: A Case Study in Domain-driven Interactive Tool Design for Biomedical Coding Scheme Exploration and Use by Natalie L. Flowers. DigitalLung: Application of High-Performance Computing to Biological System Simulation by Greg W. Burgreen, Robert Hester, Bela Soni, David Thompson, D. Keith Walters, and Keisha Walters. Consideration of Indices to Evaluate age-related Muscle Performance by Using Surface Electromyography by Hiroki Takada, Tomoki Shiozawa, Masaru Miyao, Yasuyuki Matsuura and Ma-sumi Takada. A Study on Discrete Wavelet Based Noise Removal from EEG Signals by K. Asaduzzaman, M. B. I. Reaz, F. Mohd-Yasin, K. S. Sim, M. S. Hussain. Enhancing the Communication Flow between Alzheimer Patients, Caregivers and Neuropsychologists by Abraham RodriguezRodriguez, Leidia Martel-Monagas, Aaron Lopez-Rodriguez. An improved 1-D Gel Electrophoresis Image Analysis System by Yassin Labyed, Naima Kaabouch, Richard R. Schultz, Brij B. Singh, and Barry Milavetz. Fuzzy Approach to Contrast Enhancement of Mammography Breast Images by Farhang Sahba, Anastasios Venetsanopoulos. Computational modelling of a new Thrombectomy Device for the extraction of blood clots by Romero G, Higuera I, Martinez ML, Pearce G, Perkinson N, Roffe C, Wong J.. NEURONSESSIONS: Web-based Collaborative Tool to Create Brain Computational Models by Ana Porto, Guillermo Rodriguez, Julian Dorado, Alejandro Pazos. Part VII: General Topics in Bioinformatics. Towards Automating an Inference Model on Unstructured Terminologies: OXMIS Case Study by Jeffery L Painter. Semantic Content-Based Recommendations Using Semantic Graphs by Weisen Guo and Steven B. Kraines.

Modeling Membrane Localization: Case Study of a Ras Signaling Model by Edward C Stites. A Study on Distributed PACS Systems by Aylin Kantarci and Tolga Utku Onbay. Epileptic EEG: A Comprehensive Study of Nonlinear Behavior by Moayed Daneshyari, L. Lily Kamkar, Matin Daneshyari. Computational energetic model of morphogenesis based on multi-agent Cellular Potts Model by Sebastien Tripodi , Pascal Ballet, Vincent Rodin. Standardizing the Next Generation of Bioinformatics Software Development With BioHDF (HDF5) by Christopher E Mason, Paul Zumbo, Stephan Sanders, Mike Folk, Dana Robinson, Ruth Aydt, Matrin Gollery, Mark Welsh, N. Eric Olson, Todd Smith. Multisensor Smart System on a Chip by Louiza Sellami and Robert W. Newcomb. Visual Presentation as a Welcome Alternative to Tex-tual Presentation of Gene Annotation Information by Jairav Desai, Jared M. Flatow, Jie Song, Lihua J. Zhu, Pan Du, Chiang-Ching Huang, Hui Lu, Simon M. Lin, Warren A. Kibbe. Automatic FRAP Analysis with Inhomogeneous Fluorescence Distribution and Movement Compensation by Harri Polonen, Maurice Jansen, Elina Ikonen, Ulla Ruotsalainen. Sorting Circular Permutations by Bounded Transpositions by Xuerong Feng, Bhadrachalam Chitturi, Hal Sudborough. Annotating Patents with Medline MeSH Codes via Citation Mapping by Thomas D. Griffin, Stephen K. Boyer, Isaac G. Councill. Some New Measures of Entropy, Useful Tools in Biocomputing by Garrido, Angel. Index