BIC

BIOCOMP'11

The 2011 International Conference on Bioinformatics and Computational Biology


BIOCOMP'11 Vol I -  ISBN #:  1-60132-170-8
BIOCOMP'11 Vol II - ISBN #:  1-60132-171-6
BIOCOMP'11 Set -    ISBN #:  1-60132-172-4

EDITORS:
Hamid R. Arabnia and Quoc-Nam Tran

ASSOCIATE EDITORS:
Matthew He, Andy Marsh, Ashu M. G. Solo, Jack Y. Yang

Foreword

SESSION: COMPUTATIONAL METHODS FOR MICROARRAY, GENE EXPRESSION ANALYSIS,

AND GENE REGULATORY NETWORKS

Optimization of a Microarray Probe Design Focusing on the Minimization of Cross-hybridization

Fabian Horn, Hans-Wilhelm Nutzmann, Volker Schroeckh, Reinhard Guthke, Christian Hummert

EMMA: An EM-based Imputation Technique for Handling Missing Sample-Values in Microarray Expression Profiles.

Amitava Karmaker, Edward Salinas, Stephen Kwek

Creation and Comparison of Different Chip Definition Files for Affymetrix Microarrays

Christian Hummert, Franziska Mech, Fabian Horn, Michael Weber, Susanne Drynda, Ulrike Gausmann, Reinhard Guthke

A Validation Method for Fuzzy Clustering of Gene Expression Data

Thanh Le, Katheleen Gardiner

Robust SVD Method for Missing Value Estimation of DNA Microarrays

Fen Qin, Joseph Collins, Jeonghwa Lee

Finding Biomarkers for Non-Small Cell Lung Cancer Diagnosis with Novel Data Mining Techniques

Quoc-Nam Tran

Identification of Pseudo-Periodic Gene Expression Profiles

Li-Ping Tian, Li-Zhi Liu, Fang-Xiang Wu

Gene Selection using Multidimensional False Discovery Rate

Ahmed Moussa, Mounir Maouene, Brigitte Vannier

Letting all have a say - A novel method for microRNA RT-PCR normalization

Rehman Qureshi, Ahmet Sacan

Classification of High-throughput Data Using Correlation-shared Gene Clusters

Pingzhao Hu, Hui Jiang

Markov Model Checking of Probabilistic Boolean Networks Representations of Genes

Marie Lluberes, Jaime Seguel, Jaime Ramirez-Vick

Reliability Analysis of Classification of Gene Expression Data

Sujata Dash, Bichitra Nanda Patra

SESSION: BIOINFORMATICS DATABASE, DATAMINING, AND PATTERN DISCOVERY

TECHNIQUES

Clustering on Protein Sequence Motifs using SCAN and Positional Association Rule Algorithms

Bernard Chen, Ben Nordin, Sriram Bobba, Devendar Singireddy, Brad Taylor, Sinan Kockara, Mutlu Mete

Constructing Super Rule Tree (SRT) for Protein Motif Clusters Using DBSCAN

Bernard Chen, Sait Suer, Muhyeddin Ercan, Rahul Tada, Recep Avci, Sinan Kockara

Mapping Genes to Diseases With Translational Data Mining

Modest Von Korff, Axel Klenk, Thomas Sander

Protein Sequence Motif Extraction Using Decision Forest

Bernard Chen, Cody Hudson, Minwoo Kim, Aaron Crawford, John Wright, Dongsheng Che

Matlab Toolbox for Data Reduction, Visualization, Classification and Knowledge Extraction of Complex Biological Data

Ali Mohammad-Djafari, Ghazaleh Khodabandelou, Jerome Lapuyade-Lahorgue

Portable Measurement System of the Spasticity Based on the K-means Clustering Algorithm of the Tonic Stretch Reflex Threshold

Chul-Gyu Song, Keo-Sik Kim, Min-Ho Kim, Sang-Hun Ryu

GPU Accelerated PK-means Algorithm for Gene Clustering

Wuchao Situ, Yau King Lam, Yi Xiao, Peter Wai Ming Tsang, Chi Sing Leung

Computation of Coronary Sinus Pressure Using Pattern Recognition Techniques

Loay Alzubaidi, Ammar El Hassan, Jaafar Al Ghazo

Linear Models and Biomarker Search with Microarray Data

Eulisa Rivera, Matilde Sanchez-Pena, Clara Isaza, Jaime Seguel, Mauricio Cabrera-Rios

Comparative Analysis of Krylov Iterative Methods in Support Vector Machines

Matthew Freed, Joseph Collins, Jeonghwa Lee

Fast Splice Site Classification Using Support Vector Machines in Imbalanced Data-sets

Jair Cervantes, Asdrubal Lopez Chau, Adrian Trueba Espinoza, Jose Sergio Ruiz Castilla

A Study on Acupressure Points Online Database

Zizhong Wang, Tara Santos

Human Identification via Neural Network

Parviz Eshaghi

Telomerase Gene Prediction Using Support Vector Machines

David Luper, Spandana Makeneni

SESSION: PROTEIN CLASSIFICATION + STRUCTURE PREDICTION, EVOLUTIONARY, AND

COMPUTATIONAL MOLECULAR + STRUCTURAL BIOLOGY

Solving Planted Motif Problem Using Modeling Method

Subramanyam Desaraju, Ravi Mukkamala

Predicting Sequence and Structural Specificities of RNA Binding Regions Recognized by Splicing Factor SRSF1

Xin Wang, Liran Juan, Junjie Lv, Kejun Wang, Jeremy Sanford, Yunlong Liu

Correlation of Patristic Distance with Nominal Specimen Collection Date in Inflluenza A/H1N1 Hemagglutinin-Encoding Segments

Jack Horner

Identification of Transcriptional Regulatory Elements by Functional Enrichment Analysis.

Amitava Karmaker, Stephen Kwek

An Integrated Pipeline for Protein Classification using Specific PSSMs and Existing Protein Annotations

Kyung Dae Ko, Hongfang Liu

Predicting DNA-Binding Sites by Exploring the Distribution of Atom Groups around the Surface

Jing Hu, Changhui Yan

Stuctural Analysis of Molecular Networks: AMES Mutagenicity

Laurin AJ Mueller, Karl G Kugler, Matthias Dehmer

A Study of Correlations Between the Definition and Application of the Gene Ontology

Yuji Mo, Catherine Anderson, Stephen Scott

Phylogenetic Analysis Workflow Using the BioExtract Server

Yosr Bouhlal, Douglas Jennewein, Carol Lushbough

SESSION: COMPARATIVE SEQUENCE, GENOME ANALYSIS, GENOME ASSEMBLY, AND

GENOME SCALE COMPUTATIONAL METHODS

A Regression-based Approach for Estimating Recombination Rate from Population Genomic Data

Lan Zhu, Feng Feng, Carlos Bustemante

Evaluation of the Suitability of a Zipfian Gap Model for Pairwise Sequence Alignment

Ramu Chenna, Toby Gibson

A Probabilistic Approach for Characterizing the Marking System of Multiplex Sequencing in ABI SOLiD Platform

Fabio Lobato, Pericles Machado, André Goncalves, Andrea Ribeiro-dos-Santos, Dayse Alencar, Sylvain Darnet, Adamo Santana

Enhancement on the Predictive Power of the Prediction Model for Human Genomic DNA Methylation

Hao Zheng, Shi-Wen Jiang, Hongwei Wu

Parallelization of Needleman-Wunsch String Alignment Method

Jaime Seguel, Carlos Torres

Genetic Matching: An Efficient Algorithm to Adjust Covariate Imbalance for Data Analysis and Modeling

Kao-Tai Tsai, Karl Peace

A CAM (Content Addressable Memory)-based Architecture for Molecular Sequence Matching

Parag Lala, James Parkerson

Effective Algorithms for Altering Human Chromosome Shapes

Wei Wu, Xiaoli Yang, Charles Tseng

Identification of Minimum Redundancy Tagging SNPs via Gibbs Sampling

Gaolin Zheng

Development Approach and Architecture of GenSAS : the Genome Sequence Annotation

Server

Taein Lee, Il-Hyung Cho, Cameron Peace, Sook Jung, Ping Zheng, Doreen Main

Sequence Analysis to Predict Protein Active Sites using SSHM

Satheesh Patchikolla, Srinivas Bagam, Prasada Mandala, Appa Rao Allam, Charles Babu Gundupalli

SESSION: COMPUTATIONAL METHODS FOR FILTERING, NOISE CANCELLATION, AND

SIGNAL + IMAGE PROCESSING

Quantifying Phenotypic Traits in Retinal Coronary Angiography: Automated Extraction of Retinal Vasular Networks and Localization of Optic Discs in Fundus Images

Hesam Dashti, James Driver, Nader Sheibani, Amir Assadi

Common-Path Fourier-Domain Optical Coherence Tomography using Surface Tracking Algorithm

Chul-Gyu Song, K. S. Kim, M. H. Kim, Sang-Hun Ryu, J. H. Seo

Registration of Confocal Fluorescence Endomicroscopy Images Using Phase Correlation

Feng Zhao, T. M. McGinnity

Signal Processing Algorithm for Wireless ECG Monitoring Systems

Abishek Thekkeyil Kunnath, Sahajhaksh Hariharan, Maneesha Vinodini Ramesh

Tracking of Active Cells Based on Kalman Filter in Time Lapse of Image Sequences of Neuron Stem Cells

Chunming Tang, Yanqing Wang, Ying Cui

An Efficient Soft Graph Clustering Method for PPI Networks based on Purifying and Filtering the Coupling Matrix

Ying Liu, Amir Foroushani

BRATUMASS Antenna Positioning Optimization with Genetic Algorithm

Zhongling Han, Zhifu Tao, Meng Yao, Yizhou Yao, Blair Fleet, Erik D. Goodman, John R. Deller

Application of Quarter Iteration of FRFT in BRATUMASS for Weak Signal Extraction

Zhongling Han, Zhifu Tao, Meng Yao, Yizhou Yao, Blair Fleet, Erik D. Goodman, John R. Deller

An X-Ray On Methods Aiming At Arrhythmia Classification In ECG Signals

Eduardo Luz, David Menotti

The Application of the Genetic Algorithm Tool Box at Target Enhancement Processing in Breast Cancer Microwave Imaging

Zhongling Han, Zhifu Tao, Meng Yao, Yizhou Yao, Blair Fleet, Erik D. Goodman, John R. Deller

Vitreous Imaging System - A New Method for Medical Diagnosis

Boucherit Taieb

SESSION: SOFTWARE PACKAGES AND OTHER COMPUTATIONAL TOPICS IN

BIOINFORMATICS + RELATED DISCUSSIONS

A Network of Hidden Markov Models and its Analysis

Liqing Zhang, Layne T Watson, Lenwood S. Heath

Correlation of Patristic Distance with Nominal Specimen Collection Date in Influenza A/H1N1 Neuraminidase-Encoding Segments

Jack Horner

GAPDH Architecture at Low Guanidine Concentrations: First Derivative Analysis of the Descending Slope of the UV Absorbance Peak

Jessica Kim, Christopher Theisen, Norbert Seidler

Instantiation and Adaptation of CRISP-DM to Bioinformatics Computational Processes

Santiago Gonzalez, Victor Robles, Jose Maria Pena, Ernestina Menasalvas

Analysis of Metabolic Networks: On the Similarity of the Three Domains of Life

Karl G Kugler, Laurin AJ Mueller, Matthias Dehmer

Construction and Analysis of Metabolite Network of Arabidopsis thaliana Pathways

Kasthuribai Viswanathan, Nita Parekh

A Professional Science Master Degree in Health Informatics

Kevin Daimi, Gregory Grabowski

Laterality of Motor Control before the Advent of Experimental Psychology: Revisiting David Kinnebrook's 'Error of Judgement' at Greenwich in 1796

Iraj Derakhshan

SESSION: COMPUTER-ASSISTED MEDICAL CARE + SERVICE SYSTEMS, DIAGNOSTIC TOOLS IN BIOMEDICAL, AND COMPUTER-BASED MEDICAL SYSTEMS

Diagnosis of Breast Cancer Using Averaged Proximity Measure between Samples

Roman Andrushkiw, Ekaterina Golubeva, Dmytro Klyushin, Yuri Petunin, Natalya Boroday

An Extensible Software Architecture to Facilitate Disaster Response Planning

Martin O'Neill II, Armin R. Mikler, Tamara Schneider

Computer Modeling of Diffuse Axonal Injury Mechanisms

Igor Szczyrba, Martin Burtscher, Rafal Szczyrba

A Computational Linguistics Approach to the Identification of Biological Factors that Contribute to the Development and Progression of Lung Cancer

Christopher Frenz, Cheng Luo, Egon Urgard, Andres Metspalu

The Living Experience of a Diabetic Adult in India Using Fuzzy Relational Maps (FRM)

Victor Devadoss Anthony Sany, Susanna Mystica Victor Devadoss

SleepGaze: A Wireless System for Monitoring and Detection of Sleep Disorders

K. A. Unnikrishna Menon, Davis Jose, Maneesha V. Ramesh

Doppler Ultrasound Blood Flow Measurement System for Assessing Coronary Revascularization

J Solano, M Fuentes, A Villar, J Prohias, F Garcia-Nocetti

Analysis of Electrogastrograms of the Elderly Subjects using Maximum Lyapunov Exponent - For the Evaluation of Motion Sickness induced by Stereoscopic Movies

Yasuyuki Matsuura, Masaru Miyao, Hiroki Takada

A Personalized Health Information System to Foster Preventive Medicine

Sebastian Klenk, Julia Mohrmann, Andre Burkovski, Jurgen Dippon, Peter Fritz, Gunther Heidemann

A High Throughput Computational Analysis of Claudin Gene Family in Human Ovarian Cancer

Shaukat Iqbal Malik, Sheema Sameen, Zoya Khalid

SESSION: DRUG TARGETS, IMMUNOTHERAPY, AND COMPUTATIONAL METHODS FOR

SYSTEM + MICRO BIOLOGY

Classifying HIV-1 Circulating Recombinant Forms

Steven Eliuk, Keith Ruiter, Pierre Boulanger

Self-Regulating Physiologically Based Pharmacokinetic Model and Creation of Drug Concentration Profiles in Plasma and Tissues

Stanislav Polinkevych

Identifying Co-targets to Fight Drug Resistance Based on a Random Walk Model

Liang-Chun Chen, Hsiang-Yuan Yeh, Cheng-Yu Yeh, Carlos Roberto Arias, Von-Wun Soo

The Rhesus Macaque is Three Times as Diverse but More Closely Equivalent in 'Damaging' Coding Variation as Compared to the Human

Qiaoping Yuan, Zhifeng Zhou, Stephen G. Lindell, J. Dee Higley, Betsy Ferguson, Robert C. Thompson, Juan F. Lopez, Stephen J. Suomi, Basel Baghal, Maggie Baker, Deborah C. Mash, Christina S. Barr, David Goldman

The Peak of a Pandemic? - A Phylogenetic Analysis of the H1N1 Influenza Virus from 2009 to Present

Anthony Deeter, Mark Dalman, Gayathri Nimishakavi, Zhong-Hui Duan

Protease Complement of the Thermophilic Bacterium Coprothermobacter proteolyticus

Hong Cai, Jianying Gu, Yufeng Wang

Computational Analysis on Cuminum Cyminum Compounds Against Aldose Reductase as Anti-diabetic Agents

Naresh Babu Muppalaneni, Appa Rao Allam

Etiology of the Diseases Caused by Bacterium Escherichia Coli According to an Electromagnetic Mode

Juan Esteban Correa Lopez

SESSION: MODELLING, SIMULATION AND OPTIMIZATION OF BIOLOGICAL SYSTEMS

Multi-scale Modelling of the Bile Acid and Xenobiotic System

Noel Kennedy, Paul Thompson, Huiru Zheng, Werner Dubitzky

Computerized Platform for Optimal Organ Allocations in Kidney Exchanges

Yanhua Chen, Jack Kalbfleisch, Yijiang Li, Peter Song, Yan Zhou

Application of Bioinformatics Models to Define Influenza Virus A Subtypes

Mansour Ebrahimi, Parisa Agha-Golzadeh, Esmaeil Ebrahimie, N. Shamabadi

Simulated Docking of Oseltamivir with an Avian Influenza (A/H5N1) Neuraminidase Active Site

Jack Horner

Accelerate Numerical Diffusion Solver of 2D Multi-scale and Multi-resolution Agent-based Brain Cancer Model by Employing Graphics Processing Unit Technology

Beini Jiang, Le Zhang, Wen Zhang, Allan Struthers, Michael Berens, Xiaobo Zhou

EpiGraph: A Scalable Simulation Tool for Epidemiological Studies

Gonzalo Martín, Maria-Cristina Marinescu, David E. Singh, Jesús Carretero

Altered Gliclazide Metabolic Pathway and its Implications on Increased Therapeutic Response in CYP2C9*2: Molecular Dynamics Simulation and Autodock Studies

N Renuka, Hussaina Banu, Geetha Vasanthakumar

Optimizing a Cost Matrix to Solve Rare-Class Biological Problems

Mark J. Lawson, Lenwood S. Heath, Hai Zhao, Liqing Zhang

Flow and Particle Deposition Simulations with Heat-transfer in the Nine-generation Lung Airways

Bela Soni, Naveen Arra, Shahrouz Aliabadi

A Simple Nonadditive Model of Water

Gregory Wood

Modeling as a Tool for Controlling the Production of Biofuels: Ethanol from a Biomass

Aghareed M. Tayeb, N. A. Mostafa, I. A. Ashour

Analytical and Numerical Simulation of Epidemic Models using Maple and Sage

Veronica Orjuela Contreras

Simulating The Reconstruction of Metabolic Networks Using Maple

Diego Ignacio Vélez Jaramillo

Development of a Computing Mmodel for Resistance Screening of Citrus Limon Ccultivars Infected by the Ccausal Aagent of 'Mal secco' Phoma tracheiphila

Khaled Khanchouch, Mohamed R. Hajlaoui, Hakan Kutucu

SESSION: ALGEBRAIC BIOLOGY AND BIOINFORMATICS, ABB

The Genetic Code, 8-Dimensional Hypercomplex Numbers and Dyadic Shifts

Sergey Petoukhov

Alignment-free Phylogenetic Outline of a Random-sequence Library of Non-biological

Proteins

Miguel Jimenez-Montano, Matthew He

Amino Acids, Euclidean Distance and Symmetric Matrix

Matthew He, Miguel Jimenez-Montano, Paolo Ricci

SESSION: PROTEIN STRUCTURE PROCESSING + MACHINE LEARNING + CLASSIFICATION + HPC + MODELING + GENOMICS + CLUSTERING + GENE REGULATORY NETWORKS + HEALTH INFORMATICS + MICROARRAY + BIOINFORMATICS + ASSISTIVE TECHNOLOGY + BIO-INSPIRED SYSTEMS + DATA ANALYSIS

SCOPE: An Open-Source, C++ Implementation for Calculation of Protein Energetics from First Principles

Timothy Matthew Fawcett, Stephanie Irausquin, Mikhail Simin, Homayoun Valafar

Comparative Study of Alternative Energy Functions for the HP Model of Protein Structure Prediction

Mario Garza-Fabre, Gregorio Toscano-Pulido, Eduardo Rodriguez-Tello

EST-PAC^HPC - a Web Portal for High-throughput EST Annotation and Protein Sequence Prediction

Adam Wong, Andrzej Goscinski, Christophe Lefevre

Collagen Type XI alpha-1 Chain Amino Propeptide Structural Model and Glycosaminoglycan Interactions in Silico

Chris Mallory, Owen McDougal, Julia Oxford

Probability Density Profile Analysis: A Method for Identifying Novel Protein Structures

Arjang Fahim, Stephanie Irausquin, Timothy Matthew Fawcett, Mikhail Simin, Homayoun Valafar

Mimicking Transcription Process to Recognise Promoters in E.coli

Sobha Rani Timmappareddy

Bio-Medical Data Integration Based on MetaQuerier Architecture

Khondker Hasan, Munirul Islam, M Samiullah Chowdhury, Eusuf Abdullah Mim, Naieem Khan

Expression Network Analysis of Abiotic Stress Responsive Myb in Rice

Shuchi Smita, Amit Katiyar, Dev Mani Pandey, Viswanathan Chinnusamy, Kailash Chander Bansal

Simplifying Gene Expression Microarray Comparative Analysis

Philip Church, Andrzej Goscinski, Adam Wong, Christophe Lefevre

Comparison of Affymetrix Expression Array Summarization Methods for Reproducibility and Consistency Across Studies

Xiaoyang Ruan, Ourania Kosti, Rado Goldman, Hongfang Liu

Comprehensive Comparison of Gene Set Analysis Tools

Zheng Liu, Xuejun Li, Yate-Ching Yuan, Xiwei Wu

High Performance Grid Computation of the Scattered Field Formulation for Nth Order Debye Modeling of the General Dispersive Media

Haythm Abdallah, Hala Elsadek, Hesham Eldeeb, Nader Bagherzadeh

Criteria for Annihilation of HIV-1 During HAART Therapy

Frank Nani, Mingxian Jin

Stochastic Modelling of Tumour Immune Interactions

K. S. S. Iyer, Swaminathan Sankaran, Rahul Athale

A Gaussian Packing Model For Phasing in Macromolecular Crystallography

Yan Yan, Gregory Chirikjian

Biological Data Handling Methods

Pradeep Achan, Ajit Warrier, Bhadrachalam Chitturi

A Bioinformatics Approach for Identification of Type III Signal Anchored Proteins in Rice

Amit Katiyar, Shuchi Smita, Dev Mani Pandey, Viswanathan Chinnusamy, Kailash Chander Bansal

Application of W-curves and TSP to Clustering HIV1 Sequences

Doug Cork, Steven Lembark, Nelson Michael, Jerome Kim

Electronic Health Records and Mobile Technology Use in Northwest Florida Medical Practices

Edward Rodgers

Anode Effects on Microbial Fuel Cell Efficiency

Michaela Brant, Geoffrey Chu, Mark Claire, Jane Curnutt, Ernesto Gomez, Andrea Gonzalez, Carly Gott, Michael Grigsby, Ruben Hovanesian, George Kaladjian, Jena Losch, Alex Nguyen, Alexandra

Olano, Geoffrey Payton, Amina Razzak, Kara Rotunno, Sarah Saleemi, Allison Scheppelmann, Keith Schubert, Gerardo Solis, Elizabeth Statmore, Kristin Symer

Emerging Viral Agents at Risk in Global Health Approaches to Early Diagnosis and Prompt Therapy

Giulio Tarro, Ciro Esposito

Applications of Aritificial Immune Systems

Suhair Amer

On a Body Sway Model while Maintaining Upright Posture during Exposure to a Stereoscopic Movie on a Liquid Crystal Display

Hiroki Takada, Kazuhiro Fujikake, Masaru Miyao

An Assistive Technology Computer Control System

Eduardo Alberti, Tatiany Kazmieczak , Alessandro Brawerman

A Proposal of a Comperhensive Medical Emergency Decision Support System

Asma AlJarullah, Samir El-Masri

Uncertain Gene Regulatory Networks Simplified by Gramian-Based Approach

Anke Meyer-Baese, Susanne Cappendijk, Fabian Theis