3rd International Conference on Bioinformatics and Computational Biology

Proceedings of 3rd International Conference on Bioinformatics and Computational Biology (BICOB 2011)

March 23 - 25, 2011
New Orleans, Louisiana, USA

1A: Gene & protein

Improving Transmembrane Protein Prediction by Increasing the Utilization of Local Information
Colin Kern, Li Liao, and K. Vijay-Shanker (University of Delaware, USA)

Evolutionary Algorithm for Predicting All-Atom Protein Structure.
Nashat Mansour, Iman Ghalayini, Sandra Rizk, and Mirvat El-Sibai (Lebanese American University, Lebanon)

AlienG: An Effective Computational Tool for Phylogenomic Identification of Horizontally Transferred Genes.
Jing Tian, Guiling Sun, Qin Ding, Jinling Huang, Shravanth Oruganti, and Boya Xie (East Carolina University, USA)

1B: Microarray Research and Applications

A Statistical Model for Microarrays and Optimal Detection Techniques.
Majid I. Alsagabi and Ahmed H. Tewfik (University of Minnesota, USA)

A Novel Analysis Tool to Interpret Microarray Results Using Multiple Gene Annotation.
Maakazu Umezawa (Tokyo University of Science, Japan), Miho Sera (R3 Institute Ltd. And National Institute of Advanced Industrial Science and Technology, Japan), and Ken Takeda (Tokyo University of Science, Japan)

Identification of Salt Tolerance Genes in Rice from Microarray Data using SVM-RFE.
Juexin Wang, Fan Zhang, Yan Wang, Yuan Fu (Jilin University, China), Dong Xu (Jilin University, China and University of Missouri, Columbia, USA), and Yanchun Liang (Jilin University, China)

2A: Disease and Drug

Drug Combination, The Design and Problem Landscape.
Waree Rinsurongkawong and Marc Garbey (University of Houston, USA) and Ralph G. Zinner (MD Anderson Cancer Center, USA)

Molecular Dynamics-based Computational Study on Non-Traditional Particle Modles for Improved Drug Delivery Rates
Y.J. Lin & C.J. Soong (University of Texas at Tyler)

Similarity and Prioritization of Disease Proteins using Path Length Measure.
Anurag Nagar and Hisham Al-Mubaid (University of Houston-Clear Lake, USA)

Computational Modeling of Breast Conserving Surgery: a Cosmetic Outcome Indicator from Virtual Surgery.
David Thanoon and Marc Garbey (University of Houston, USA) and Barbara Bass (The Methodist Hospital Research Institute, USA)

2B: Biological and Regulatory Networks

Community Detection in Biological Networks using a Variational Bayes Approach.
Tejaswini Narayanan and Shankar Subramaniam (University of California, San Diego, USA)

On the Predecessor Problem in Boolean Network Models of Regulatory Networks.
Johannes Georg Klotz, Steffen Schober and Martin Bossert (Ulm University, Germany)

A Scalable Information Theory Based Gene Regulatory Network Inference Method from Time Series and Knock-Out Data.
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri (The University of Southern Mississippi, USA) and Edward J. Perkins (U.S. Army Engineer Research and Development Center, USA)

DMPFinder - Finding Differentiating Pathways with Gaps from Two Goups of Metabolic Networks.
Henry C.M. Leung, S.Y. Leung, Carlos L. Xiang, S.M. Yiu, and Francis Y.L. Chin (The University of Hong Kong, Hong Kong)

3A: Machine Learning

MSubCellProt: Predicting Protein Multiple Subcellular Localization using Machine Learning.
Prabha Garg, Anju Sharma, Rajender Kumar, Pawan Gupta, and Nilanjan Roy (National Institute of Pharmaceutical Education and Research, India)

TAC-ELM: Metagenomic Taxonomic Classification with Extreme Learning Machines.
Zeehasham Rasheed and Huzefa Rangwala (George Mason University, USA)

An Efficient Approach for Discovering Interesting Patterns from Biomedical Data.
Raj Singh and Vikas Yadav (University of Houston Clear Lake, USA)

A Learning Approach for Word Sense Disambiguation in the Biomedical Domain.
Hisham Al-Mubaid and Sandeep Gungu (University of Houston-Clear Lake, USA)

3B: Petri Nets Modeling

Krebs Cycle and Glycolysis Petri Net Models and Simulations for Biochemical Education.
Melissa Pegues, Nicholas Drozda, Seung-yun Kim, and Robert Warburton (Shepherd University, USA)

Modeling and Simulation of Steroid Hormone Biosynthesis and Disease State using Petri Nets.
Nicholas Drozda, Melissa Pegues, Seung-yun Kim, and Robert Warburton (Shepherd University, USA)

Modeling and Simulation of Biochemical Processes using Petri Nets: Steroid Hormone Biosynthesis and Action of Aldosterone.
Melissa Pegues, Nicholas Drozda, Seung-yun Kim, and Robert Warburton (Shepherd University, USA)

4A: Bioinformatics Applications

Extracting Family History Diagnosis from Clinical Texts.
Neal Lewis (San Francisco State University, USA), Daniel Gruhl (IBM Almaden Research Center, USA), and Hui Yang (San Francisco State University, USA)

A Systematic Approach to Evaluate Sustained Stochastic Oscillations.
Jorge Julvez (University of Zaragoza, Spain), Marta Kwiatkowska (University of Oxford, UK), Gethin Norman (University of Glasgow, UK), and David Parker (University of Oxford, UK)

Hemodynamic Uncertainties onf Wall Shear Stress in Major Arteries.
Guillaume Tran-Son-Tay and Marc Garbey (University of Houston, USA) and Mark Davies (The Methodist Hospital, USA)

A Novel Multi-GPU Neural Simulator.
Corey Thibeault, Roger Hoang, and Frederick C. Harris Jr. (University of Nevada, Reno, USA)

4B: Data Mining Applications in Bioinformatics

Mining Temporal Patterns from iTRAQ Mass Spectrometry(LC-MS/MS) Data.
Fahad Saeed, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert (National Institutes of Health, USA)

Multi-layered Vector Spaces for Classifying and Analyzing Biological Sequences.
Can Akkoc (The Middle East Technical University, Turkey), Tom Johnsten (University of South Alabama, USA) and Ryan Benton (University of Louisiana at Lafayette, USA)

M-Fish Image Analysis with Improved Adaptive Fuzzy C-Means Clustering Based Segmentation and Sparse Representation Classification.
Hongbao Cao and Yu-Ping Wang (Tulane University, USA)

Integrated Analysis of Gene Expression and Copy Number Data using Sparse Representation Based Clustering Model.
Hongbao Cao and Yu-Ping Wang (Tulane University, USA)

5A: DNA and RNA

A Scalable Method for Identifying DNA Substrings Using Functions.
Pragyan P. Mohanty and Spyros Tragoudas (Southern Illinois University, USA)

An Information Theoretic Approach for the Analysis of RNA and DNA Binding Sites.
Sheng Li and Huzefa Rangwala (George Mason University, USA)

Profiling Microbial Communities using SSU rRNA Sequence and LH-PCR Data.
Nuttachat Wisittipanit, Huzefa Rangwala, Masoumeh Sikaroodi (George Mason University, USA) Ali Keshavarzian, Ece A. Mutlu (Rish University Medical Center, USA), and Patrick Gillevet (George Mason University, USA)

PARSES: A Pipeline for Analysis of RNA-Seq Exogenous Sequences.
Joseph R. Coco (University of New Orleans, USA), Erik K. Flemington (Tulane Cancer Center, USA), and Christopher M. Taylor (University of New Orleans, USA)

A Simple Algorithm for Solving the All-Pairs Minimum Value Cut Problem Using DNA Computing.
Marzieh Khodaee (University of Tehran, Iran), Vahid Hashem and Mohammad Aminisharifabad (University of Saarlandes, Germany)

5B: Data Analysis and Modeling - 1

Identifying and Implementing the Underlying Operators for Nuclear Magnetic Resonance based Metabolomics Data Analysis.
Aswin Manjunatha (Wright State University, USA), Paul Anderson (Wright-Patterson AFB, USA), Ajith Ranabahu and Amith Sheth (Wright State University, USA)

Parallel BLAST Analysis and Performance Evaluation.
Gabriel Silva and Juliana Correa (Federal University of Rio de Janeir-UFRJ, Brazil)

Efficient Parallel Execution of Sequence Similarity Analysis Via Dynamic Load Balancing.
James D. Jackson and Philip J. Hatcher (University of New Hampshire, USA)

Single Nucleotide Polymorphism Detection via Cheminformatics Analysis of Nanopore-Blockades Engineered for Event Transduction.
Stephen Winters-Hilt (University of New Orleans, USA)

6A: Data Analysis and Modeling - 2

EASAL (Efficient Atlasing, Analysis and Search of Molecular Assembly Landscapes).
Aysegul Ozkan and Meera Sitharam (University of Florida, USA)

A Hidden Markov Model Approach to Identifying Novel Functional Modules.
Kris Sankaran (Stanford University, USA) and Siva Sankaran (California State University, Northridge, USA)

Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer.
Haijun Gong, Qinsi Wang, Paolo Zuliani (Carnegie Mellon University, USA), James Faeder (University of Pittsburgh, USA), Michael Lotze (University of Pittsburgh Cancer Institute, USA), and Edmund Clarke (Carnegie Mellon University, USA)

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