IUP : Intrinsic Unstructured Protein Prediction - A Software Tool

Jack Yang, Mary Yang

Novel Efficient Granular Computing Model for Protein Sequence Motifs and Structure Information Discovery

Bernard Chen, Phang C. Tai, Robert Harrison, Yi Pan

On Integrating Peptide Sequence Analysis and Relational Distance-Based Indexing

Weijia Xu, Rui Mao, Shu Wang, Daniel Miranker

Assessing protein function using a combination of supervised and unsupervised learning

Jack Yang, Mary Yang, Okan K. Ersoy

A Language Modeling Text Mining Approach to the Annotation of Protein Community

Xiaodan Zhang, Daniel Wu, Xiaohua Zhou, Xiaohua Hu

Partition Frequency Distance based Filter Method for Finding Approximate Repetitions in DNA Sequences

Di Wang, Guoren Wang, Baichen Chen, Qingquan Wu, Changyong Yu, Yi Zhao, Ge Yu

Finding Patterns in Biological Sequences by Longest Common Subsequences and Shortest Common Supersequences

Kang Ning, Hoong Kee Ng, Hon Wai Leong

Mining the Database of Transcription Binding Sites

Wei Peng, Tao Li, Giri Narasimhan

Extending Pattern Branching to Handle Challenging Instances

Jaime Davila, Sanguthevar Rajasekaran

Discovering DNA Motifs with Nucleotide Dependency

Francis Chin, Henry Leung

Prediction of labor for pregnant women using high-resolution mass spectrometry data

J-H Oh, J. Gao, A. Nandi, P.Gurnani, P. B.Greenwood, K.P. Rosenblatt

Exploratory Tools for Follow-Up Studies to Microarray Experiments

Kaushik Sinha, Ruoming Jin, Gagan Agrawal, Helen Piontkivska

Mining Positive and Negative Co-regulation Patterns from Microarray Data

Yuhai Zhao, Guoren Wang, Ying Yin, Ge Yu

Building a Classifier for Integrated Microarray Datasets through Two-Stage Approach

Youngmi Yoon, Jongchan Lee, Sanghyun Park

IntClust: A Software Package for Clustering Replicated Microarray Data

Wei Peng, Tao Li

Quick Hierarchical Biclustering on Microarray Gene Expression Data

Liping Ji, Kenneth Mock, Kian-Lee Tan

An improved algorithm for the regular expression constrained multiple sequence alignment problem

Abdullah Arslan, Dan He

Large Grain Size Stochastic Optimization Alignment

Perry Ridge, Hyrum Carroll, Dan Sneddon, Mark Clement, Quinn Snell

Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model

Sakti Pramanik, Qiang Xue, James Cole

A Tool for Supporting Integration Across Multiple Flat-File Datasets

Xuan Zhang, Gagan Agrawal

Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignments

Rimon Mikhaiel, Guohui Lin, Eleni Stroulia

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees

Usman Roshan, Dennis Livesay, Satish Chikkagoudar

Learning the Tree of Phenotypes Using Genomic Data and VISDA

Yuanjian Feng, Zuyi Wang, Yitan Zhu, Jianhua Xuan, David Miller, Robert Clarke, Eric Hoffman, Yue Wang

Visualization of DNA/RNA Structure using Temporal CGRs

Margaret Dunham, Donya Quick, Yuhang Wang, Monnie McGee, Jim Waddle

Isolation and Visualization of Codon Usage Biases

Douglas Raiford, Dan Krane, Travis Doom, Michael Raymer

Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration

Daniel A. Keim, Daniela Oelke, Royal Truman, Klaus Neuhaus

Evidence of Multiple Maximum Likelihood Points for a Phylogenetic Tree

B-B Zhou, M. Tarawneh, D. Chu, P. Wang, C.Wang, A. Zomaya, R.Brent

A New Kernel Method for RNA Classification

Xiaoming Wu, Jason T.L. Wang, Katherine G. Herbert

RADAR: An Interactive Web-Based Toolkit for RNA Data Analysis and Research

Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian, Kaizhong Zhang

Parsimony based approach to test the Evolving Master Gene hypothesis for human Alu repeats

Sridhar Ramachandran, Travis Doom, Michael Raymer, Dan Krane

An algorithm for string edit distance allowing substring reversals

Abdullah Arslan

Unsupervised Gene Selection For High Dimensional Data

Young Bun Kim, Jean Gao

Using Gene Clustering to Identify Discriminatory Genes with Higher Classification Accuracy

Zhipeng Cai, Lizhe Xu, Yi Shi, Mohammad Salavatipour, Randy Goebel, Guohui Lin

Semi-Supervised Clustering Models for Clinical Risk Assessment

Yongyang Huo, Francisco Azuaje, Paul McCullagh, Roy Harper

Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction Networks

Chuan Lin, Daxin Jiang, Aidong Zhang

Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric

Elinor Velasquez, Emmanuel R. Yera, Rahul Singh

Assigning Schema Labels Using Ontology and Hueristics

Xuan Zhang, Ruoming Jin, Gagan Agrawal

Optimal Multi-Objective Control Method for Discrete Genetic Regulatory Networks

Osman Abul, Reda Alhajj, Faruk Polat

Methods for Random Modularization of Biological Networks

Zachary Saul, Vladimir Filkov

Efficient Modularization of Weighted Protein Interaction Networks using k-Hop Graph Reduction

Young-Rae Cho, Woochang Hwang, Aidong Zhang

A Computational Inference Framework for analyzing Gene Regulation Pathway using Microarray Data

D-G Shin, J. Bluis, Y-A Kim, W. Krueger, R.i Nori, N. Viniconis, H-W Wang, A. Wong, D. Rowe

The Automation of SIBIOS Workflow Composition

Xiang Xiao, Malika Mahoui, Zina Ben Miled, Bhavna Choudhury

Using MEDLINE as Standard Corpus for Measuring Semantic Similarity in the Biomedical Domain

Hisham Al-Mubaid, Hoa A. Nguyen

Leveraging Chemical Background Knowledge for the Prediction of Growth Inhibition

Lothar Richter, Stefan Hechtl, Stefan Kramer

A Supervised Learning Approach to Predicting Coronary Heart Disease Complications in Type 2 Diabetes Mellitus Patients

Marisol Giardina, Francisco Azuaje, Paul McCullagh, Roy Harper

Noninvasive Study of the Human Heart using Independent Component Analysis

Yi Zhu, T-L Chen, W. Zhang, T-P Jung, J-R Duann, S. Makeig, C-K Cheng

False Discovery rates in Identifying Functional DNA Motifs

Osman Abul, Geir Kjetil Sandave, Finn Drablos

The Role of Timing in Speech Perception and Speech Production Processes and its Effects on Language Impaired Individuals

Anna Esposito & Nikolaos Bourbakis

Analysis of Invariant Meta-features for Learning and Understanding Disable People’s Emotional Behavior Related to Their Health Conditions

N. Bourbakis ,A. Esposito & D. Kavraki