BICoB-2012 ACCEPTED PAPERS

 

003

A New Approach to RNA Pseudoknot Prediction

Junilda Spirollari, Jason T. L. Wang (New Jersey Institute of Technology, USA), and Shawn Xiong Wang (California State University, USA)

 

103

Gene Selection for Cancer Classification by Multiple PCA with Sparsity

Yanwei Huang (Fuzhou University, China and Virginia Tech, USA), Mingming Liu, Liqing Zhang (Virginia Tech, USA)

 

105

ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing

Mary-Huard, Tristan        

 

107

HSPp-BLAST: Highly Scalable Parallel PSI-BLAST for Very Large-scale Sequence Searches

Bhanu Rekepalli, Aaron Vose and Paul Giblock (University of Tennessee, USA and Oak Ridge National Laboratory, USA)

 

108

GRAAu: Genome Rearrangement Algorithm Auditor

Gustavo Rodrigues Galvăo and Zanoni Dias (University of Campinas, Brazil)

 

109

Detecting STR Peaks in Degraded DNA Samples

Emanuela Marasco, Arun Ross, Jeremy Dawson, Tina Moroose, and Tanya Ambrose (West Virginia University, USA)

 

110

SMAlign: Alignment of DNA Sequences with Gap Constraints

Faisal Alobaid, Kishan Mehrotra, Chilukuri Mohan and Ramesh Raina (Syracuse University, USA)

 

 

111

On the Performance of Sorting Permutations by Prefix Operations

Gustavo Rodrigues Galvăo and Zanoni Dias (University of Campinas, Brazil)

 

112

Histogram Difference String Distance for Enhancing Ontology Integration in Bioinformatics

Alex Rudniy, James Geller and Min Song (New Jersey Institute of Technology, USA)

 

114

Efficient Algorithm for Restricted LCS Problem

Effat Farhana (Bangladesh University of Engineering and Technology and Ahsanullah University of Science and Technology,, Bangladesh), and M. Sohel Rahman (Ahsanullah University of Science and Technology, Bangladesh)

 

115

Directed Dot Plots - Enhancing Sequence Alignments with Principles of Perception

David Cox (Independent Researcher, Raleigh, NC, USA)

 

116

New Algorithm for Selecting Degenerate Primers to Clone DNA using a Short Peptide Sequence

Farag A. Elshaari, Fatum A. Elshaari, and Mohamed A. Elshaari (University of Benghazi, Libya)

 

117

Automating Mass Spectrometry Proteomics Analysis

Xian Yang, Yike Guo (Imperial College London, UK), Paul Skipp (University of Southampton, UK), and Anthony Rowe (Imperial College London, UK)

 

120

Applying Feature-Based Resampling to Protein Structure Prediction

Trent Higgs, Bela Stantic (Griffith University, Australia), Md Tamjidul Hoque (IUPUI, USA), and Abdul Sattar (Griffith University, Australia and NICTA Queensland Research Laboratory, Australia)

 

121

Global Alignment of Protein-Protein Interaction Networks for Analyzing Evolutionary Changes of Network Frameworks

Aika Terada and Jun Sese (Tokyo Institute of Technology, Japan)

 

122

Analysis of Functional Linkages between Nucleosome Dynamics and Trans-regulatory Factors

Bich Hai Ho, Ngoc Tu Le, and Tu Bao Ho (JAIST, Japan)

 

123

Transcriptional Analysis of Messanger-RNA and Micro-RNA Array Data Reveals Global Negative Correlation in Human Stem Cell Derived Cardiomyocyte Clusters

Jane Synnergren (University of Skövde, Sweden) and Peter Sartipy (Cellartis AB, Sweden)

 

124

HMM with Mixture as Emission Distribution: Analysis of Differential Expression and Detection of New Transcripts usingTiling Array Data

Caroline Berard               

 

125

Impact of Receptor Clustering on the Membrane-based Stage of a Signalling Pathway

Bertrand R. Caré and Hédi A. Soula (University of Lyon, France)

 

126

An Exact Algorithm for Reconstructing Genomic Scaffolds

Zhihui  Liu (Shandong Institute of Business and Technology, China), Brendan Mumey, Kelly Spendlove, and Binhai Zhu (Montana State University, USA)

 

127

Local Search Techniques for Placing Unique Restriction Sites in Synthetic Genomes

Mahfuza Sharmin, Monjura Afrin, and M. Sohel Rahman (Bangladesh University of Engineering and Technology, Bangladesh)

 

129

Density-based Imputation Method for Fuzzy Cluster Analysis of Gene Expression Microarray Data

Thanh Le, Tom Altman, and Katheleen J. Gardiner (University of Colorado Denver, USA)

 

132

Formal Methods to Specify Crosstalk Among Different Signalling Pathways

Xian Yang and Jeremy T. Bradley (Imperial College London, UK)

 

134

Pairwise Bionetwork Comparisons: A Java Package for Graphs Global Alignment and Local Alignment

Yunkai Liu and Lei Zhang (Gannon University, USA)

 

135

Prediction of Type III Secretion Apparatus in Unannotated Bacterial Genomes

Manonmani Kumar (Duke University, USA), Vineet Sadarangani (Indian Institutes of Science Education and Research, India), Sathish AP Kumar (National University, USA), and Sunando Datta (Indian Institutes of Science Education and Research, India)

 

138

A Provenance Data Model to Manage RNA-SEQ Projects

Renato de Paula, Ruben Cruz Huacarpuma, Maristela T. Holanda, Maria Emilia M. T. Walter (University of Brazil, Brazil)

 

141

Comparative Analysis of Machine Learning Techniques for the Prediction of the DMPK Parameters Intrinsic Clearance and Plasma Protein Binding

Edward Lowe, Jr., Mariusz Butkiewicz, Zollie White III, Matthew Spellings, Albert Omlor, and Jens Meiler (Vanderbilt University, USA)

 

142

Analyzing Memetic Algorithm Behavior in DNA Fragment Assembly Problem for Noisy Data

Jesun Sahariar Firoz, M. Sohel Rahman and Tanay Kumar Saha (Bangladesh University of Engineering and Technology, Bangladesh)

 

143

Finding Collections of Protein Modules in Protein-Protein Interaction Networks

Pierre-Nicolas Mougel, Christophe Rigotti, and Olivier Gandrillon (University of Lyon, France)

 

145

Multifractal analysis and Chaos Game Representation of Human Chromosomes: A Study of Interaction between Chromosomes

Juan Gutierrez Cardenas (University of Helsinki, Finland)

 

147

Topological Properties of the Configuration Spaces of Proteins

Nurit Haspel and Eduardo González (University of Massachusetts Boston, USA)

 

149

A Novel Multivariate Quantification Strategy for Complex Mass Spectrometry Data

Mingon Kang, Dong-Chul Kim, and Jean Gao (University of Texas at Arlington, USA)

 

150

Preliminary Design of a Phylogenetic Query Portal based on Declarative Programming Languages Technology

Brandon Chisham, Hieu Nguyen, Khoi  Nguyen, Enrico Pontelli, and Tran Son (New Mexico State University, USA)

 

151

Comparison of miRNA Target Prediction Algorithms Using Computational Methods

Tamer Ali Aldwairi, Lifang Yan, Kanchana S. Weerasinghe, and Andy D. Perkins (Mississippi State University, USA)

 

152

Dynamics and Docking Simulations of Type I Collagen and Matrix Metalloproteinase 1

Chien M. Nguyen, Xiongwu Wu, and Bernard R. Brooks (NHLBI/NIH, USA)

 

153

A Fully-Integrated Servo Feedback Loop for MICS

Hussain A. Alzaher (King Fahd University of Petroleum & Minerals, Saudi Arabia)

 

155

Mining Maximal-Homogeneous Subnetworks using Protein Interaction Networks and Gene Profiles

Saeed Salem, Shadi Banitaan, Ibrahim Aljarah, and Rami Alroobi (North Dakota State University, USA)

 

156

A Text Mining and Visualization Tool for Generating Protein Interaction Hypothesis

Xiaohui Yuan – coming tomorrow – please include

 

157

A Scalable Method for Arbitrary String Searches in DNA Sequence

Phaninder Alladi, Pragyan P. Mohanty, and Spyros Tragoudas (Southern Illinois University, USA)

 

158

Mapping Biomedical Entities to MeSH to Recognize Hierarchical Relationships

Yan Dong and Hui Yang (San Francisco State University, USA)

 

160

Parallel Algorithm for Center-star Sequence Alignments with Applications to Short Reads

Fahad Saeed (NIH, USA) and Ashfaq A. Khokhar (University of Illinois at Chicago, USA)

 

161

Knowledge-based Consensus Methods for Secondary Structure Prediction of Transmembrane Beta-barrel Proteins

Saad Sheikh (Ecole Polytechnique, France and University of Florida, USA), Van Du T Tran (Ecole Polytechnique, France and University of Evry, France), Philippe Chassignet and Jean-Marc Steyaert (Ecole Polytechnique, France)

 

162

An Algorithm for Combining Graphs Based on Shared Knowledge

Hisham Al-Mubaid and Said Bettayeb (University of Houston-Clear Lake, USA)

 

 

Go back to BICOB-2012 homepage