Program Information

ISBRA08 Program (.pdf)


Tuesday, May 6, 2008  

5:00pm- 7:00pm Registration and Reception Residence Inn Atlanta downtown

 

Wednesday, May 7, 2008  

8:50am- 9:00am Welcome Message ALC005
 
9:00am- 10:00am Plenary Session Chair: Ion Mandoiu ALC005
  Invited Keynote talk: Set-level Analyses for Genome-wide Association Data, Dan Nicolae  
 
10:00am- 10:30am Coffee Break  
 
10:30am- 12:30pm Parallel Sessions  
 
Session 1A: Phylogenetics I ALC005 Chair: Russell Schwartz Session 1B: Sequence Analysis I ALC002 Chair: Giri Narasimhan
Hierarchical Clustering using Constraints, Mariana Kant, Maurice LeBon, David Sankoff Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences, Ankit Agrawal, Volker Brendel, Xiaoqiu Huang
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches, Mukul S. Bansal, Oliver Eulenstein Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition, Ankit Agrawal, Arka Ghosh, Xiaoqiu Huang
A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes, Xintao Wei, Lenore Cowen, Carla Brodley, Arthur Brady, D. Sculley, Donna Slonim Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats, Todd Treangen, Aaron Darling, Mark A. Ragan, Xavier Messeguer
An Approach for Determining Evolutionary Distance in Network-based Phylogenetic Analysis, Tingting Zhou, Keith C.C. Chan, Yi Pan, Zhenghua Wang Improved Alignment of Protein Sequences Based on Common Parts, David Hoksza
 
12:30pm- 2:00pm Lunch  
 
2:00pm- 3:00pm Plenary Session Chair: Alexander Zelikovsky ALC005
  Invited Keynote talk: Computing P-values for Peptide Identifications in Mass Spectrometry, Andrey Gorin  
 
3:00pm- 3:30pm Coffee Break  
 
3:30pm- 5:00pm Parallel Sessions  
 
Session 2A: Phylogenetics II ALC005 Chair: Mariana Kant Session 2B: Sequence Analysis II ALC002 Chair: Luonan Chen
PFP: a Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes, Dongsheng Che, Guojun Li, Shane Jensen, Jun Liu, Ying Xu Physicochemical Correlation Between Amino Acid Sites in Short Sequences under Selective Pressure, David Stiven Campo Rendon, Zoya Dimitrova, Yury Khudyakov
Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure, Leonid Zaslavsky, Tatiana Tatusova HCV Quasispecies Assembly using Network Flows, Kelly Westbrooks, Irina Astrovskaya, David Campo Rendon, Yury Khudyakov, Piotr Berman, Alex Zelikovsky
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution, Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring, Matthew Goto, Eric Schwabe
 
5:00pm- 5:30pm Coffee Break  
5:30pm- 7:00pm Tutorial A (ALC005) Chair: Raj Sunderraman   Poster Session A
 
Comparative Genomic Analysis Giri Narasimhan   An emerging trend in the post-genome sequencing era is the use of high-througput technology to sequence many closely related genomes. Large sequencing centers have started sequencing genomes of interest at an astonishing rate, making it imperative for systematic and comprehensive comparative genomic analyses to be applied. An important goal of comparing a pair (or a set) of entire genomes is to understand the genetic basis of phenotypic differences.   A wide variety of comparative genomics tools exist for the comparison of whole genomes. This tutorial will survey a number of these tools. Comparative genomic analysis is a multi-faceted task and involves the study of many aspects of the genome. We will discuss methods to perform this analysis with the goal of identifying and/or understanding orthologs, synteny, paralogs, insertions and deletions of genomic regions and their characterization, inversions and other genome rearrangements, SNPs, pseudogenes, gene isoforms and alternative splicing, whole genome alignment, phylogenetic analysis, recombination and horizontal gene transfer, functional annotations, gene ontology (GO) and associated issues, metabolic and functional pathways, GC-content and GC-skew, transcription start sites and operons, transcription factors, regulatory elements, transcription factor binding sites, regulons, regulatory networks, protein-protein interaction networks, and much more.

•  A Probabilistic Approach to Inferring Protein Interactions with GO Annotations, Eyad Almasri, Peter Larsen and Yang Dai

•  2LR- Tagging: Linear Regression with Controlled Overfitting, Irina Astrovskaya, Diana Mohan Babu and Alex Zelikovsky

•  Biological Image Segmentation with Wavelets, Evelyn Brannock and Michael Weeks

•  DFT-Based Ab Initio Heuristics for Identifying Coding Regions, Robert Brown, Markus Hitz and Bryson Payne

•  Graph comparison : Homo-Home Morphism in Metabolic Pathways, Qiong Cheng, Robert Harrison and Alex Zelikovsky

•  Construction of Function Regulatory Module using Knowledge Base Gene Classification in Saccharomyces Cerevisiae, SooYoung Cho and YoungSeek Lee

•  Finding Novel Genes and Correcting Annotations through Tandem Mass Spectrometry, Robert Day, Tema Fridman and Andrey Gorin

•  PrimerHunter: A Primer Selection Tool for Avian Influenza Subtype Identification, Jorge Duitama, Mazhar Khan, Ion Mandoiu, Dipu Nair and Craig Nelson

•  Text-Mining: An Automated, Systematic Approach for the Large-Scale Identification of Biological Relationships in Text, Elvena Fong, Guozhen Liu and Xiao Zeng

•  Brain Computer Interfaces, Carson Herrick and Michael Weeks

•  Comparative Genomic Analysis of Transcription Factors in Symbiotic Fungus Laccaria Bicolor and other Pathogenic and Nonpathogenic Basidiomycetes and Ascomycetes, Preti Jain, Gopi Podila and Ramazan Aygun

•  Genotype Error Detection and Imputation using Hidden Markov Models of Haplotype Diversity, Justin Kennedy, Ion Mandoiu and Bogdan Pasaniuc

 

 


Thursday, May 8, 2008
9:00am- 10:00am Plenary Session Chair: Ion Mandoiu ALC005
  Invited Keynote talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies, Andrew Allen  
 
10:00am- 10:30am Coffee Break  
 
10:30am- 12:30pm Parallel Sessions  
 
Session 3A: Biological Networks ALC005 Chair: Raj Sunderraman Session 3B: Microarray Data Analysis ALC002 Chair: Wei Zhong
Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data, Eyad Almasri, Peter Larsen, Guanrao Chen, Yang Dai Mean Squared Residue Based Biclustering Algorithms, Stefan Gremalschi, Gulsah Altun
Integrative Network Component Analysis for Regulatory Network Reconstruction, Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke, Eric Hoffman Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information, Ting Gong, Jianhua Xuan, Li Chen, Rebecca Riggins, Yue Wang, Eric Hoffman, Robert Clarke
A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks, Min Li, Jianxin Wang, Jianer Chen A Novel Measure for Redundant Gene Elimination Based on Discriminative Contribution, Xue-Qiang Zeng, Guo-Zheng Li, Jack Yang, Mary Qu Yang
Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-Occurrence Graph, Alexandre P. Francisco, Arlindo Oliveira, Ana T. Freitas Network-Based Inference of Cancer Progression from Microarray Data, Yongjin Park , Stanley Shackney, Russell Schwartz
 
12:30pm- 2:00pm Lunch  
 
2:00pm- 3:00pm Plenary Session Chair: Robert Harrison ALC005
  Invited Keynote talk: Quiet Revolution: Connectivity in the Cancer Research Community, Kenneth Buetow  
 
3:00pm- 3:30pm Coffee Break  
 
3:30pm- 5:00pm Parallel Sessions  
 
Session 4A: Biomedical Image Processing and Visualization ALC005 Chair: Saeid Belkasim Session 4B: RNA and Protein Structure ALC002 Chair: Sanguthevar Rajasekaran
Wavelet-based 3-D Multifractal Spectrum with Applications in Breast MRI Images, Gordana Derado, Kichun Lee, Orietta Nicolis, F. DuBois Bowman, Mary Newell, Fabrizio F. Rugger, Brani Vidakovic Pattern Matching in RNA Structures, Kejie Li, Reazur Rahman, Aditi Gupta, Prasad Siddavatam, Michael Gribskov
Accurate Inverse Consistent Non-Rigid Image Registration and its Application on Automatic Re-Contouring, Qingguo Zeng, Yunmei Chen The Use of a Conformational Alphabet for Fast Alignment of Protein Structures, Wei-Mou Zheng
GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies, Matthew Eavenson, Maciej Janik, Shravya Nimmagadda, John Miller, Krys Kochut, William York On-The-Fly Rotamer Pair Energy Evaluation in Protein Design, Andrew Leaver-Fay, Jack Snoeyink, Brian Kuhlman
 
5:00pm- 5:30pm Coffee Break  

 

5:30pm- 7:00pm Tutorial B (ALC005) Chair: Raj Sunderraman   Poster Session B
 
Sequential and Parallel Algorithms for Motif Search Sanguthevar Rajasekaran   The problem of identifying meaningful patterns (i.e., motifs) from biological data has been studied extensively due to its paramount importance. Motifs are fundamental functional elements in proteins vital for understanding gene function, human disease, and identifying potential therapeutic drug targets. Several versions of the motif search problem have been identified in the literature. In this tutorial we focus on three such versions, namely, simple motif search, planted (l, d)-motif search and edit-distance based motif search. Numerous sequential and parallel algorithms have been proposed for these three versions. In this talk we survey some of these algorithms.

•  Non-Parametric Clustering for Studying RNA Conformations, Xavier Le Faucheur, Eli Hershkovits, Rina Tannenbaum and Allen Tannenbaum

•  A Clustering-Based Approach for Filtering False Positive MicroRNA Candidates, Wing-Sze Leung, Marie C. M. Lin, David W. Cheung and S. M. Yiu

•  From Gene Sequence to Protein Function: 3D Metal-Binding-Site Predictions from Translated DNA Sequences, Ronen Levy, Marvin Edelman and Vladimir Sobolev

•  Choice of Distance Measures for Detecting Horizontal Gene Transfer, Hua Li, Lavanya Kannan and Arcady Mushegian

•  Bivariate Genome-wide Association Analysis to Determine Genetic Variants of Drug Response, Hua Li and Dongxiao Zhu

•  Self-Organizing Maps for Haplotype Assembly from SNP Fragments, Zhenping Li, Rui-Sheng Wang and Luonan Chen

•  Text-Mining Guided Rescue of Transcription Factor Binding Sites Missed in UCSC Predictions, Guozhen Liu, Elvena Fong and Xiao Zeng

•  Phylogenomics of Metazoans Based on SVD Analysis, Arun Seetharam and Gary Stuart

•  Error Tolerant Sibship Reconstruction in Wild Populations, Saad Sheikh, Tanya Berger-Wolf, Mary Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse and Bhaskar DasGupta

•  Implementation of HL7 Application Programming Interface using LabVIEW, Dong Ik Shin and Soo Jin Huh

•  A Quantile Approach to Analyzing Differential Methylation Hybridization (DMH) Microarrays, Shuying Sun, Dustin Potter, Pearlly Yan, Tim Huang and Shili Lin •  Distance-Dependent

Bayesian Potentials for Protein Docking, Xiuping Tao, Andrew J. Bordner, Thomas Schulthess and Andrey Gorin

 

7:00pm- 9:00pm Banquet Atlanta Marriott Downtown

 

 
Friday, May 9, 2008

9:00am- 10:00am Plenary Session Chair: Alexander Zelikovsky ALC005
  Invited Keynote talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling, Yury Khudyakov  
 
10:00am- 10:30am Coffee Break  
 
10:30am- 12:30pm Parallel Sessions  
 
Session 5A: Clustering & Classification ALC005 Chair: Yanqing Zhang Session 5B: ODGEA Session I ALC002 Chair: Radha Krishna Murthy Karuturi
Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction, Shibinn Qiu, Terran Lane ODGEA Opening Remarks
Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients, Wei Zhong, Rick Chow, Richard Stolz, Jieyue He, Marsha Dowell A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling, Huimin Geng, Hesham Ali, Wing Chan
Computational Mutagenesis of E. coli Lac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity, Majid Masso, Kahkeshan Hijazi, Nida Parvez, Iosif Vaisman Evolutionary Algorithm for Feature Subset Selection in Predicting Tumor Outcomes using Microarray Data, Qihua Tan, Mads Thomassen, Kirsten Jochumsen, Jing Hua Zhao, Kaare Christensen, Torben Kruse
Evaluating Genetic Algorithms in Protein-Ligand Docking, Rafael Ordog, Vince Grolmusz Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data, Peter Larsen, Eyad Almasri, Guanrao Chen, Yang Dai
 
12:30pm- 2:00pm Lunch  
 
2:00pm- 3:00pm Plenary Session Chair: Yi Pan ALC005
  Invited Keynote talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments, Kwok Tsui  
 
3:00pm- 3:30pm Coffee Break  
 
3:30pm- 5:00pm Parallel Sessions  
 
Session 6A: Databases & Software Tools ALC005 Chair: Jing Li Session 6B: ODGEA Session II ALC002 Chair: Qihua Tan
Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI, Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis, Juntao Li, Jianhua Liu, Radha Krishna Murthy Karuturi
Supporting Computational Systems Science: Genomic Analysis Tool Federations using Aspects and AOP, David Stotts, Keith Lee, Ivan Rusyn Bagging Multiple Comparisons from Microarray Data, Dimitris Politis
BioDQ: Data Quality Estimation and Management for Genomics Databases, Alexandra Martinez, Joachim Hammer, Sanjay Ranka Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products, Shandar Ahmad
   

News


Poster submission deadline is extended to March 28, 2008.

Registration is open. Each paper requires one FULL registration by February 19, 2008.

The 1st International Workshop on Optimal Data Mining in Gene Expression Analysis (ODGEA 2008) will be held in conjunction with ISBRA 2008, for details please visit the ODGEA 2008 website.

ISBRA 2008 will be held on May 6-9, 2008 at Georgia State University in Atlanta, GA.

ISBRA 2008 keynote speakers:

Andrew Scott Allen

Kenneth Buetow

Andrey Gorin

Yury Khudyakov

Dan Nicolae

Kwok Tsui

Tutorials:

Giri Narasimhan

Sanguthevar Rajasekaran

Important Dates


Poster submission deadline: March 28, 2008.

Paper submission deadline:

December 21, 2007 (main symposium)

January 14, 2008 (ODGEA 2008)

Notification of acceptance for papers:
January 25, 2008

Final version submission: February 15, 2008

Sponsors


GSU Department of Computer Science

GSU Biomedical Computational Center

GSU Molecular Basis of Disease Program

GSU Student Chapter of ACM