Conference Program

Wednesday, August 27, 2008
7:00–8:15 AM BREAKFAST and Late Registration
8:15–8:30 AM Opening Remarks
8:30–9:45 AM Session I: Structural Bioinformatics - I
8:30 AM Optimizing Bayes Error for Protein Structure Model Selection by Stability Mutagenesis
Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg
8:55 AM Feedback Algorithm and Web-Server for Protein Structure Alignment
Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa
9:20 AM Predicting Flexible Length Linear B-cell Epitopes
Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar
9:45–10:15 AM COFFEE BREAK
10:15 AM–12:00 PM Session II: Pathways, Networks and Biological Systems
10:15 AM INVITED TALK: Robert Murphy
Carnegie Mellon University
Automated Proteome-Wide Determination and Modeling of Subcellular Location for Systems Biology
10:45 AM Using Relative Importance Methods to Model High-throughput Gene Perturbation Screens
Ying Jin, Naren Ramakrishnan, Lenwood S. Heath, Richard F. Helm
11:10 AM Consistent Alignment of Metabolic Pathways without Abstraction
Ferhat Ay, Tamer Kahveci, Valerie de Crécy-Lagard
11:35 AM Detecting pathways transcriptionally correlated with clinical parameters
Igor Ulitsky, Ron Shamir
12:00–1:30 PM LUNCH - Dohrmann Grove
1:30–2:30 PM POSTER SESSION - Abstracts online
2:30–3:20 PM Session III: Genomics - I
2:30 PM An ORFome Assembly Approach to Metagenomics Sequences Analysis
Yuzhen Ye, Haixu Tang
2:55 PM A Probabilistic Coding Based Quantum Genetic Algorithm for Multiple Sequence Alignment
Hongwei Huo, Vojislav Stojkovic, Qiaoluan Xie, Xubang Shen
3:50–5:30 PM Session IV: Structural Bioinformatics - II
3:50 PM Fast and Accurate Multi-class Protein Fold Recognition with Spatial Sample Kernels
Pavel Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
4:15 PM Designing Secondary Structure Profiles for Fast ncRNA Identification
Yanni Sun, Jeremy Buhler
4:40 PM Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction
Mark Moll, Lydia E. Kavraki
5:05 PM A Hausdorff-Based NOE Assignment Algorithm Using Rotamer Patterns and Protein Backbone Determined from Residual Dipolar Couplings and Rotamer Patterns
Jianyang (Michael) Zeng, Chittaranjan Tripathy, Pei Zhou, Bruce R. Donald
6:00 PM DINNER - Dohrmann Grove



Thursday, August 28, 2008
7:00–8:30 AM BREAKFAST and Late Registration
8:30–9:45 AM Session V: Computational Methods
8:30 AM Knowledge representation and data mining for biological imaging
Wamiq M. Ahmed
8:55 AM Fast Multisegment Alignments for Temporal Expression Profiles
Adam A. Smith, Mark Craven
9:20 AM Graph Wavelet Alignment Kernels for Drug Virtual Screening
Aaron Smalter, Jun Huan, Gerald Lushington
9:45–10:15 AM COFFEE BREAK
10:15–11:50 AM Session VI: Computational Genomics - I
10:15 AM The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid
Chunfang Zheng, P. Kerr Wall, Jim Leebens-Mack, Claude de Pamphilis, Victor A. Albert, David Sankoff
10:40 AM Error Tolerant Sibship Reconstruction in Wild Populations
Saad I. Sheikh, Tanya Y. Berger-Wolf, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta
11:05 AM INVITED TALK: Clyde Hutchison
J. Craig Venter Institute
The quest for a minimal cellular genome: A synthetic genomics approach
11:50 AM–1:15 PM LUNCH - Dohrmann Grove
1:15–2:15 PM POSTER SESSION - Abstracts online
2:15–3:15 PM Session VII
2:15 PM KEYNOTE ADDRESS: Matthew Scott
Stanford University Medical School
Signal Transduction in Development and Cancer
4:00–5:40 PM Session VIII: Proteomics
4:00 PM A Max-Flow Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data
Jianxing Feng, Rui Jiang, Tao Jiang
4:25 PM MSDash: Mass Spectrometry Database and Search
Zhan Wu, Gilles Lajoie, Bin Ma
4:50 PM Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction
Erliang Zeng, Chris Ding, Giri Narasimhan, Stephen R. Holbrook
5:15 PM GaborLocal: Peak Detection in Mass Spectrum by Gabor Filters and Gaussian Local Maxima
Nha Nguyen, Heng Huang, Soontorn Oraintara, An Vo
6:00 PM DINNER - Dohrmann Grove



Friday, August 29, 2008
7:00–8:30 AM BREAKFAST and Late Registration
8:30–9:20 AM Session IX: Genomics - II
8:30 AM Scalable Computation of Kinship and Identity Coefficients on Large Pedigrees
En Cheng, Brendan Elliott, Z. Meral Ozsoyoglu
8:55 AM Voting Algorithms for the Motif Finding Problem
Xiaowen Liu, Bin Ma, Lusheng Wang
9:50–11:40 AM Session X: Structural Bioinformatics - III
9:50 AM INVITED TALK: William Swope
IBM Almaden Research Center
Simulations of Protein Folding on the BlueGene Supercomputer at IBM
10:20 AM Iterative Non-Sequential Protein Structural Alignment
Saeed Salem, Mohammed J. Zaki
10:45 AM Combining Sequence and Structural Profiles for Protein Solvent Accessibility Prediction
Rajkumar Bondugula, Dong Xu
11:10 AM INVITED TALK: Eric Lai
Memorial Sloan-Kettering Cancer Center
Small RNAs in Drosophila
11:40 AM–1:10 PM LUNCH - Dohrmann Grove
1:10–2:10 PM POSTER SESSION - Abstracts online
2:10–3:00 PM Session XI: Computational Genomics - II
2:10 PM On the accurate construction of consensus genetic maps
Yonghui Wu, Timothy J. Close, Stefano Lonardi
2:35 PM Efficient Haplotype Inference from Pedigrees with Missing Data using Linear Systems with Disjoint-Set Data Structures
Xin Li, Jing Li
3:45–4:35 PM Session XII: Structural Bioinformatics - IV
3:45 PM Extensive Exploration of the Conformational Space Improves Rosetta Results for Short Protein Domains
Yaohang Li, Andrew J. Bordner, Yuan Tian, Xiuping Tao, Andrey Gorin
4:10 PM Improving Homology Models for Protein-Ligand Binding Sites
Chris Kauffman, Huzefa Rangwala, George Karypis
4:40 PM Closing Remarks


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