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 |
| 3:20–3:50 PM | COFFEE BREAK |
| 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 |
| 3:15–4:00 PM | COFFEE BREAK |
| 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 |
| 9:20–9:50 AM | COFFEE BREAK |
| 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 |
| 3:00–3:45 PM | COFFEE BREAK |
| 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 |