Contents
Committees vii
Referees ix
Preface xi
Keynote Addresses
Exploring the Ocean's Microbes: Sequencing the Seven Seas 1
Marvin E.
Frazier, et. al.
Don’t Know Much About Philosophy: The Confusion Over Bio-Ontologies 3
Mark A. Musen
Invited Talks
Biomedical Informatics
Research Network (BIRN): Building a National Collaboratory for
BioMedical and Brain Research 5
Mark H.
Ellisman
Protein Network Comparative Genomics 7
Trey Ideker
Systems Biology in Two Dimensions: Understanding and Engineering Membranes as Dynamical Systems 9
Eric Jakobsson
Bioinformatics at Microsft Research 11
Simon Mercer
Movie Crunching in Biological Dynamic Imaging 13
Jean-Christophe
Olivo-Marin
Engineering Nucleic Acid-Based Molecular Sensors for Probing and Programming Cellular Systems 15
Christina D.
Smolke
Reactome: A Knowledgebase of Biological Pathways 17
Structural Bioinformatics
Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction 19
Kevin W. DeRonne and George Karypis
Transmembrane Helix and Topology
Prediction Using Hierarchical SVM Classifiers and
an Alternating Geometric Scoring Function 31
Allan Lo, Hua-Sheng Chiu, Ting-Yi Su and Wen-Lian Hsu
Protein Fold Recognition Using the Gradient Boost Algorithm 43
Feng Jiao, Jinbo Xu, Libo Yu and Dale Schuurmans
A Graph-Based Automated NMR Backbone Resonance Sequential Assignment 55
Xiang Wan and Guohui Lin
A Data-Driven, Systematic
Search Algorithm for Structure Determination of
Denatured or Disordered Proteins 67
Lincong Wang and Bruce Randall Donald
Multiple Structure Alignment by Optimal RMSD Implies that the Average Structure is a Consensus 79
Xueyi Wang and
Jack Snoeyink
Identification of α-Helices from Low Resolution Protein Density Maps 89
Alessandro Dal Palu, Enrico Pontelli, Jing He and Yonggang
Lu
Efficient Annotation of Non-coding RNA Structures Including Pseudoknots via Automated Filters 99
Chunmei Liu, Yinglei Song, Ping Hu, Russell L.
Malmberg and Liming Cai
Thermodynamic Matchers: Strengthening the Significance of RNA Folding Energies 111
Thomas Hoechsmann, Matthias Hoechsmann and Robert
Giegerich
Microarray Data Analysis and Applications
PEM: A General Statistical Approach
for Identifying Differentially Expressed Genes
in Time-course cDNA Microarray Experiment without Replicate 123
Xu Han, Wing-Kin Sung and Lin Feng
Efficient Generalized Matrix
Approximations for Biomarker Discovery and Visualization in
Wenyuan Li,
Yanxiong Peng, Hung-Chung Huang, and Ying Liu
Computational Genomics and Genetics
Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) 145
Yufeng Wu and Dan Gusfield
Sorting Genomes by Translocations and Deletions 157
Xingqin Qi, Shuguang Li, Guojun Li and Ying Xu
Turning Repeats To Advantage: Scaffolding Genomic Contigs Using LTR Retrotransposons 167
Ananth Kalyanaraman, Srinivas Aluru and Patrick S.
Schnable
Whole Genome Composition Distance for HIV-1 Genotyping 179
Xiaomeng Wu, Randy Goebel, Xiu-Feng Wan, and Guohui
Lin
Efficient Recursive Linking
Algorithm for Computing the Likelihood of an Order of a Large
Optimal Imperfect Phylogeny Reconstruction and Haplotyping (IPPH) 199
Srinath Sridhar, Guy E. Blelloch, R. Ravi and
Russell Schwartz
Toward an Algebraic Understanding of Haplotype Inference by Pure Parsimony 211
Daniel G. Brown and Ian M. Harrower
Global Correlation Analysis
Between Redundant Probe Sets Using a Large Collection of
Arabidopsis ATH1 Expression Profiling Data 223
Xiangqin Cui and Ann Loraine
Motif Sequence Identification
Jun Huana, Deepak Bandyopadhyaya, Jan Prinsa, Jack
Snoeyinka, Alexander Tropshab and Wei Wang
An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting 239
Xin Chen and Tao Jiang
Detection of Cleavage Sites for HIV-1 Protease in Native Proteins 249
Liwen You
A Methodology for Motif Discovery Employing Iterated Cluster Re-assignment 257
Osman Abul, Geir Kjetil Sandve and Finn Drabløs
Biological Pathways and Systems
Identifying Biological Pathways via Phase Decomposition and Profile Extraction 269
Yi Zhang and Zhidong Deng
Expectation-Maximization Algorithms for Fuzzy Assignment of Genes to Cellular Pathways 281
Liviu Popescu and Golan Yona
Classification of Drosophila
Embryonic Developmental Stage Range Based on Gene
Jieping Ye, Jianhui Chen, Qi Li, and Sudhir Kumar
Evolution versus Intelligent
Design: Comparing the Topology of Protein-Protein Interaction
Qiaofeng Yang, Georgos Siganos, Michalis Faloutsos
and Stefano Lonardi
Protein Functions and Computational Proteomics
Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction 311
Brian Y. Chen, Drew H. Bryant, Viacheslav Y.
Fofanov, David M. Kristensen,
Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge
and
Protein Subcellular Localization Prediction Based on Compartment-Specific Biological Features 325
Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung
and Wen-Lian Hsu
Predicting the Binding Affinity of MHC Class II Peptides 331
Fatih Altiparmak, Altuna Akalin and Hakan Ferhatosmanoglu
Codon-Based Detection of
Positive Selection Can Be Biased by Heterogeneous Distribution of
Polar Amino Acids Along Protein Sequences 335
Xuhua Xia and Sudhir Kumar
Bayesian Data Integration: A Functional Perspective 341
Curtis Huttenhower and Olga Troyanska
An Iterative Algorithm to Quantify the Factors Influencing Peptide Fragmentation for MS/MS Spectrum 353
Chungong Yu, Yu Lin, Shiwei Sun, Zhuo Zhang,
Jinjin Cai, Jingfen Zhang, Runsheng Chen, Dongbo Bu
Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing 361
Changjiang Xu and Bin Ma
Biomedical Applications
Expectation-Maximization Method for Reconstructing Tumor Phylogenies from Single-Cell Data 371
Gregory Pennington, Charles A. Smith,
Simulating In Vitro Epithelial Morphogenesis in Multiple Environments 381
Mark R. Grant, Sean H. J. Kim and C. Anthony Hunt
A Combined Data Mining Approach
for Infrequent Events: Analyzing HIV Mutation Changes
Based on Treatment History 385
Ray S. Lin, Soo-Yon Rhee, Robert W. Shafer, and
Amar K. Das
A Systems Biology Case Study of Ovarian Cancer Drug Resistance 389
Jake Y. Chen, Changyu Shen, Zhong Yan, Dawn P. G.
Brown and Mu Wang
Author Index 399