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FRONT MATTER
| i |
| Keynote Address |
QUANTITATIVE ASPECTS OF GENE REGULATION IN BACTERIA: AMPLIFICATION, THRESHOLD, AND COMBINATORIAL CONTROL
Terry Hwa | 3 |
WHOLE-GENOME ANALYSIS OF DORSAL GRADIENT THRESHOLDS IN THE DROSOPHILA EMBRYO
Julia Zeitlinger, Rob Zinzen, Dmitri Papatsenko, Rick Young and Mike Levine | 5 |
| Invited Talks |
LEARNING PREDICTIVE MODELS OF GENE REGULATION
Christina Leslie | 9 |
THE PHYLOFACTS PHYLOGENOMIC ENCYCLOPEDIAS: STRUCTURAL PHYLOGENOMIC ANALYSIS ACROSS THE TREE OF LIFE
Kimmen Sjölander | 11 |
MAPPING AND ANALYSIS OF THE HUMAN INTERACTOME NETWORK
Kavitha Venkatesan | 13 |
GENE-CENTERED PROTEIN-DNA INTERACTOME MAPPING
A. J. Marian Walhout | 15 |
| Proteomics |
ALGORITHM FOR PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY BASED ON BETTER PREPROCESSING AND ANTI-SYMMETRIC COMPUTATIONAL MODEL
Kang Ning and Hon Wai Leong | 19 |
ALGORITHMS FOR SELECTING BREAKPOINT LOCATIONS TO OPTIMIZE DIVERSITY IN PROTEIN ENGINEERING BY SITE-DIRECTED PROTEIN RECOMBINATION
Wei Zheng, Xiaoduan Ye, Alan M. Friedman and Chris Bailey-Kellogg | 31 |
AN ALGORITHMIC APPROACH TO AUTOMATED HIGH-THROUGHPUT IDENTIFICATION OF DISULFIDE CONNECTIVITY IN PROTEINS USING TANDEM MASS SPECTROMETRY
Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher | 41 |
| Biomedical Application |
CANCER MOLECULAR PATTERN DISCOVERY BY SUBSPACE CONSENSUS KERNEL CLASSIFICATION
Xiaoxu Han | 55 |
EFFICIENT ALGORITHMS FOR GENOME-WIDE TAGSNP SELECTION ACROSS POPULATIONS VIA THE LINKAGE DISEQUILIBRIUM CRITERION
Lan Liu, Yonghui Wu, Stefano Lonardi and Tao Jiang | 67 |
TRANSCRIPTIONAL PROFILING OF DEFINITIVE ENDODERM DERIVED FROM HUMAN EMBRYONIC STEM CELLS
Huiqing Liu, Stephen Dalton and Ying Xu | 79 |
| Pathways, Networks and Systems Biology |
BAYESIAN INTEGRATION OF BIOLOGICAL PRIOR KNOWLEDGE INTO THE RECONSTRUCTION OF GENE REGULATORY NETWORKS WITH BAYESIAN NETWORKS
Dirk Husmeier and Adriano V. Werhli | 85 |
USING INDIRECT PROTEIN-PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION
Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong and Limsoon Wong | 97 |
FINDING LINEAR MOTIF PAIRS FROM PROTEIN INTERACTION NETWORKS: A PROBABILISTIC APPROACH
Henry C. M. Leung, M. H. Siu, S. M. Yiu, Francis Y. L. Chin and Ken W. K. Sung | 111 |
A MARKOV MODEL BASED ANALYSIS OF STOCHASTIC BIOCHEMICAL SYSTEMS
Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal K. Das | 121 |
AN INFORMATION THEORETIC METHOD FOR RECONSTRUCTING LOCAL REGULATORY NETWORK MODULES FROM POLYMORPHIC SAMPLES
Manjunatha Jagalur and David Kulp | 133 |
USING DIRECTED INFORMATION TO BUILD BIOLOGICALLY RELEVANT INFLUENCE NETWORKS
Arvind Rao, Alfred O. Hero, III, David J. States and James Douglas Engel | 145 |
DISCOVERING PROTEIN COMPLEXES IN DENSE RELIABLE NEIGHBORHOODS OF PROTEIN INTERACTION NETWORKS
Xiao-Li Li, Chuan-Sheng Foo and See-Kiong Ng | 157 |
MINING MOLECULAR CONTEXTS OF CANCER VIA IN-SILICO CONDITIONING
Seungchan Kim, Ina Sen and Michael Bittner | 169 |
| Genomics |
PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA
Xi Wang, Sanghamitra Bandyopadhya, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang and Xuegong Zhang | 183 |
CLUSTERING OF MAIN ORTHOLOGS FOR MULTIPLE GENOMES
Zheng Fu and Tao Jiang | 195 |
DECONVOLUTING THE BAC-GENE RELATIONSHIPS USING A PHYSICAL MAP
Yonghui Wu, Lan Liu, Timothy J. Close and Stefano Lonardi | 203 |
A GRAMMAR BASED METHODOLOGY FOR STRUCTURAL MOTIF FINDING IN ncRNA DATABASE SEARCH
Daniel Quest, William Tapprich and Hesham Ali | 215 |
IEM: AN ALGORITHM FOR ITERATIVE ENHANCEMENT OF MOTIFS USING COMPARATIVE GENOMICS DATA
Erliang Zeng, Kalai Mathee and Giri Narasimhan | 227 |
MANGO: A NEW APPROACH TO MULTIPLE SEQUENCE ALIGNMENT
Zefeng Zhang, Hao Lin and Ming Li | 237 |
LEARNING POSITION WEIGHT MATRICES FROM SEQUENCE AND EXPRESSION DATA
Xin Chen, Lingqiong Guo, Zhaocheng Fan and Tao Jiang | 249 |
| Structural Bioinformatics |
EFFECTIVE LABELING OF MOLECULAR SURFACE POINTS FOR CAVITY DETECTION AND LOCATION OF PUTATIVE BINDING SITES
Mary Ellen Bock, Claudio Garutti and Concettina Guerra | 263 |
EXTRACTION, QUANTIFICATION AND VISUALIZATION OF PROTEIN POCKETS
Xiaoyu Zhang and Chandrajit Bajaj | 275 |
UNCOVERING THE STRUCTURAL BASIS OF PROTEIN INTERACTIONS WITH EFFICIENT CLUSTERING OF 3-D INTERACTION INTERFACES
Z. Aung, S.-H. Tan, S.-K. Ng and K.-L. Tan | 287 |
ENHANCED PARTIAL ORDER CURVE COMPARISON OVER MULTIPLE PROTEIN FOLDING TRAJECTORIES
Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota and Yusu Wang | 299 |
fRMSDPred: PREDICTING LOCAL RMSD BETWEEN STRUCTURAL FRAGMENTS USING SEQUENCE INFORMATION
Huzefa Rangwala and George Karypis | 311 |
CONSENSUS CONTACT PREDICTION BY LINEAR PROGRAMMING
Xin Gao, Dongbo Bu, Shuai Cheng Li, Ming Li and Jinbo Xu | 323 |
IMPROVEMENT IN PROTEIN SEQUENCE-STRUCTURE ALIGNMENT USING INSERTION/DELETION FREQUENCY ARRAYS
Kyle Ellrott, Jun-tao Guo, Victor Olman and Ying Xu | 335 |
COMPOSITE MOTIFS INTEGRATING MULTIPLE PROTEIN STRUCTURES INCREASE SENSITIVITY FOR FUNCTION PREDICTION
Brian Y. Chen, Drew H. Bryant, Amanda E. Cruess, Joseph H. Bylund, Viacheslav Y. Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge and Lydia E. Kavrak | 343 |
| Ontology, Database and Text Mining |
AN ACTIVE VISUAL SEARCH INTERFACE FOR MEDLINE
Weijian Xuan, Manhong Dai, Barbara Mirel, Justin Wilson, Brian Athey, Stanley J. Watson and Fan Meng | 359 |
RULE-BASED HUMAN GENE NORMALIZATION IN BIOMEDICAL TEXT WITH CONFIDENCE ESTIMATION
William W. Lau, Calvin A. Johnson and Kevin G. Becker | 371 |
CBioC: BEYOND A PROTOTYPE FOR COLLABORATIVE ANNOTATION OF MOLECULAR INTERACTIONS FROM THE LITERATURE
C. Baral, G. Gonzalez, A. Gitter, C. Teegarden, A. Zeigler and G. Joshi-Topé | 381 |
| Biocomputing |
SUPERCOMPUTING WITH TOYS: HARNESSING THE POWER OF NVIDIA 8800GTX AND PLAYSTATION 3 FOR BIOINFORMATICS PROBLEMS
Justin Wilson, Manhong Dai, Elvis Jakupovic, Stanley Watson and Fan Meng | 387 |
EXACT AND HEURISTIC ALGORITHMS FOR WEIGHTED CLUSTER EDITING
Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truß and Sebastian Böcker | 391 |
METHODS FOR EFFECTIVE VIRTUAL SCREENING AND SCAFFOLD-HOPPING IN CHEMICAL COMPOUNDS
Nikil Wale, George Karypis and Ian A. Watson | 403 |
| Transcriptomics and Phylogeny |
IMPROVING THE DESIGN OF GENECHIP ARRAYS BY COMBINING PLACEMENT AND EMBEDDING
Sérgio A. de Carvalho, Jr. and Sven Rahmann | 417 |
MODELING SPECIES-GENES DATA FOR EFFICIENT PHYLOGENETIC INFERENCE
Wenyuan Li and Ying Liu | 429 |
RECONCILIATION WITH NON-BINARY SPECIES TREES
B. Vernot, M. Stolzer, A. Goldman and D. Durand | 441 |
BACK MATTER
| 453 |
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