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CSB 2007 On-line Proceedings

Sponsors p. iii

Preface p. vii

Committees p. ix

Referees p. xi

Keynote Addresses

Quantitative Aspects of Gene Regulation in Bacteria: Amplification, Threshold, and Combinatorial Control p. 3
Terry Hwa

Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo p. 5
Julia Zeitlinger, Rob Zinzen, Dmitri Papatsenko, Rick Young, Mike Levine

Invited Talks

Learning Predictive Models of Gene Regulation p. 9
Christina Leslie

The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life p. 11
Kimmen Sjöander

Mapping and Analysis of the Human Interactome Network p. 13
Kavitha Venkatesan

Gene-Centered Protein-Dna Interactome Mapping p. 15
A. J. Marian Walhout


Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-Symmetric Computational Model p. 19
Kang Ning, Hon Wai Leong

Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination p. 31
Wei Zheng, Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg

An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry p. 41
Timothy Lee, Rahul Singh, Ten-Yang Yen, Bruce Macher

Biomedical Applications

Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification p. 55
Xiaoxu Han

Efficient Algorithms for Genome-Wide tagSNP Selection Across Populations via the Linkage Disequilibrium Criterion p. 67
Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang

Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells p. 79
Huiqing Liu, Stephen Dalton, Ying Xu

Pathways, Networks and Systems Biology

Bayesian Integration of Biological Prior Knowledge into the Reconstruction of Gene Regulatory Networks with Bayesian Networks p. 85
Dirk Husmeier, Adriano V. Werhli

Using Indirect Protein-Protein Interactions for Protein Complex Predication p. 97
Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong

Finding Linear Motif Pairs from Protein Interaction Networks: A Probabilistic Approach p. 111
Henry C.M. Leung, M.H. Siu, S.M. Yiu, Francis Y.L. Chin, Ken W.K. Sung

A Markov Model Based Analysis of Stochastic Biochemical Systems p. 121
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajial K. Das

An Information Theoretic Method for Reconstructing Local Regulatory Network Modules from Polymorphic Samples p. 133
Manjunatha Jagalur, David Kulp

Using Directed Information to Build Biologically Relevant Influence p. 145
Arvind Rao, Alfred O. Hero, David J. States, James Douglas Engel

Discovering Protein Complexes in Dense Reliable Neighborhoods of Protein Interaction Networks p. 157
Xiao-Li Li, Chuan-Sheng Foo, See-Kiong Ng

Mining Molecular Contexts of Cancer via In-Silico Conditioning p. 169
Seungchan Kim, Ina Sen, Micheal Bittner


Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA p. 183
Xi Wang, Sanghamitra Bandyopadhyay, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, Xuegong Zhang

Clustering of Main Orthologs for Multiple Genomes p. 195
Zheng Fu, Tao Jiang

Deconvoluting the BAC-Gene Relationships Using a Physical Map p. 203
Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi

A Grammar Based Methodology for Structural Motif Finding in ncRNA Database Search p. 215
Daniel Quest, William Tapprich, Hesham Ali

IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data p. 227
Erliang Zeng, Kalai Mathee, Giri Narasimhan

MANGO: A New Approach to Multiple Sequence Alignment p. 237
Zefeng Zhang, Hao Lin, Ming Li

Learning Position Weight Matrices from Sequence and Expression Data p. 249
Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang

Structural Bioinformatics

Effective Labeling of Molecular Surface Points for Cavity Detection and Location of Putative Binding Sites p. 263
Mary Ellen Bock, Claudio Garutti, Conettina Guerra

Extraction, Quantification and Visualization of Protein Pockets p. 275
Xiaoyu Zhang, Chandrajit Bajaj

Uncovering the Structural Basis of Protein Interactions with Efficient Clustering of 3-D Interaction Interfaces p. 287
Zeyar Aung, Soon-Heng Tan, See-Kiong Ng, Kian-Lee Tan

Enhanced Partial Order Curve Comparison Over Multiple Protein Folding Trajectories p. 299
Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang

fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information p. 311
Huzefa Rangwala, George Karypis

Consensus Contact Prediction by Linear Programming p. 323
Xin Gao, Dongbo Bu, Shuai Cheng Li, Ming Li, Jinbo Xu

Improvement in Protein Sequence-Structure Alignment Using Insertion/Deletion Frequency Arrays p. 335
Kyle Ellrott, Jun-Tao Guo, Victor Olman, Ying Xu

Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction p. 343
Brian Y. Chen, Drew H. Bryant, Amanda E. Cruess, Joseph H. Bylund, Viacheslav Y. Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki

Ontology, Database and Text Mining

An Active Visual Search Interface for Medline p. 359
Weijian Xuan, Manhong Dai, Barbara Mirel, Justin Wilson, Brian Athey, Stanley J. Watson, Fan Meng

Rule-Based Huamn Gene Normalization in Biomedical Text with Confidence Estimation p. 371
William W. Lau, Calvin A. Johnson, Kevin G. Becker

CBioC: Beyond a Prototype for Collaborative Annotation of Molecular Interactions from the Literature p. 381
Chitta Baral, Graciela Gonzalez, Anthony Gitter, Craig Tegarden, Amanda Zeigler, G. Joshi-Topé


Supercomputing with Toys: Harnessing the Power of NVIDIA 8800GTX and Playstation 3 for Bioinformatics Problem p. 387
Justin Wilson, Manhong Dai, Elvis Jakupovic, Stanley Watson, Fan Meng

Exact and Heuristic Algorithms for Weighted Cluster Editing p. 391
Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truß, Sebastian Böcker

Method for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds p. 403
Nikil Wale, George Karypis, Ian A. Watson

Transcriptomics and Phylogeny

Improving the Design of Genechip Arrays by Combining Placement and Embedding p. 417
Ségio Anibal de Carvalho, Sven Rahmann

Modeling Species-Genes Data for Efficient Phylogenetic Inference p. 429
Wenyuan Li, Ying Liu

Reconcilation with Non-Binary Species Trees p. 441
Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand

Author Index p. 453