[2007 Conference Home Page][LSS Home Page]
Sponsors p. iii
Preface p. vii
Committees p. ix
Referees p. xi
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
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
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
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
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
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
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