| Preface |
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vii | |
| Committees |
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ix | |
| Referees |
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xi | |
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Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control |
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3 | (2) |
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Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo |
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5 | (4) |
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Learning Predictive Models of Gene Regulation |
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9 | (2) |
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The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life |
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11 | (2) |
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Mapping and Analysis of the Human Interactome Network |
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13 | (2) |
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Gene-Centered Protein-DNA Interactome Mapping |
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15 | (4) |
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Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-Symmetric Computational Model |
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19 | (12) |
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Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination |
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31 | (10) |
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An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry |
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41 | (14) |
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Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification |
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55 | (12) |
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Efficient Algorithms for Genome-Wide tagSNP Selection Across Populations via the Linkage Disequilibrium Criterion |
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67 | (12) |
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Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells |
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79 | (6) |
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Pathways, Networks and Systems Biology |
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Bayesian Integration of Biological Prior Knowledge into the Reconstruction of Gene Regulatory Networks with Bayesian Networks |
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85 | (12) |
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Using Indirect Protein-Protein Interactions for Protein Complex Predication |
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97 | (14) |
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Finding Linear Motif Pairs from Protein Interaction Networks: A Probabilistic Approach |
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111 | (10) |
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A Markov Model Based Analysis of Stochastic Biochemical Systems |
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121 | (12) |
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An Information Theoretic Method for Reconstructing Local Regulatory Network Modules from Polymorphic Samples |
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133 | (12) |
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Using Directed Information to Build Biologically Relevant Influence |
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145 | (12) |
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Discovering Protein Complexes in Dense Reliable Neighborhoods of Protein Interaction Networks |
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157 | (12) |
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Mining Molecular Contexts of Cancer via In-Silico Conditioning |
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169 | (14) |
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Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA |
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183 | (12) |
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Sanghamitra Bandyopadhyay |
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Clustering of Main Orthologs for Multiple Genomes |
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195 | (8) |
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Deconvoluting the BAC-Gene Relationships Using a Physical Map |
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203 | (12) |
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A Grammar Based Methodology for Structural Motif Finding in ncRNA Database Search |
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215 | (12) |
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IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data |
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227 | (10) |
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Mango: A New Approach to Multiple Sequence Alignment |
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237 | (12) |
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Learning Position Weight Matrices from Sequence and Expression Data |
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249 | (14) |
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Structural Bioinformatics |
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Effective Labeling of Molecular Surface Points for Cavity Detection and Location of Putative Binding Sites |
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263 | (12) |
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Extraction, Quantification and Visualization of Protein Pockets |
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275 | (12) |
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Uncovering the Structural Basis of Protein Interactions with Efficient Clustering of 3-D Interaction Interfaces |
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287 | (12) |
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Enhanced Partial Order Curve Comparison Over Multiple Protein Folding Trajectories |
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299 | (12) |
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fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information |
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311 | (12) |
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Consensus Contact Prediction by Linear Programming |
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323 | (12) |
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Improvement in Protein Sequence-Structure Alignment Using Insertion/Deletion Frequency Arrays |
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335 | (8) |
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Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction |
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343 | (16) |
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Ontology, Database and Text Mining |
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An Active Visual Search Interface for Medline |
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359 | (12) |
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Rule-Based Huamn Gene Normalization in Biomedical Text with Confidence Estimation |
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371 | (10) |
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CBioC: Beyond a Prototype for Collaborative Annotation of Molecular Interactions from the Literature |
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381 | (6) |
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Supercomputing with Toys: Harnessing the Power of NVIDIA 8800GTX and Playstation 3 for Bioinformatics Problem |
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387 | (4) |
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Exact and Heuristic Algorithms for Weighted Cluster Editing |
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391 | (12) |
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Method for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds |
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403 | (14) |
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Transcriptomics and Phylogeny |
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Improving the Design of Genechip Arrays by Combining Placement and Embedding |
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417 | (12) |
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Sergio Anibal de Carvalho Jr. |
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Modeling Species-Genes Data for Efficient Phylogenetic Inference |
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429 | (12) |
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Reconcilation with Non-Binary Species Trees |
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441 | (12) |
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| Author Index |
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453 | |
