Preface |
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vi | |
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A Twentieth Anniversary Tribute to PSB |
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1 | (7) |
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CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT "OMICS" DATA |
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8 | (2) |
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Cell Index Database (CELLX): A Web Tool for Cancer Precision Medicine |
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10 | (10) |
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Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors |
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20 | (12) |
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Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors |
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32 | (12) |
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Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma |
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44 | (12) |
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An Integrated Framework for Reporting Clinically Relevant Biomarkers from Paired Tumor/Normal Genomic and Transcriptomic Sequencing Data In Support of Clinical Trials in Personalized Medicine |
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56 | (12) |
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Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials. Gov |
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68 | (12) |
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CANCER PATHWAYS: AUTOMATIC EXTRACTION, REPRESENTATION, AND REASONING IN THE "BIG DATA" ERA |
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80 | (4) |
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Identifying Mutation Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network |
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84 | (12) |
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Binning Somatic Mutations Based on Biological Knowledge for Predicting Survival: An Application in Renal Cell Carcinoma |
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96 | (12) |
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Topological Features in Cancer Gene Expression Data |
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108 | (12) |
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Distant Supervision for Cancer Pathway Extraction from Text |
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120 | (12) |
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Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders |
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132 | (12) |
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Automated Gene Expression Pattern Annotation in the Mouse Brain |
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144 | (12) |
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CHARACTERIZING THE IMPORTANCE OF ENVIRONMENTAL EXPOSURES, INTERACTIONS BETWEEN THE ENVIRONMENT AND GENETIC ARCHTECTURE, AND GENETC INTERACTIONS: NEW METHODS FOR UNDERSTANDING THE ETIOLOGY OF COMPLEX TRAITS AND DISEASE |
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156 | (5) |
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Measures of Exposure Impact Genetic Association Studies: An Example in Vitamin K Levels and VKORC1 |
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161 | (10) |
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A Bipartite Network Approach to Inferring Interactions Between Environmental Exposures and Human Diseases |
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171 | (12) |
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A Screening-Testing Approach for Detecting Gene-Environment Interactions Using Sequential Penalized and Unpenalized Multiple Logistic Regression |
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183 | (12) |
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Variable Selection Method for the Identification of Epistatic Models |
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195 | (12) |
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Genome-Wide Genetic Interaction Analysis of Glaucoma Using Expert Knowledge Derived from Human Phenotype Networks |
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207 | (12) |
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Identification of Gene-Gene and Gene-Environment Interactions Within the Fibrinogen Gene Cluster for Fibrinogen Levels in Three Ethnically Diverse Populations |
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219 | (12) |
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Development of Exposome Correlations Globes to Map Out Environment-Wide Associations |
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231 | (12) |
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Mitochondrial Variation and the Risk of Age-Related Macular Degeneration Across Diverse Populations |
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243 | (12) |
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iPINBPA: An Integrative Network-Based Functional Module Discovery Tool for Genome-Wide Association Studies |
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255 | (12) |
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CROWDSOURCING AND MINING CROWD DATA |
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267 | (3) |
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Reputation-Based Collaborative Network Biology |
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270 | (12) |
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Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts |
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282 | (12) |
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Crowdsourcing Image Annotation for Nucleus Detection and Segmentation in Computational Pathology: Evaluating Experts, Automated Methods, and the Crowd |
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294 | (12) |
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Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance |
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306 | (12) |
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Refining Literature Curated Protein Interactions Using Expert Opinions |
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318 | (12) |
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Crowdsourcing RNA Structural Alignments with an Online Computer Game |
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330 | (12) |
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PERSONALIZED MEDICINE: FROM GENOTYPES, MOLECULAR PHENOTYPES AND THE QUANTIFIED SELF, TOWARDS IMPROVED MEDICINE |
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342 | (5) |
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KLEAT: Cleavage Site Analysis of Transcriptomes |
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347 | (12) |
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Causal Inference in Biology Networks with Integrated Belief Propagation |
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359 | (12) |
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Machine Learning from Concept to Clinic: Reliable Detection of BRAF V600E DNA Mutations in Thyroid Nodules Using High-Dimensional RNA Expression Data |
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371 | (12) |
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A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets |
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383 | (12) |
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Drug-induced mRNA Signatures Are Enriched for the Minority of Genes that Are Highly Heritable |
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395 | (12) |
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An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships |
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407 | (12) |
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PEAX: Interactive Visual Analysis and Exploration of Complex Clinical Phenotype and Gene Expression Association |
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419 | (12) |
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T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes |
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431 | (12) |
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Meta-Analysis of Differential Gene Co-Expression: Application to Lupus |
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443 | (12) |
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Melancholic Depression Prediction by Identifying Representative Features in Metabolic and Microarray Profiles with Missing Values |
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455 | (12) |
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BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data |
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467 | (12) |
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Human Evolutionary Genomics and the Search for the Genes that Made Us Human |
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479 | (3) |
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Discovery Informatics in Biological and Biomedical Sciences: Research Challenges and Opportunities |
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482 | (1) |
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Inviting the Public: The Impact on Informatics Arising from Emerging Global Health Research Paradigms |
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483 | (5) |
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Training the Next Generation of Quantitative Biologists in the Era of Big Data |
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488 | (5) |
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ERRATUM: Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit |
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493 | |