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Pacific Symposium on Biocomputing 2017 : Kohala Coast, Hawaii, USA, 4-8 January 2017 / edited by Russ B. Altman ... [et al.]. -- Boca Raton, FL ; London : CRC Press, 2017 .—(58.1057/P117/2017) |
Contents
Preface vii
COMPUTATIONAL
APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION
Session
Introduction 1
Identification
and Analysis of Bacterial Genomic Metabolic Signatures
When
should we NOT transfer functional annotation between sequence paralog$ ?
ProSNet:
integrating homology with molecular networks for protein function
prediction 27
On the
power and limits of sequence similarity based clustering of proteins into families 39
IMAGING
GENOMICS
Session
Introduction
Adaptive
testing of SNP-brain functional connectivity association via a modular network
analysis 58
Exploring
Brain Transcriptomic Patterns: A Topological Analysis Using Spatial Expression
Networks 70
Integrative
Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated
with Genetic Variations 82
Identification
of Discriminative Imaging Proteomics Associations in Alzheimer's Disease via a
Novel Sparse Correlation Model 94
Enforcing
Co-expression in Multimodal Regression Framework 105
METHODS
TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH
Session Introduction 117
Exploring
the Reproducibility of Probabilistic Causal Molecular Network Models 120
Reproducible
Drug Repurposing: When Similarity Does Not Suffice 132
Empowering
Multi-Cohort Gene Expression Analysis to Increase Reproducibility 144
Rabix:
An Open-Source Workflow Executor Supporting Recomputability and Interoperability
of
Work: flow
Descriptions 154
Data
Sharing and Reproducible Clinical Genetic Testing: Successes and
Challenges 166
PATTERNS
IN BIOMEDICAL DATA-HOW DO WE FIND THEM?
Session
Introduction 177
Learning
Attributes of Disease Progression from Trajectories of Sparse Lab Values 184
Computer
Aided Image Segmentation and Classification for Viable and Non-Viable Tumor
Identification in Osteosarcoma 195
Missing
Data Imputation in the Electronic Health Record Using Deeply Learned Autoencoders 207
A Deep
Learning Approach for Cancer Detection and Relevant Gene Identification 219
Development
and Performance of Text-Mining Algorithms to Extract Socioeconomic Status from
De-Identified Electronic Health Records
230
Genome-Wide
Interaction with Selected Type 2 Diabetes Loci Reveals Novel Loci for Type 2
Diabetes in African Americans 242
Deep
Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep
Neural Networks 254
Meta-Analysis
of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD
Disease Status 266
Predictive
Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide
Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort 276
Learning
Parsimonious Ensembles for Unbalanced Computational Generates Problems 288
Methods
for Clustering Time Series Data Acquired from Mobile Health Apps 300
A New
Relevance Estimator for the Compilation and Visualization of Disease Patterns
and Potential Drug Targets 312
Network
Map of Adverse Health Effects Among Victims of Intimate Partner Violence 324
Discovery
of Functional and Disease Pathways by Community Detection in Protein-Protein
Interaction Networks 336
PRECISION
MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY
Session Introduction 348
Opening
the Door to the Large Scale Use of Clinical Lab Measures for Association
Testing: Exploring Different Methods for Defining Phenotypes 356
A
Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg Equilibrium 368
Temporal
Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of
Diabetes and Sleep Apnea 380
MicroRNA-Augmented
Pathways (mirAP) and Their Applications to Pathway Analysis and Disease Subtyping 390
Frequent
Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with
Frequently Dysregulated Disease Pathways and Predicts prognosis 402
Human
Kinases Display Mutational Hotspots at Cognate Positions Within Cancer 414
MUSE: A
Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction 426
ceRNA
Search Method Identified a MET-activated Subgroup Among EGFR DNA Amplified Lung
Adenocarcinoma Patients 438
Improved
Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data when Using
Gene Activity State Estimates 449
methylDMV:
Simultaneous Detection of Differential DNA Methylation and Variability with
Confounder Adjustment 461
Identify
Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and
Cancer Somatic Mutations 473
Identifying
Cancer Specific Metabolic Signatures Using Constraint-Based Models 485
Differential
Pathway Dependency Discovery Associated with Drug Response across Cancer Cell
Lines 497
A
Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk
Scores and Identifying Disease Targets in Clear Cell Kidney Cancer 509
De Novo
Mutations in Autism Implicate the Synaptic Elimination Network
Identifying
Genetic Associations with Variability in Metabolic Health and Blood Count
Laboratory Values: Diving into the Quantitative Traits by Leveraging
Longitudinal Data from an EHR 533
Strategies
for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African
American Individuals in a Clinical Population
SINGLE-CELL
ANALYSIS AND MODELLING OF CELL POPULATION
Session
Introduction 557
Production
of a Preliminary Quality Control Pipeline for Single Nuclei RNA-Seq and Its
Application in the Analysis of Cell Type Diversity of Post-Mortem Human Brain
Neocortex 564
Tracing
Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome
Trajectories 576
An
Updated Debarcoding Tool for Mass Cytometry with Cell Type-Specific and Cell
Sample-Specific Stringency Adjustment
588
Mapping
Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse
Single Cell RNA Sequencing 599
A
Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder
Cancer Metastases to the Lung 611
Scalable
Visualization for High-dimensional Single-cell Data 623
WORKSHOPS
Harnessing
Big Data for Precision Medicine: Infrastructures and Applications 635
The
Training of Next Generation Data Scientists in Biomedicine 640
No-Boundary
Thinking in Bioinformatics 646
Open
Data for Discovery Science 649
