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A Fast and Flexible Framework for Network-Assisted Genomic Association
Published in , 1900
Abstract
We present an accessible, fast, and customizable network propagation system for pathway boosting and interpretation of genome-wide association studies. This system — NAGA (Network AssistedGenomic Association) — taps the NDEx biological network resource to gain access to thousands of protein networks and select those most relevant and performative for a specific association study. The method works efficiently, completing genome-wide analysis in under 5 minutes on a modern laptop computer. We show that NAGA recovers many known disease genes from analysis of schizophrenia genetic data, and it substantially boosts associations with previously unappreciated genes such as amyloid beta precursor. On this and seven other gene-disease association tasks, NAGA out-performs conventional approaches in recovery of known disease genes and replicability of results. Protein interactions associated with disease are visualized and annotated in Cytoscape, which, in addition to standard programmatic interfaces, allows for downstream analysis.
Assessing the associations between known genetic variants and substance use in people with HIV in the United States
Published in , 1900
Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior
Published in , 1900
Abstract
Whole-brain recordings give us a global perspective of the brain in action. In this study, we describe a method using light field microscopy to record near-whole brain calcium and voltage activity at high speed in behaving adult flies. We first obtained global activity maps for various stimuli and behaviors. Notably, we found that brain activity increased on a global scale when the fly walked but not when it groomed. This global increase with walking was particularly strong in dopamine neurons. Second, we extracted maps of spatially distinct sources of activity as well as their time series using principal component analysis and independent component analysis. The characteristic shapes in the maps matched the anatomy of subneuropil regions and, in some cases, a specific neuron type. Brain structures that responded to light and odor were consistent with previous reports, confirming the new technique’s validity. We also observed previously uncharacterized behavior-related activity as well as patterns of spontaneous voltage activity.
Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks
Published in , 1900
pyNBS: a Python implementation for network-based stratification of tumor mutations
Published in , 1900
Thousands of missing variants in the UK Biobank are recoverable by genome realignment
Published in , 1900