idekeradmin – UC San Diego

PubMed

A multi-scale map of cell structure fusing protein images and interactions 2021-11-25
The cell is a multi-scale structure with modular organization across at least four orders of magnitude¹. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately^(2,3). Here we integrate immunofluorescence images in the Human Protein Atlas⁴ with affinity […]
Yue Qin
A protein interaction landscape of breast cancer 2021-09-30
[Figure: see text].
Minkyu Kim
Interpretation of cancer mutations using a multiscale map of protein systems 2021-09-30
[Figure: see text].
Fan Zheng
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity 2021-09-30
[Figure: see text].
Danielle L Swaney
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy 2021-09-24
The fate of influenza A virus (IAV) infection in the host cell depends on the balance between cellular defence mechanisms and viral evasion strategies. To illuminate the landscape of IAV cellular restriction, we generated and integrated global genetic loss-of-function screens with transcriptomics and proteomics data. Our multi-omics analysis revealed a subset of both IFN-dependent and […]
Laura Martin-Sancho
Genetic dissection of complex traits using hierarchical biological knowledge 2021-09-17
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical biological knowledge to associate genetic mutations with phenotypic outcomes, yielding substantial predictive power and mechanistic insight. Here, we use […]
Hidenori Tanaka
Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction 2021-08-27
Behaviors and disorders related to self-regulation, such as substance use, antisocial behavior and attention-deficit/hyperactivity disorder, are collectively referred to as externalizing and have shared genetic liability. We applied a multivariate approach that leverages genetic correlations among externalizing traits for genome-wide association analyses. By pooling data from ~1.5 million people, our approach is statistically more powerful […]
Richard Karlsson Linnér
Stress-induced aberrations in sensory processing predict worse cognitive outcomes in healthy aging adults 2021-08-19
It is well recognized that not all individuals age equivalently, with functional dependence attributable, at least in part, to stress accumulated across the lifespan. Amongst these dependencies are age-related declines in cognitive function, which may be the result of impaired inhibitory processing (e.g., sensory gating). Herein, we examined the unique roles of life and biological […]
Rachel K Spooner
A convergent molecular network underlying autism and congenital heart disease 2021-08-19
Patients with neurodevelopmental disorders, including autism, have an elevated incidence of congenital heart disease, but the extent to which these conditions share molecular mechanisms remains unknown. Here, we use network genetics to identify a convergent molecular network underlying autism and congenital heart disease. This network is impacted by damaging genetic variants from both disorders in […]
Sara Brin Rosenthal
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients 2021-07-05
Cell-line screens create expansive datasets for learning predictive markers of drug response, but these models do not readily translate to the clinic with its diverse contexts and limited data. In the present study, we apply a recently developed technique, few-shot machine learning, to train a versatile neural network model in cell lines that can be […]
Jianzhu Ma