idekeradmin – UC San Diego

PubMed

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
Unveiling Complexity and Multipotentiality of Early Heart Fields 2021-06-24
Rationale: Extraembryonic tissues, including the yolk sac and placenta, and the heart within the embryo, work to provide crucial nutrients to the embryo. The association of congenital heart defects (CHDs) with extraembryonic tissue defects further supports the potential developmental relationship between the heart and extraembryonic tissues. Although the development of early cardiac lineages has been […]
Qinqguan Zhang
Mapping the multiscale structure of biological systems 2021-06-17
Biological systems are by nature multiscale, consisting of subsystems that factor into progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy, an ever-increasing diversity of technologies can be applied to characterize the corresponding biological units and their relations, resulting in large networks of physical or functional proximities-e.g., proximities of amino […]
Leah V Schaffer
Functional landscape of SARS-CoV-2 cellular restriction 2021-04-30
A deficient interferon (IFN) response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been implicated as a determinant of severe coronavirus disease 2019 (COVID-19). To identify the molecular effectors that govern IFN control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human IFN-stimulated genes (ISGs) on viral […]
Laura Martin-Sancho
Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging 2021-04-06
A growing literature suggests a relationship between HIV-infection and a molecular profile of age acceleration. However, despite the widely known high prevalence of HIV-related brain atrophy and HIV-associated neurocognitive disorder (HAND), epigenetic age acceleration has not been linked to HIV-related changes in structural MRI. We applied morphological MRI methods to study the brain structure of […]
Brandon J Lew
Author Correction: A census of pathway maps in cancer systems biology 2021-01-14
No abstract
Brent M Kuenzi
HiDeF: identifying persistent structures in multiscale 'omics data 2021-01-08
In any 'omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here, we use the concept of persistent homology, drawn […]
Fan Zheng
Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences 2021-01-05
No abstract
Nikolaos Vakirlis
Multiscale community detection in Cytoscape 2020-10-23
Detection of community structure has become a fundamental step in the analysis of biological networks with application to protein function annotation, disease gene prediction, and drug discovery. This recent impact creates a need to make these techniques and their accompanying visualization schemes available to a broad range of biologists. Here we present a service-oriented, end-to-end […]
Akshat Singhal
Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells 2020-10-23
Most drugs entering clinical trials fail, often related to an incomplete understanding of the mechanisms governing drug response. Machine learning techniques hold immense promise for better drug response predictions, but most have not reached clinical practice due to their lack of interpretability and their focus on monotherapies. We address these challenges by developing DrugCell, an […]
Brent M Kuenzi