idekeradmin – UC San Diego

PubMed

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
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms 2020-10-16
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein […]
David E Gordon
Functional Landscape of SARS-CoV-2 Cellular Restriction 2020-10-07
A deficient interferon response to SARS-CoV-2 infection has been implicated as a determinant of severe COVID-19. To identify the molecular effectors that govern interferon control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human interferon stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to […]
Laura Martin-Sancho
Association of Epigenetic Metrics of Biological Age With Cortical Thickness 2020-09-14
CONCLUSIONS AND RELEVANCE: To our knowledge, this is the first study to investigate vertexwise cortical thickness in relation to DNAm-based biological age, and the findings suggest that this metric of biological age may yield additional insight on healthy and pathological cortical aging compared with standard measures of chronological age alone.
Amy L Proskovec
Genomic Landscape of Appendiceal Neoplasms 2020-09-11
CONCLUSION: Epithelial appendiceal cancers and goblet cell carcinoids show differences in KRAS and GNAS mutation frequencies and have mutation profiles distinct from CRC. This study highlights the benefit of performing molecular profiling on rare tumors to identify prognostic and predictive biomarkers and new therapeutic targets.
Celina S-P Ang