Software tools, databases and resources in metabolomics: updates from 2018 to 2019

K O'Shea, BB Misra - Metabolomics, 2020 - Springer
Metabolomics has evolved as a discipline from a discovery and functional genomics tool,
and is now a cornerstone in the era of big data-driven precision medicine. Sample …

Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts

JW Guarnieri, JM Dybas, H Fazelinia, MS Kim… - Science translational …, 2023 - science.org
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host
mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating …

[PDF][PDF] Role of miR-2392 in driving SARS-CoV-2 infection

JT McDonald, FJ Enguita, D Taylor, RJ Griffin, W Priebe… - Cell reports, 2021 - cell.com
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene
regulation that have a major impact on many diseases and provide an exciting avenue …

[HTML][HTML] Metabolomics for evaluating flavor-associated metabolites in plant-based products

S Pavagadhi, S Swarup - Metabolites, 2020 - mdpi.com
Plant-based diets (PBDs) are associated with environmental benefits, human health
promotion and animal welfare. There is a worldwide shift towards PBDs, evident from the …

[HTML][HTML] Targeted down regulation of core mitochondrial genes during SARS-CoV-2 infection

JW Guarnieri, JM Dybas, H Fazelinia, MS Kim, J Frere… - BioRxiv, 2022 - ncbi.nlm.nih.gov
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-
19 patients, but the timing and organs affected vary among reports. Here, we reveal the …

[PDF][PDF] System-wide transcriptome damage and tissue identity loss in COVID-19 patients

J Park, J Foox, T Hether, DC Danko, S Warren… - Cell Reports …, 2022 - cell.com
The molecular mechanisms underlying the clinical manifestations of coronavirus disease
2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and …

[HTML][HTML] African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and …

U Singh, KM Hernandez, BJ Aronow, ES Wurtele - Scientific reports, 2021 - nature.com
The COVID-19 pandemic has affected African American populations disproportionately with
respect to prevalence, and mortality. Expression profiles represent snapshots of combined …

pyrpipe: a Python package for RNA-Seq workflows

U Singh, J Li, A Seetharam… - NAR genomics and …, 2021 - academic.oup.com
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis
tools, enable unprecedented biological insight. There is a pressing requirement for a …

Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks, and plastoglobular functions

EJS Michel, L Ponnala… - Journal of Experimental …, 2021 - academic.oup.com
Plastoglobules are dynamic protein–lipid microcompartments in plastids enriched for
isoprenoid-derived metabolites. Chloroplast plastoglobules support formation, remodeling …

[HTML][HTML] Landscape of the dark transcriptome revealed through re-mining massive RNA-Seq data

J Li, U Singh, Z Arendsee, ES Wurtele - Frontiers in Genetics, 2021 - frontiersin.org
The “dark transcriptome” can be considered the multitude of sequences that are transcribed
but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 …