Published in Cell Systems
The response to SARS-CoV-2 infection differs from person to person, with some patients developing more severe symptoms than others. In this paper, Caterina La Porta and Stefano Zapperi show that the immune recognition of SARS-CoV-2 viral peptides differs widely among individuals and could thus explain why they may respond differently to the virus.
Published in Cell Systems
HLA haplotype frequencies are used to evaluate and design SARS-CoV-2 peptide vaccines. The methods presented optimize the presentation likelihood of a diverse set of vaccine peptides to maximize vaccine immunogenicity. The proposed SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine pe...
Published in Cell Systems
Alda-Catalinas et al. developed a pooled CRISPR-activation screen combined with single-cell transcriptomics to identify regulators of zygotic genome activation (ZGA) using an in vitro proxy of early mouse embryos, embryonic stem cells. After interrogation of 230 candidate regulators, 24 hits were identified using multi-omics factor analysis (MOFA+)...
Published in Cell Systems
Racism and COVID-19 represent a pandemic on a pandemic for Blacks. The pandemics find themselves synergized to the detriment of Blacks and their health. The complexity of the combination of these pandemics are evident when examining the interplay between racist policing practices and health.
Published in Cell Systems
In this work, Bunina et al. profiled transcriptome, proteome, and chromatin accessibility dynamics during differentiation of mouse embryonic stem cells to postmitotic neurons. They revealed extensive associations between molecular layers within and across differentiation time points and uncovered an unexpected interaction of two chromatin-bound pro...
Published in Cell Systems
Where the SARS-CoV-2 genome localizes inside human cells remains understudied but may regulate viral replication and host response. We use a machine-learning model to predict subcellular residency of the SARS-CoV-2 genome and its encoded transcripts, as well as for other coronaviruses. Our predictions suggest new hypotheses for SARS-CoV-2 mechanism...
Published in Cell Systems
Messner et al. present a standardized, low-cost, ultra-high-throughput platform for serum and plasma proteomics designed for clinical use and apply it to a cohort of hospitalized COVID-19 patients. They identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19.
Published in Cell Systems
Mordstein et al. report an unexpected effect of splicing in human cells, whereby splicing preferentially enhances the expression of genes with low GC content. This might partially explain the high number of introns found in mammalian genomes.
Published in Cell Systems
Published in Cell systems
Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function and is thus of great interest fo...
