How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time?
Published in Cell Systems
How Has the COVID-19 Pandemic Changed How You Will Approach Research and Lab Work in the Future?
...Published in Cell Systems
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact P...
Published in Cell Systems
An integrated model of peptide-HLA immunogenicity based on data from COVID-19 patients and machine learning is used to evaluate and design COVID-19 vaccines for cellular immunity. Human population coverage gaps are predicted for COVID-19 subunit vaccines, and augmentation strategies are proposed to close these gaps. Compact peptide vaccine designs ...
A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disea...
Published in Cell Systems
Virally encoded factors resembling host factors hijack host molecular machines in a phenomenon called molecular mimicry. Lasso et al. use 3D protein structural information to identify over 6,000,000 instances of structural mimicry, >70% of which cannot be discerned through protein sequence alone. Their work provides the first systematic analysis of...
Large-Scale Multi-omic Analysis of COVID-19 Severity
...Published in Cell Systems
Leukocyte mRNA expression and plasma protein, metabolite, and lipid levels were measured in 102 COVID-19 and 26 non-COVID-19 patient samples. 219 diverse biomolecules were strongly associated with COVID-19 status and severity and pointed to dysregulation of processes related to lipid transport, blood coagulation, acute phase response, endotheliopat...
A Mentee’s Baby Registry: Supporting New Academic Parents in 2020
Published in Cell Systems
The lack of childcare infrastructure in the COVID-19 pandemic has highlighted many systemic problems faced by academic caregivers, and particularly new parents. This commentary uses the lessons from the pandemic to highlight the potential role of mentors in supporting caregiver responsibilities.
Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling
...Published in Cell Systems
This study demonstrates that transcriptional variability of the toll-like receptor signaling is constrained by mean mRNA responses through gene-specific modulation of transcriptional bursting.
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks
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.
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distrib...
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...
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation...
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+)...
