Systems & Computational Biology
On the relation of gene essentiality to intron structure: a computational and deep learning approachA deep learning classifier predicts gene essentiality by intron sequence. A unique set of intron features of essential genes was found and its importance demonstrated by a high-performing classifier.
Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiationL929 cell supernatant is commonly used to differentiate murine macrophages from bone marrow. The supernatant and its effect on macrophage phenotype was characterised by proteomics and the authors identified novel immunoregulatory proteins.
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq dataA systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.
PieParty: visualizing cells from scRNA-seq data as pie chartsPieParty visualizes every cell in scRNA-seq experiments as pie charts, where every slice of a pie chart corresponds to the expression of a single gene.
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case studyThis study describes complementary network-based and sequence similarity methods to identify drug repurposing opportunities predicted to directly target viral proteins, highlighting results for five human pathogens.
A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWASThis paper describes the economical optimization of DNA extraction, short and long read sequencing, and bioinformatic assembly, which in turn improves mapping and variant resolution of short-read sequenced, same-breed dogs for association studies. This methodology is applicable for any investigators planning a genome-wide association study.
The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cellsUsing ChIP-seq and functional genomic analyses, the study shows that the Paf1 complex occupies transcriptional enhancers and positively regulates their activity.
The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cellsThe RNA-binding protein SRSF6 recognizes a purine-rich consensus motif consisting of GAA triplets, and its downregulation in human pancreatic β-cells affects alternative splicing in a position-dependent manner.
FIREWORKS: a bottom-up approach to integrative coessentiality network analysisA tool to create bias-adjusted coessentiality networks reveals functional relationships between genes, context-specific rewiring of genetic networks, determinants of essentiality, and therapeutic targets for challenging proteins.
Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic networkUsing genomic and structural information from SARS-CoV-2, we created a biomass function capturing its amino and nucleic acid requirements and incorporated this into a metabolic model of the human lung cell to predict metabolic perturbations that inhibit virus reproduction.