Systems & Computational Biology
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.
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics dataWe describe and provide an array of diverse methods to predict cellular positions in tissue from RNA-seq data selecting mapping genes according to their spatial/statistical properties and their effect on improving the cell positioning.
Predicting gene regulatory networks from cell atlasesIntegrated single-cell gene regulatory network from three mouse cell atlases captures global and cell type–specific regulatory modules and crosstalk, important for cellular identity.
multicrispr: gRNA design for prime editing and parallel targeting of thousands of targetsA bioinformatics R package for a fast and generic guideRNA design, optimized for large-scale perturbation assays.
Peptide-based quorum sensing systems in Paenibacillus polymyxaDiscovery of conserved communication systems in the agriculturally important Paenibacillus bacteria. These systems are widespread, and some species encode more than 25 different peptide-receptor pairs.