Systems & Computational Biology
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.
Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolutionGenome-wide analysis of R-loop alterations in U2OS cells deficient of DDX5, XRN2, and PRMT5 identify >50,650 DRIP-seq peaks spanning ∼4.5% of the genomic sequence. R-loops near TSS generated intergenic antisense transcription.
Splicing of enhancer-associated lincRNAs contributes to enhancer activityAnalysis of enhancer-associated lincRNA transcripts shows their efficient and conserved splicing contributes to cognate enhancer activity and cis-regulation of target gene expression.
Metabolome-based prediction of yield heterosis contributes to the breeding of elite riceMetabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions.
A comprehensive resource for retrieving, visualizing, and integrating functional genomics dataThis study presents qcGenomics, a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multi-dimensional data integration.
Phenotypic proteomic profiling identifies a landscape of targets for circadian clock–modulating compoundsThis study provides comprehensive insights into the mechanism of action and cellular effects of circadian period–modulating compounds, which is critical for clearly defining molecular targets to modulate daily rhythms for therapeutic benefit.