Systems & Computational Biology
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.
ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s researchADAPTABLE is a webserver and database of antimicrobial peptides that uses sequence and property alignment to highlight their mode of action against the threat of resistance in medicine and agriculture.
TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosisThis work summarizes cellular apoptotic and signaling response to TRAIL across 10 cell lines and for the first time links signaling diversity to nongenetic resistance. This high-dimensional, single-cell approach toward TRAIL resistance sets a standard in studying nongenetic resistance.
Detecting sequence signals in targeting peptides using deep learningDuring the development of TargetP 2.0, a state-of-the-art method to predict targeting signal, we find a previously overlooked biological signal for subcellular targeting using the output from a deep learning method.