Systems & Computational Biology
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.
Sufficiency analysis of estrogen responsive enhancers using synthetic activatorsEnhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription.
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.
Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptomeA genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeSBRAPeS is a software for B-cell receptor reconstruction in single cells from very short (25–30 bp) read lengths, which achieves similar success rates and accuracy as applying other methods on long reads.
KAP1 is an antiparallel dimer with a functional asymmetryThis study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1.
Targeted variant detection using unaligned RNA-Seq readsThis study introduces km, an approach leveraging k-mer decomposition to identify targeted mutations. It can detect single-base mutations, insertions and deletions, as well as fusions. An analysis of over 10,000 RNA-seq samples shows fast mutation detection via km.