Systems & Computational Biology
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.
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.
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.
Dietary restriction induces posttranscriptional regulation of longevity genesBy modulating posttranscriptional processes, including RNA editing, miRNA biogenesis, and intron retention, dietary restriction enacts some of its pro-longevity benefits in Caenorhabditis elegans through posttranscriptional regulation of gene expression.
Cellular response upon proliferation in the presence of an active mitotic checkpointCells that replicate with an active mitotic checkpoint remain capable to mount multiple times an efficient arrest, are bigger than unperturbed cells, rely more heavily on Cdh1, and have an altered protein expression profile.
Competition in the chaperone-client network subordinates cell-cycle entry to growth and stressGrowth and cell-cycle entry compete for multifunctional chaperones subjugating the critical size and proliferation to the growth potential of the cell.
A network of human functional gene interactions from knockout fitness screens in cancer cellsThe function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell.