Systems & Computational Biology
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.
The PI3K and MAPK/p38 pathways control stress granule assembly in a hierarchical mannerPI3K and p38 act in a hierarchical manner to enhance mTORC1 activity and stress granule formation; although PI3K is the main driver, the impact of p38 gets apparent as PI3K activity declines.
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogsComparison of observed exon–exon junction counts to those predicted from estimated transcript abundances can identify genes with misannotated or misquantified transcripts.
An integrative machine learning approach for prediction of toxicity-related drug safetyThis method allows the prediction of toxicity-related drug clinical trial failures, withdrawals from the market, and idiosyncratic toxicity risk by combining biological network analysis with machine learning.
Interaction modulation through arrays of clustered methyl-arginine protein modificationsExtensively modifiable arrays of clustered arginines in a large set of human proteins function as regulatory protein interaction platforms. Quantitative immunoprecipitation assays defined two distinct cumulative binding mechanisms operating across an array of 18 methyl-arginine motifs in SYNCRIP.
RNase E cleavage shapes the transcriptome of Rhodobacter sphaeroides and strongly impacts phototrophic growthThis study identifies the cleavage sites of the endoribonuclease RNase E in the Rhodobacter sphaeroides transcriptome and demonstrates its effect on oxidative stress resistance and phototrophic growth.
Proteins of generalist and specialist pathogens differ in their amino acid compositionPrimitive amino acids and disorder content in secreted proteins are distinctively enriched in generalist compared with host-specific pathogens.
Dynamic m6A methylation facilitates mRNA triaging to stress granulesm6A modification in the 5′ vicinity of the coding sequence of transcripts provides a selective mechanism for triaging mRNAs to stress granules and is mediated by the YTHDF3 “reader” protein.