Systems & Computational Biology
A new metabolic model of Drosophila melanogaster and the integrative analysis of Parkinson’s diseaseThe reconstruction of a comprehensive and literature-curated Drosophila metabolic model, iDrosophila1, provided a powerful platform for studying metabolism with systems medicine perspective.
Evaluation of genetic demultiplexing of single-cell sequencing data from model speciesThe authors demonstrate that scRNA-seq sample pooling followed by genetics-based separation of individuals is an effective means to identify individual samples in a variety of commonly studied species.
Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling networkThe site-specific function of EGFR’s C-terminal tyrosines is interrogated by phosphotyrosine phosphoproteomics to build a data-driven model that links cell response to signaling nodes and elucidates novel associations in the EGFR signaling network.
Antibody reliability influences observed mRNA–protein correlations in tumour samplesUpadhya and Ryan show that the reliability of antibodies used for RPPA profiling influences the mRNA-protein correlations observed in tumour cohorts.
Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and diseaseZ-DNABERT uses the transformer algorithm to map genomic Z-DNA. We validate the approach using chemical footprinting data from live cells. We show the utility of the approach by mapping the Z-flipons discovered to Mendelian disease variants and various quantitative traits.
Gapless provides combined scaffolding, gap filling, and assembly correction with long readsgapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads.
Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in gliomaGlioma patients often relapse because of resistance to radiation therapy. The transfer of the metabolic enzyme NAMPT via microvesicles and the accompanying elevated levels of NAD are found to be a mechanism by which glioma cells become resistant to radiation.
Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cellsWe used affinity purification of KRAS in different genetic and growth contexts to determine KRAS-mediated complexes, their rewiring in specific contexts, and their link to functional outcomes.
RAS and PP2A activities converge on epigenetic gene regulationThis study reveals a hidden regulatory layer in epigenetic gene expression in cancer by co-operative phosphoregulation by RAS and tumor suppressor phosphatase PP2A.
Assessing the impacts of various factors on circular RNA reliabilityThis study systematically assesses the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability, providing a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.