| Molecular Systems Biology, Volume 15, Issue 8, |
Articles
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Methods
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Open AccessHigh‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
e8849 | First Published: 01 August 2019
A comprehensive proteomics analysis reveals the effects of high‐fat diet and free fatty acid overload on signaling pathways in murine livers and hepatocytes. It shows concomitant diet‐induced changes of metabolic and receptor‐adjacent signaling nodes and a lack of response to insulin.
Open AccessElucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data
e8828 | First Published: 06 August 2019
The endothelin B receptor signalling pathway is mapped in human melanoma cells using time‐resolved quantitative phosphoproteomics. The protein phosphorylation data is combined with prior knowledge to build a logic model of the pathway.
Open AccessCRISPR screens are feasible in TP53 wild‐type cells
e8679 | First Published: 08 August 2019
A recent study by Haapaniemi et al (2018) reported that intact p53 signaling hampers CRISPR‐based functional genomic screens. Brown et al report good performance of genome‐scale screens in TP53 wild‐type cells and reiterate best practices for CRISPR screening.
Open AccessReply to “CRISPR screens are feasible in TP53 wild‐type cells”
e9059 | First Published: 08 August 2019
Haapaniemi et al address the issues raised by Brown et al and discuss several differences between the analyses performed by the two groups.
Open AccessInaccuracy of the log‐rank approximation in cancer data analysis
e8754 | First Published: 12 August 2019
The log‐rank test statistic is very broadly used in biology. Unfortunately, P‐values based on the popular chi‐square approximation are often inaccurate and can be misleading.
Open AccessMultiplex transcriptional characterizations across diverse bacterial species using cell‐free systems
e8875 | First Published: 14 August 2019
A cell‐free framework (DRAFTS) is developed to quantitatively characterize transcriptional activities of thousands of bacterial regulatory sequences.
Open AccessSystematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli
e9008 | First Published: 23 August 2019
To probe the depth of our current knowledge on protein‐metabolite interactions, the interactions between 29 enzymes from Escherichia colicentral metabolism and 55 intracellular metabolites were systematically mapped using ligand‐detected NMR.
Open AccessGenetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases
e8939 | First Published: 27 August 2019
Genetic screens of yeast transcription response dynamics identify partially uncoupled parameters (response intensity and duration) and their differential regulation. Epistasis analysis of individual parameters uncovers two distinctly regulated response phases.
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