Protein Interaction Networks
Published in In the World of Scientific Discoveries Series A
Bioengineering and systems biology.
Published in Annals of Biomedical Engineering
Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis.
Published in Proceedings of the National Academy of Sciences
The circadian clock generates daily rhythms in mammalian liver processes, such as glucose and lipid homeostasis, xenobiotic metabolism, and regeneration. The mechanisms governing these rhythms are not well understood, particularly the distinct contributions of the cell-autonomous clock and central pacemaker to rhythmic liver physiology. Through mic...
Systematic identification of functional orthologs based on protein network comparison.
Published in Genome Research
Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying functionally related proteins that supplements sequence-based comparisons with information on conserved protein-protein interactions. First, the protein interac...
PKCĪµ promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria.
Published in Cell
The transcription factor ATF2 elicits oncogenic activities in melanoma and tumor suppressor activities in nonmalignant skin cancer. Here, we identify that ATF2 tumor suppressor function is determined by its ability to localize at the mitochondria, where it alters membrane permeability following genotoxic stress. The ability of ATF2 to reach the mit...
Hierarchical modularity and the evolution of genetic interactomes across species.
...Published in Molecular Cell
To date, cross-species comparisons of genetic interactomes have been restricted to small or functionally related gene sets, limiting our ability to infer evolutionary trends. To facilitate a more comprehensive analysis, we constructed a genome-scale epistasis map (E-MAP) for the fission yeast Schizosaccharomyces pombe, providing phenotypic signatur...
Modeling transcriptome dynamics in a complex world.
Published in Cell
An accurate prediction of how extrinsic stimuli influence changes in gene expression has been challenging. In this issue, Nagano and colleagues successfully model genome-wide mRNA expression changes under variable environmental conditions in rice, raising hopes that scientists will soon be able to predict genome-wide transcriptional responses in a ...
Leveraging models of cell regulation and GWAS data in integrative network-based association studies.
Published in Nature Genetics
A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.
...Published in Cell Reports
Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. ...
Molecular networks in context.
Published in Nature Biotechnology
