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Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation

https://doi.org/10.1039/C5MB00310E

McManus, Joel; Cheng, Zhe; Vogel, Christine (July 2015, Molecular BioSystems)

Abstract Technological advances now enable routine measurement of mRNA and protein abundances, and estimates of their rates of synthesis and degradation that inform on their values and the degree of change in response to stimuli. Importantly, more and more data on time-series experiments are emerging, e.g. of cells responding to stress, enabling first insights into a new dimension of gene expression regulation – its dynamics and how it allows for very different response signals across genes. This review discusses recently published methods and datasets, their impact on what we now know about the relationships between concentrations and synthesis rates of mRNAs and proteins in yeast and mammalian cells, their evolution, and new hypotheses on translation regulatory mechanisms generated by approaches that involve ribosome footprinting.
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A synopsis on aging—Theories, mechanisms and future prospects

https://doi.org/10.1016/j.arr.2016.06.005

da Costa, João Pinto; Vitorino, Rui; Silva, Gustavo M.; Vogel, Christine; Duarte, Armando C.; Rocha-Santos, Teresa (August 2016, Ageing Research Reviews)

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Systems Approaches to the Eukaryotic Stress Response

https://doi.org/10.1371/journal.pcbi.1004757

Vogel, Christine; Alexandrov, Theodore (March 2016, PLOS Computational Biology)

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Mass spectrometry analysis of K63-ubiquitinated targets in response to oxidative stress

https://doi.org/10.1016/j.dib.2015.05.002

Silva, Gustavo Monteiro; Vogel, Christine (September 2015, Data in Brief)

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K63 polyubiquitination is a new modulator of the oxidative stress response

https://doi.org/10.1038/nsmb.2955

Silva, Gustavo M; Finley, Daniel; Vogel, Christine (January 2015, Nature Structural & Molecular Biology)

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One third of dynamic protein expression profiles can be predicted by a simple rate equation

https://doi.org/10.1039/c4mb00358f

Tchourine, Konstantine; Poultney, Christopher S.; Wang, Li; Silva, Gustavo M.; Manohar, Sandhya; Mueller, Christian L.; Bonneau, Richard; Vogel, Christine (January 2014, Mol. BioSyst.)

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