Determination of in vivo RNA kinetics using RATE-seq
B Neymotin, R Athanasiadou, D Gresham - Rna, 2014 - rnajournal.cshlp.org
The abundance of a transcript is determined by its rate of synthesis and its rate of degradation;
however, global methods for quantifying RNA abundance cannot distinguish variation in …
however, global methods for quantifying RNA abundance cannot distinguish variation in …
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae
B Neymotin, V Ettorre, D Gresham - G3: Genes, Genomes …, 2016 - academic.oup.com
Degradation of mRNA contributes to variation in transcript abundance. Studies of individual
mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, …
mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, …
Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen
…, N Brandt, F Abdul-Rahman, B Neymotin… - Molecular biology of …, 2016 - Am Soc Cell Biol
Cell growth rate is regulated in response to the abundance and molecular form of essential
nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental …
nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental …
Hit-and-Run” transcription: de novo transcription initiated by a transient bZIP1 “hit” persists after the “run
Background Dynamic transcriptional regulation is critical for an organism’s response to
environmental signals and yet remains elusive to capture. Such transcriptional regulation is …
environmental signals and yet remains elusive to capture. Such transcriptional regulation is …
Emergence of physiological oscillation frequencies in a computer model of neocortex
Coordination of neocortical oscillations has been hypothesized to underlie the “binding”
essential to cognitive function. However, the mechanisms that generate neocortical oscillations …
essential to cognitive function. However, the mechanisms that generate neocortical oscillations …
Optimizing computer models of corticospinal neurons to replicate in vitro dynamics
SA Neymotin, BA Suter… - Journal of …, 2017 - journals.physiology.org
Corticospinal neurons (SPI), thick-tufted pyramidal neurons in motor cortex layer 5B that
project caudally via the medullary pyramids, display distinct class-specific electrophysiological …
project caudally via the medullary pyramids, display distinct class-specific electrophysiological …
Detecting spontaneous neural oscillation events in primate auditory cortex
Electrophysiological oscillations in the brain have been shown to occur as multicycle events,
with onset and offset dependent on behavioral and cognitive state. To provide a baseline …
with onset and offset dependent on behavioral and cognitive state. To provide a baseline …
Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex
A large number of physiomic pathologies can produce hyperexcitability in cortex. Depending
on severity, cortical hyperexcitability may manifest clinically as a hyperkinetic movement …
on severity, cortical hyperexcitability may manifest clinically as a hyperkinetic movement …
A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
R Athanasiadou, B Neymotin, N Brandt… - PLoS computational …, 2019 - journals.plos.org
A fundamental assumption, common to the vast majority of high-throughput transcriptome
analyses, is that the expression of most genes is unchanged among samples and that total …
analyses, is that the expression of most genes is unchanged among samples and that total …
Measuring the quality of neuronal identification in ensemble recordings
SA Neymotin, WW Lytton, AV Olypher… - Journal of …, 2011 - Soc Neuroscience
Technological advances in electrode construction and digital signal processing now allow
recording simultaneous extracellular action potential discharges from many single neurons, …
recording simultaneous extracellular action potential discharges from many single neurons, …