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 …

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, …

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 …

Hit-and-Run” transcription: de novo transcription initiated by a transient bZIP1 “hit” persists after the “run

J Doidy, Y Li, B Neymotin, MB Edwards, K Varala… - BMC genomics, 2016 - Springer
Background Dynamic transcriptional regulation is critical for an organism’s response to
environmental signals and yet remains elusive to capture. Such transcriptional regulation is …

Emergence of physiological oscillation frequencies in a computer model of neocortex

SA Neymotin, H Lee, E Park, AA Fenton… - Frontiers in …, 2011 - frontiersin.org
Coordination of neocortical oscillations has been hypothesized to underlie the “binding”
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 …

Detecting spontaneous neural oscillation events in primate auditory cortex

SA Neymotin, I Tal, A Barczak, MN O'Connell… - Eneuro, 2022 - eneuro.org
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 …

Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex

SA Neymotin, S Dura-Bernal, P Lakatos… - Frontiers in …, 2016 - frontiersin.org
A large number of physiomic pathologies can produce hyperexcitability in cortex. Depending
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 …

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, …