What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

N Neelagandan, I Lamberti, HJF Carvalho… - Open …, 2020 - royalsocietypublishing.org
Protein synthesis from mRNA is an energy-intensive and tightly controlled cellular process.
Translation elongation is a well-coordinated, multifactorial step in translation that undergoes …

Translation dynamics of single mRNAs in live cells

T Morisaki, ON Wiggan… - Annual review of …, 2023 - annualreviews.org
The translation of messenger RNA (mRNA) into proteins represents the culmination of gene
expression. Recent technological advances have revolutionized our ability to investigate this …

Bursting translation on single mRNAs in live cells

NM Livingston, J Kwon, O Valera, JA Saba, NK Sinha… - Molecular cell, 2023 - cell.com
Stochasticity has emerged as a mechanism of gene regulation. Much of this so-called"
noise" has been attributed to bursting transcription. Although bursting transcription has been …

Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene

LS Forero-Quintero, W Raymond, T Handa… - Nature …, 2021 - nature.com
The carboxyl-terminal domain of RNA polymerase II (RNAP2) is phosphorylated during
transcription in eukaryotic cells. While residue-specific phosphorylation has been mapped …

Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells

A Koch, L Aguilera, T Morisaki, B Munsky… - Nature structural & …, 2020 - nature.com
Viruses use internal ribosome entry sites (IRES) to hijack host ribosomes and promote cap-
independent translation. Although they are well-studied in bulk, the dynamics of IRES …

Imaging translational control by Argonaute with single-molecule resolution in live cells

CA Cialek, G Galindo, T Morisaki, N Zhao… - Nature …, 2022 - nature.com
A major challenge to our understanding of translational control has been deconvolving the
individual impact specific regulatory factors have on the complex dynamics of mRNA …

Nucleotide and codon usage biases involved in the evolution of African swine fever virus: a comparative genomics analysis

F Pu, R Wang, X Yang, X Hu, J Wang… - Journal of Basic …, 2023 - Wiley Online Library
Since African swine fever virus (ASFV) replication is closely related to its host's machinery,
codon usage of viral genome can be subject to selection pressures. A better understanding …

Lighting up single-mRNA translation dynamics in living cells

CA Cialek, AL Koch, G Galindo, TJ Stasevich - Current opinion in genetics …, 2020 - Elsevier
Over the past five years, technological advances have made it possible to image the
translation of single mRNA in the natural context of living cells. With these advances …

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis

MA Ramirez Sierra, TR Sokolowski - PLOS Computational Biology, 2024 - journals.plos.org
Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a
central challenge in developmental biology, particularly in early mammalian development …

Computational Experiments in Computer Science Research: A Literature Survey

P Landeta-López, C Guevara-Vega - IEEE Access, 2024 - ieeexplore.ieee.org
Computational experiments have been important since the 70s to find solutions to problems
using computers, and even more now with the advancement of technology, especially …