The emerging landscape of spatial profiling technologies
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …
profiling methods as a major pillar for cellular atlas building of complex samples, from …
Mechanisms of cellular mRNA transcript homeostasis
S Berry, L Pelkmans - Trends in Cell Biology, 2022 - cell.com
For most genes, mRNA transcript abundance scales with cell size to ensure a constant
concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with …
concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with …
PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
The Polycomb repressive system plays a fundamental role in controlling gene expression
during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 …
during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 …
[HTML][HTML] A guidebook of spatial transcriptomic technologies, data resources and analysis approaches
L Yue, F Liu, J Hu, P Yang, Y Wang, J Dong… - Computational and …, 2023 - Elsevier
Advances in transcriptomic technologies have deepened our understanding of the cellular
gene expression programs of multicellular organisms and provided a theoretical basis for …
gene expression programs of multicellular organisms and provided a theoretical basis for …
Making use of noise in biological systems
Y Ilan - Progress in biophysics and molecular biology, 2023 - Elsevier
Disorder and noise are inherent in biological systems. They are required to provide systems
with the advantages required for proper functioning. Noise is a part of the flexibility and …
with the advantages required for proper functioning. Noise is a part of the flexibility and …
Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions
Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers
measured using smFISH (single molecule fluorescence in situ hybridization) with the …
measured using smFISH (single molecule fluorescence in situ hybridization) with the …
Reduction in gene expression noise by targeted increase in accessibility at gene loci
Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by
periods of quiescence. Here, we show that the intermittent access of the promoters to …
periods of quiescence. Here, we show that the intermittent access of the promoters to …
[HTML][HTML] A guide to ERK dynamics, part 2: downstream decoding
A Ram, D Murphy, N DeCuzzi, M Patankar… - Biochemical …, 2023 - portlandpress.com
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular
processes, including cell division, death, and differentiation. In this second installment of a …
processes, including cell division, death, and differentiation. In this second installment of a …
Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning
E Moen, E Borba, G Miller, M Schwartz, D Bannon… - Biorxiv, 2019 - biorxiv.org
Live-cell imaging experiments have opened an exciting window into the behavior of living
systems. While these experiments can produce rich data, the computational analysis of …
systems. While these experiments can produce rich data, the computational analysis of …
[HTML][HTML] Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …
telegraph model which includes synthesis and degradation of mRNA, and switching of the …