[HTML][HTML] Modeling and interpretation of single-cell proteogenomic data
Biological functions stem from coordinated interactions among proteins, nucleic acids and
small molecules. Mass spectrometry technologies for reliable, high throughput single-cell …
small molecules. Mass spectrometry technologies for reliable, high throughput single-cell …
Trajectory inference from single-cell genomics data with a process time model
Single-cell transcriptomics experiments provide gene expression snapshots of
heterogeneous cell populations across cell states. These snapshots have been used to infer …
heterogeneous cell populations across cell states. These snapshots have been used to infer …
Incorporating extrinsic noise into mechanistic modelling of single-cell transcriptomics
K Öcal - bioRxiv, 2023 - biorxiv.org
A mechanistic understanding of single-cell transcriptomics data requires differentiating
between intrinsic, extrinsic and technical noise, but an abundance of the latter often …
between intrinsic, extrinsic and technical noise, but an abundance of the latter often …
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA-sequencing
Single-cell transcriptomics reveals significant variations in the transcriptional activity across
cells. Yet, it remains challenging to identify mechanisms of transcription dynamics from static …
cells. Yet, it remains challenging to identify mechanisms of transcription dynamics from static …
Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression
What features of transcription can be learnt by fitting mathematical models of gene
expression to mRNA count data? Given a suite of models, fitting to data selects an optimal …
expression to mRNA count data? Given a suite of models, fitting to data selects an optimal …
New and notable: Revisiting the “two cultures” through extrinsic noise
In the classic article (1), Leo Breiman bears witness to the divergence between “two
cultures” of statistics that emerged in the wake of readily accessible computing technology …
cultures” of statistics that emerged in the wake of readily accessible computing technology …
Principles of bursty mRNA expression and irreversibility in single cells and extrinsically varying populations
J Holehouse - arXiv preprint arXiv:2405.12897, 2024 - arxiv.org
The canonical model of mRNA expression is the telegraph model, describing a gene that
switches on and off, subject to transcription and decay. It describes steady-state mRNA …
switches on and off, subject to transcription and decay. It describes steady-state mRNA …
What can we learn when fitting a simple telegraph model to a complex gene expression model?
F Jiao, J Li, T Liu, Y Zhu, W Che… - PLOS Computational …, 2024 - journals.plos.org
In experiments, the distributions of mRNA or protein numbers in single cells are often fitted to
the random telegraph model which includes synthesis and decay of mRNA or protein, and …
the random telegraph model which includes synthesis and decay of mRNA or protein, and …
Transcriptome-wide analysis of cell cycle-dependent bursty gene expression from single-cell RNA-seq data using mechanistic model-based inference
Bursty gene expression is quantified by two intuitive parameters: the burst frequency and the
burst size. While these parameters are known to be cell-cycle dependent for some genes, a …
burst size. While these parameters are known to be cell-cycle dependent for some genes, a …