Studying and modelling dynamic biological processes using time-series gene expression data

Z Bar-Joseph, A Gitter, I Simon - Nature Reviews Genetics, 2012 - nature.com
Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

Common markers of proliferation

ML Whitfield, LK George, GD Grant… - Nature Reviews Cancer, 2006 - nature.com
When normal tissue and tumour samples are compared by microarray analysis, the biggest
differences most often occur in the expression levels of genes that control cell proliferation …

[HTML][HTML] Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells

S Marguerat, A Schmidt, S Codlin, W Chen… - Cell, 2012 - cell.com
Data on absolute molecule numbers will empower the modeling, understanding, and
comparison of cellular functions and biological systems. We quantified transcriptomes and …

Escape of Intracellular Shigella from Autophagy

M Ogawa, T Yoshimori, T Suzuki, H Sagara… - Science, 2005 - science.org
The degradation of undesirable cellular components or organelles, including invading
microbes, by autophagy is crucial for cell survival. Here, Shigella, an invasive bacteria, was …

Counting cytokinesis proteins globally and locally in fission yeast

JQ Wu, TD Pollard - Science, 2005 - science.org
We used fluorescence microscopy to measure global and local concentrations of 28
cytoskeletal and signaling proteins fused to yellow fluorescent protein (YFP) in the fission …

Rapidly regulated genes are intron poor

DC Jeffares, CJ Penkett, J Bähler - Trends in genetics, 2008 - cell.com
We show that genes with rapidly changing expression levels in response to stress contain
significantly lower intron densities in yeasts, thale cress and mice. Therefore, we propose …

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

D Mahdessian, AJ Cesnik, C Gnann, F Danielsson… - Nature, 2021 - nature.com
The cell cycle, over which cells grow and divide, is a fundamental process of life. Its
dysregulation has devastating consequences, including cancer,–. The cell cycle is driven by …

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

A Santos, R Wernersson, LJ Jensen - Nucleic acids research, 2015 - academic.oup.com
The eukaryotic cell division cycle is a highly regulated process that consists of a complex
series of events and involves thousands of proteins. Researchers have studied the …

Current approaches to gene regulatory network modelling

T Schlitt, A Brazma - BMC bioinformatics, 2007 - Springer
Many different approaches have been developed to model and simulate gene regulatory
networks. We proposed the following categories for gene regulatory network models …

Secrets of a double agent: CDK7 in cell-cycle control and transcription

RP Fisher - Journal of cell science, 2005 - journals.biologists.com
In metazoans, cyclin-dependent kinase 7 (CDK7) has essential roles in both the cell-division
cycle and transcription, as a CDK-activating kinase (CAK) and as a component of the …