cell-cycle

Computational Cell Biology Simulator & In Silico Drug Testing Platform — C++20/Metal, Novak-Tyson CDK ODE, Fick Diffusion, PhysiPKPD Pharmacodynamics

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Predict cell cycle phase in a continuum from single-cell RNA-seq data

Track single cells and profile the cell cycle with PCNA fluorescence images

Single-cell transcriptome analysis by fluorescence labeling

Interactive cell cycle analysis

What's all this talk about cell cycle models?

ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast | T.D.G.A. Mondeel, P. Holland, J. Nielsen and M. Barberis | 2019 | https://doi.org/10.1093/nar/gkz603

RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions

Track single-cells and profile the cell cycle with PCNA images.

"Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming" published in eLife (2022)

Circadian-cell cycle coupling orchestrates cell growth (Nature Physics 2025)

Bottom-up dynamical modeling of biological systems using ordinary, partial, and stochastic differential equations.

A web application for ingesting flow cytometry data, modeling cell-cycle distributions with the Dean-Jett-Fox model, and generating highly customizable, publication-ready plots.

Cell-cycle phase scoring for single cells, separating proliferating from resting populations.

Molekulaarse rakubioloogia kursuse rakutsükli loeng

IFAC2020

Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs | Thierry D.G.A. Mondeel, Oleksandr Ivanov, Hans V. Westerhoff, Wolfram Liebermeister and Matteo Barberis | NPJ Syst. Biol. Appl. (2020) | https://doi.org/10.1038/s41540-020-0125-0

An interactive web application for exploring cell cycle models