cell-cycle

Physics-first, uncertainty-honest in-silico cell and drug-response simulator (Python). Validated docking/ADMET input layer (Vina, OpenFF, xTB), cell-level PK/PD modules, and a cell/colony engine under construction toward a validated interactive dish.

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?

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

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

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

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

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

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

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.

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

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

Molekulaarse rakubioloogia kursuse rakutsükli loeng

IFAC2020

An interactive web application for exploring cell cycle models