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.

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

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

Mechanistic Pan-Cancer Signaling Model

Interactive cell cycle analysis

What's all this talk about cell cycle models?

This is to show oscillations in the number of cells in G1 and in G2 phase of cell cycle.

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)

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

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

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

Molekulaarse rakubioloogia kursuse rakutsükli loeng

IFAC2020

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.