Everything about Gillespie algorithm

🧭 Start here: a 6-step reading path

1. Read the overview: Gillespie algorithmA 5-minute orientation
2. Skim a recent paper: A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuitsInfluential work since 2022
3. Pick up a classic book: Stochastic modelling for systems biologyThe most-reprinted book on the subject
4. Read the landmark paper: Continuous time boolean modeling for biological signaling: application of Gillespie algorithmCited 145 times
5. Go sideways: Stochastic simulationA closely related topic
6. Go sideways: Tau-leapingA closely related topic

🏆 Landmark papers (most cited)

• Continuous time boolean modeling for biological signaling: application of Gillespie algorithm

  Gautier Stoll, Eric Viara, Emmanuel Barillot · 2012 · BMC Systems Biology · 145 citations

• Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm

  David Bernstein · 2005 · Physical Review E · 119 citations

• Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

  Christian L. Vestergaard, Mathieu Génois · 2015 · PLOS Computational Biology · 109 citations

• STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm

  Andrzej M. Kierzek · 2002 · Bioinformatics · 103 citations

• Cellular growth and division in the Gillespie algorithm

  T. Lu, D. Volfson, L. Tsimring · 2004 · Systems Biology · 98 citations

• A Gillespie Algorithm for Non-Markovian Stochastic Processes

  Naoki Masuda, Luis E. C. Rocha · 2018 · SIAM Review · 82 citations

• Modeling Langmuir isotherms with the Gillespie stochastic algorithm

  J. Epstein, J. Michael, C. Mandona · 2015 · Journal of Chromatography A · 9 citations

• Application of the Gillespie algorithm to a granular intruder particle

  J Talbot, P Viot · 2006 · Journal of Physics A: Mathematical and General · 9 citations

🆕 Influential since 2022

• A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

  Krishna Rijal, Pankaj Mehta · 2025 · eLife · 6 citations

• Gillespie algorithm for quantum jump trajectories

  Marco Radaelli, Gabriel T. Landi, Felix C. Binder · 2024 · Physical Review A · 5 citations

• Geospatial model of COVID-19 spreading and vaccination with event Gillespie algorithm

  Alexander Temerev, Liudmila Rozanova, Olivia Keiser · 2022 · Nonlinear Dynamics · 5 citations

• A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

  Krishna Rijal, Pankaj Mehta · 2025 · eLife · 3 citations

• Simulating epidemic peak dynamics on complex networks using efficient Gillespie algorithms

  Yulian Kuryliak, Michael T.M. Emmerich, Dmytro Dosyn · 2025 · Infection, Genetics and Evolution · 2 citations

📚 Books worth reading

• Stochastic modelling for systems biologyDarren James Wilkinson · 2006
• 📕Gillespie Algorithms for Stochastic Multiagent Dynamics in Populations and NetworksNaoki Masuda, Christian L. Vestergaard · 2023
• A bibliography of Russian literature and patents on loose abrasive finishingA. P. Babichev · 2004

Ranked by number of editions on Open Library, a rough measure of how lasting a book is.

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