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Perspective: Stochastic algorithms for chemical kinetics

The Journal of chemical physics, 2013-05, Vol.138 (17), p.170901

2013

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CBMOS: a GPU-enabled Python framework for the numerical study of center-based models

BMC bioinformatics, 2022-01, Vol.23 (1), p.55-55, Article 55

2022

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Contributions of cell behavior to geometric order in embryonic cartilage

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011658-e1011658

2023

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Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010683-e1010683

2022

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Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009830

2022

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URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

BMC systems biology, 2012-06, Vol.6 (1), p.76-76, Article 76

2012

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Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

PLoS computational biology, 2016-12, Vol.12 (12), p.e1005220-e1005220

2016

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Federated learning for predicting compound mechanism of action based on image-data from cell painting

Artificial intelligence in the life sciences, 2024-06, Vol.5, p.100098, Article 100098

2024

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Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration

Nature communications, 2022-11, Vol.13 (1), p.6949-17, Article 6949

2022

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Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes

SIAM journal on scientific computing, 2009-01, Vol.31 (3), p.1774-1797

2009

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Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators

BMC bioinformatics, 2021-06, Vol.22 (1), p.339-17, Article 339

2021

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BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data

BMC bioinformatics, 2018-06, Vol.19 (1), p.240-240, Article 240

2018

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Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions

Multiscale modeling & simulation, 2012-01, Vol.10 (2), p.585-611

2012

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Hierarchical algorithm for the reaction-diffusion master equation

The Journal of chemical physics, 2020-01, Vol.152 (3), p.034104-034104

2020

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FedQAS: Privacy-Aware Machine Reading Comprehension with Federated Learning

Applied sciences, 2022-03, Vol.12 (6), p.3130

2022

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Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning

Bioinformatics (Oxford, England), 2019-12, Vol.35 (24), p.5199-5206

2019

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Analysis of neural crest-derived clones reveals novel aspects of facial development

Science advances, 2016-08, Vol.2 (8), p.e1600060-e1600060

2016

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Reaction rates for mesoscopic reaction-diffusion kinetics

Physical review. E, Statistical, nonlinear, and soft matter physics, 2015-02, Vol.91 (2), p.023312-023312, Article 023312

2015

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Efficient Hierarchical Storage Management Empowered by Reinforcement Learning

IEEE transactions on knowledge and data engineering, 2023-06, Vol.35 (6), p.5780-5793

2023

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A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis

The Journal of chemical physics, 2021-05, Vol.154 (18), p.184105-184105

2021

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A Hierarchy of Approximations of the Master Equation Scaled by a Size Parameter

Journal of scientific computing, 2008-02, Vol.34 (2), p.127-151

2008

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Scalable machine learning-assisted model exploration and inference using Sciope

Bioinformatics, 2021-04, Vol.37 (2), p.279-281

2021

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Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning

The Journal of chemical physics, 2017-12, Vol.147 (23), p.234101-234101

2017

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The machine learning life cycle and the cloud: implications for drug discovery

Expert opinion on drug discovery, 2021-09, Vol.16 (9), p.1071-1079

2021

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Reaction-diffusion master equation in the microscopic limit

Physical review. E, Statistical, nonlinear, and soft matter physics, 2012-04, Vol.85 (4 Pt 1), p.042901-042901, Article 042901

2012

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Perspective: Stochastic algorithms for chemical kinetics

CBMOS: a GPU-enabled Python framework for the numerical study of center-based models

Contributions of cell behavior to geometric order in embryonic cartilage

Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

Federated learning for predicting compound mechanism of action based on image-data from cell painting

Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration

Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes

Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators

BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data

Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions

Hierarchical algorithm for the reaction-diffusion master equation

FedQAS: Privacy-Aware Machine Reading Comprehension with Federated Learning

Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning

Analysis of neural crest-derived clones reveals novel aspects of facial development

Reaction rates for mesoscopic reaction-diffusion kinetics

Efficient Hierarchical Storage Management Empowered by Reinforcement Learning

A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis

A Hierarchy of Approximations of the Master Equation Scaled by a Size Parameter

Scalable machine learning-assisted model exploration and inference using Sciope

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning

The machine learning life cycle and the cloud: implications for drug discovery

Reaction-diffusion master equation in the microscopic limit

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