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Spatio-temporal model of endogenous ROS and raft-dependent WNT/beta-catenin signaling driving cell fate commitment in human neural progenitor cells

PLoS computational biology, 2015-03, Vol.11 (3), p.e1004106-e1004106

2015

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Relating simulation studies by provenance—Developing a family of Wnt signaling models

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009227-e1009227

2021

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VPMBench: a test bench for variant prioritization methods

BMC bioinformatics, 2021-11, Vol.22 (Suppl 5), p.1-543, Article 543

2021

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Potential based, spatial simulation of dynamically nested particles

BMC bioinformatics, 2019-11, Vol.20 (1), p.607-16, Article 607

2019

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Long-term stimulation with alternating electric fields modulates the differentiation and mineralization of human pre-osteoblasts

Frontiers in physiology, 2022-09, Vol.13, p.965181-965181

2022

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Implications of different membrane compartmentalization models in particle-based in silico studies

Royal Society open science, 2023-07, Vol.10 (7), p.221177-221177

2023

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Simulation studies of social systems: telling the story based on provenance patterns

Royal Society open science, 2024-08, Vol.11 (8), p.240258-24

2024

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Receptor/Raft Ratio Is a Determinant for LRP6 Phosphorylation and WNT/β-Catenin Signaling

Frontiers in cell and developmental biology, 2021-08, Vol.9, p.706731-706731

2021

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Using a Digital Twin of an Electrical Stimulation Device to Monitor and Control the Electrical Stimulation of Cells in vitro

Frontiers in bioengineering and biotechnology, 2021-12, Vol.9, p.765516-765516

2021

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ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology

IEEE/ACM transactions on computational biology and bioinformatics, 2017-11, Vol.14 (6), p.1339-1349

2017

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detectCilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

Bioinformatics and biology insights, 2024-01, Vol.18, p.11779322241280431

2024

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Composing problem solvers for simulation experimentation: a case study on steady state estimation

PloS one, 2014-04, Vol.9 (4), p.e91948-e91948

2014

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Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

Journal of cell science, 2020-08, Vol.133 (15)

2020

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A Model-Driven Approach for Conducting Simulation Experiments

Applied sciences, 2022-08, Vol.12 (16), p.7977

2022

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Artifact-Based Workflows for Supporting Simulation Studies

IEEE transactions on knowledge and data engineering, 2020-06, Vol.32 (6), p.1064-1078

2020

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Elucidating the sources of β-catenin dynamics in human neural progenitor cells

PloS one, 2012-08, Vol.7 (8), p.e42792-e42792

2012

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Synchronous speculative simulation of tightly coupled agents in continuous time on CPUs and GPUs

Simulation (San Diego, Calif.), 2024-01, Vol.100 (1), p.5-21

2024

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HIV pre-exposure prophylaxis during the SARS-CoV-2 pandemic: Results from a prospective observational study in Germany

Frontiers in public health, 2022-08, Vol.10, p.930208-930208

2022

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ROS Dependent Wnt/β-Catenin Pathway and Its Regulation on Defined Micro-Pillars-A Combined In Vitro and In Silico Study

Cells (Basel, Switzerland), 2020-07, Vol.9 (8), p.1784

2020

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Rule-based multi-level modeling of cell biological systems

BMC systems biology, 2011-10, Vol.5 (179), p.166-166

2011

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SESSL: A domain-specific language for simulation experiments

ACM transactions on modeling and computer simulation, 2014-02, Vol.24 (2), p.1-25

2014

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Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology

Briefings in bioinformatics, 2010-05, Vol.11 (3), p.290-300

2010

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Reproducible and flexible simulation experiments with ML-Rules and SESSL

Bioinformatics, 2018-04, Vol.34 (8), p.1424-1427

2018

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Creating PROV-DM Graphs from Model Databases

2022 Winter Simulation Conference (WSC), 2022, p.2118-2129

2022

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Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry

Molecular biology of the cell, 2021-01, Vol.32 (2), p.186-210

2021

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Spatio-temporal model of endogenous ROS and raft-dependent WNT/beta-catenin signaling driving cell fate commitment in human neural progenitor cells

Relating simulation studies by provenance—Developing a family of Wnt signaling models

VPMBench: a test bench for variant prioritization methods

Potential based, spatial simulation of dynamically nested particles

Long-term stimulation with alternating electric fields modulates the differentiation and mineralization of human pre-osteoblasts

Implications of different membrane compartmentalization models in particle-based in silico studies

Simulation studies of social systems: telling the story based on provenance patterns

Receptor/Raft Ratio Is a Determinant for LRP6 Phosphorylation and WNT/β-Catenin Signaling

Using a Digital Twin of an Electrical Stimulation Device to Monitor and Control the Electrical Stimulation of Cells in vitro

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology

detectCilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

Composing problem solvers for simulation experimentation: a case study on steady state estimation

Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

A Model-Driven Approach for Conducting Simulation Experiments

Artifact-Based Workflows for Supporting Simulation Studies

Elucidating the sources of β-catenin dynamics in human neural progenitor cells

Synchronous speculative simulation of tightly coupled agents in continuous time on CPUs and GPUs

HIV pre-exposure prophylaxis during the SARS-CoV-2 pandemic: Results from a prospective observational study in Germany

ROS Dependent Wnt/β-Catenin Pathway and Its Regulation on Defined Micro-Pillars-A Combined In Vitro and In Silico Study

Rule-based multi-level modeling of cell biological systems

SESSL: A domain-specific language for simulation experiments

Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology

Reproducible and flexible simulation experiments with ML-Rules and SESSL

Creating PROV-DM Graphs from Model Databases

Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry

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