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BioNetGen 2.2: advances in rule-based modeling

Bioinformatics (Oxford, England), 2016-11, Vol.32 (21), p.3366-3368

2016

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Unified tumor growth mechanisms from multimodel inference and dataset integration

PLoS computational biology, 2023-07, Vol.19 (7), p.e1011215-e1011215

2023

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An unbiased metric of antiproliferative drug effect in vitro

Nature methods, 2016-06, Vol.13 (6), p.497

2016

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An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

PLoS biology, 2021-06, Vol.19 (6), p.e3000797

2021

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Real-time luminescence enables continuous drug-response analysis in adherent and suspension cell lines

Cancer biology & therapy, 2022-12, Vol.23 (1), p.358-368

2022

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Unsupervised logic-based mechanism inference for network-driven biological processes

PLoS computational biology, 2021-06, Vol.17 (6), p.e1009035-e1009035

2021

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Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity

Cancers, 2023-02, Vol.15 (5), p.1477

2023

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Concepts of multi-level dynamical modelling: understanding mechanisms of squamous cell carcinoma development in Fanconi anemia

Frontiers in genetics, 2023, Vol.14, p.1254966-1254966

2023

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A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase

PloS one, 2018-02, Vol.13 (2), p.e0192087-e0192087

2018

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Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective

PLoS computational biology, 2017-02, Vol.13 (2), p.e1005352-e1005352

2017

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Exact hybrid particle/population simulation of rule-based models of biochemical systems

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003544-e1003544

2014

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Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

The Journal of chemical physics, 2010-03, Vol.132 (9), p.094101-094101-14

2010

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Processes in DNA damage response from a whole-cell multi-omics perspective

iScience, 2022-11, Vol.25 (11), p.105341-105341, Article 105341

2022

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Modeling heterogeneous tumor growth dynamics and cell–cell interactions at single-cell and cell-population resolution

Current opinion in systems biology, 2019-10, Vol.17, p.24-34

2019

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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Journal of integrative bioinformatics, 2020-07, Vol.17 (2)

2020

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A biochemical necroptosis model explains cell-type-specific responses to cell death cues

Biophysical journal, 2023-03, Vol.122 (5), p.817-834

2023

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Quantifying Drug Combination Synergy along Potency and Efficacy Axes

Cell systems, 2019-02, Vol.8 (2), p.97-108.e16

2019

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Thunor: visualization and analysis of high-throughput dose-response datasets

Nucleic acids research, 2021-07, Vol.49 (W1), p.W633

2021

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A Nonquiescent “Idling” Population State in Drug-Treated, BRAF-Mutated Melanoma

Biophysical journal, 2018-03, Vol.114 (6), p.1499-1511

2018

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Modeling for (physical) biologists: an introduction to the rule-based approach

Physical biology, 2015-07, Vol.12 (4), p.045007-045007

2015

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A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

The Journal of chemical physics, 2006-10, Vol.125 (14), p.144107-144107-10

2006

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Molecular chemisorption as the theoretically preferred pathway for water adsorption on ideal rutile TiO2(110)

Physical review letters, 2004-08, Vol.93 (8), p.086105.1-086105.4

2004

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52. Computational modeling of signaling pathways and cell-cell interactions driving tumor-induced bone disease

Journal of bone oncology, 2024-04, Vol.45, p.100590, Article 100590

2024

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GPU-powered model analysis with PySB/cupSODA

Bioinformatics (Oxford, England), 2017-11, Vol.33 (21), p.3492-3494

2017

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Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

Wiley interdisciplinary reviews. Mechanisms of disease, 2014-01, Vol.6 (1), p.13-36

2014

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BioNetGen 2.2: advances in rule-based modeling

Unified tumor growth mechanisms from multimodel inference and dataset integration

An unbiased metric of antiproliferative drug effect in vitro

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

Real-time luminescence enables continuous drug-response analysis in adherent and suspension cell lines

Unsupervised logic-based mechanism inference for network-driven biological processes

Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity

Concepts of multi-level dynamical modelling: understanding mechanisms of squamous cell carcinoma development in Fanconi anemia

A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective

Exact hybrid particle/population simulation of rule-based models of biochemical systems

Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

Processes in DNA damage response from a whole-cell multi-omics perspective

Modeling heterogeneous tumor growth dynamics and cell–cell interactions at single-cell and cell-population resolution

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

A biochemical necroptosis model explains cell-type-specific responses to cell death cues

Quantifying Drug Combination Synergy along Potency and Efficacy Axes

Thunor: visualization and analysis of high-throughput dose-response datasets

A Nonquiescent “Idling” Population State in Drug-Treated, BRAF-Mutated Melanoma

Modeling for (physical) biologists: an introduction to the rule-based approach

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

Molecular chemisorption as the theoretically preferred pathway for water adsorption on ideal rutile TiO2(110)

52. Computational modeling of signaling pathways and cell-cell interactions driving tumor-induced bone disease

GPU-powered model analysis with PySB/cupSODA

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

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