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References from Mechanistic modeling of cell viability assays with in silico lineage tracing. Local targets link to admitted publications; unresolved targets remain external evidence.
A whole-cell computational model predicts phenotype from genotype
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An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control
2022 · External reference
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
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Fundamental behaviors emerge from simulations of a living minimal cell
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Stimulus-dependent dynamics of p53 in single cells
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Modeling a snap-action, variable-delay switch controlling extrinsic cell death
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Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics
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Computational modeling of mammalian signaling networks
10.1002/wsbm.52 · 2010 · External reference
A hybrid model of mammalian cell cycle regulation
10.1371/journal.pcbi.1001077 · 2011 · External reference
Modeling single-neuron dynamics and computations: a balance of detail and abstraction
10.1126/science.1127240 · 2006 · External reference
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
10.1038/msb.2011.50 · 2011 · External reference
Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis
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Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models
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Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients
2015 · External reference
MAPK signal pathways in the regulation of cell proliferation in mammalian cells
10.1038/sj.cr.7290105 · 2002 · External reference
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
10.1038/msb.2008.74 · 2009 · External reference
Modeling T cell antigen discrimination based on feedback control of digital ERK responses
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The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation
10.1126/science.1071914 · 2002 · External reference
The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway
2003 · External reference
Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts
10.1074/jbc.m304968200 · 2003 · External reference
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens
10.1371/journal.pcbi.1005985 · 2018 · External reference
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
2018 · External reference
Recon 2.2: from reconstruction to model of human metabolism
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Predicting ligand-dependent tumors from multi-dimensional signaling features
10.1038/s41540-017-0030-3 · 2017 · External reference
Genome scale metabolic modeling of cancer
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Integration of clinical data with a genome-scale metabolic model of the human adipocyte
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Global reconstruction of the human metabolic network based on genomic and bibliomic data
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An atlas of human metabolism
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A blueprint for human whole-cell modeling
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Multiscale models of cell signaling
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Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
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Multiscale model of the different modes of cancer cell invasion
10.1093/bioinformatics/btad374 · 2023 · External reference
Representing dynamic biological networks with multi-scale probabilistic models
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A multi-approach and multi-scale platform to model CD4+ T cells responding to infections
10.1371/journal.pcbi.1009209 · 2021 · External reference
A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery
10.3389/fimmu.2023.1112985 · 2023 · External reference
A mechanistic modeling framework reveals the key principles underlying tumor metabolism
10.1371/journal.pcbi.1009841 · 2022 · External reference
Mechanism-Based Modeling of Tumor Growth and Treatment Response Constrained by Multiparametric Imaging Data
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Recent applications of quantitative systems pharmacology and machine learning models across diseases
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A Review of Quantitative Systems Pharmacology Models of the Coagulation Cascade: Opportunities for Improved Usability
10.3390/pharmaceutics15030918 · 2023 · External reference
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
10.1039/c3mb25489e · 2013 · External reference
BioModels—15 years of sharing computational models in life science
2020 · External reference
Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
10.1038/nature11735 · 2012 · External reference
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
2013 · External reference
Correlating chemical sensitivity and basal gene expression reveals mechanism of action
10.1038/nchembio.1986 · 2016 · External reference
Modeling breast cancer proliferation, drug synergies, and alternating therapies
10.1016/j.isci.2023.106714 · 2023 · External reference
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
10.1371/journal.pcbi.1005991 · 2018 · External reference
Mathematical Modeling of Impacts of Patient Differences on Renin-Angiotensin System and Applications to COVID-19 Lung Fibrosis Outcomes
2024 · External reference
Agent-based methods facilitate integrative science in cancer
10.1016/j.tcb.2022.10.006 · 2023 · External reference
Unresolved reference
2018 · External reference
10.3389/fbioe.2020.00249
10.3389/fbioe.2020.00249 · External reference
Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production
10.1093/bioinformatics/btaa969 · 2021 · External reference
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling
10.1038/s41467-022-31138-1 · 2022 · External reference
Modeling the cell division cycle: cdc2 and cyclin interactions
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A multi-center study on the reproducibility of drug-response assays in mammalian cell lines
10.1016/j.cels.2019.06.005 · 2019 · External reference
Characterization of the novel and specific PI3Kα inhibitor NVP-BYL719 and development of the patient stratification strategy for clinical trials
10.1158/1535-7163.mct-13-0865 · 2014 · External reference
The potent and selective cyclin-dependent kinases 4 and 6 inhibitor ribociclib (LEE011) is a versatile combination partner in preclinical cancer models
10.18632/oncotarget.26215 · 2018 · External reference
Identification and characterization of a novel chemotype MEK inhibitor able to alter the phosphorylation state of MEK1/2
10.18632/oncotarget.747 · 2012 · External reference
Unresolved reference
External reference
Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs
10.1038/nmeth.3853 · 2016 · External reference
Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop
10.1038/s41467-022-34536-7 · 2022 · External reference
Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics
10.1038/sdata.2017.166 · 2017 · External reference
Treating cancer with selective CDK4/6 inhibitors
10.1038/nrclinonc.2016.26 · 2016 · External reference
Targeting cell-cycle machinery in cancer
10.1016/j.ccell.2021.03.010 · 2021 · External reference
The double dealing of cyclin D1
10.1080/15384101.2019.1706903 · 2020 · External reference
Oxidative DNA base damage in MCF-10A breast epithelial cells at clinically achievable concentrations of doxorubicin
10.1016/j.bcp.2007.03.022 · 2007 · External reference
More than apples and oranges - Detecting cancer with a fruit fly’s antenna
10.1038/srep03576 · 2014 · External reference
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2013 · External reference
Kinetic analysis of regulatory events in G1 leading to proliferation or quiescence of Swiss 3T3 cells
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Unresolved reference
2008 · External reference
Unresolved reference
2007 · External reference
Mammalian cells cycle without the D-type cyclin-dependent kinases Cdk4 and Cdk6
10.1016/j.cell.2004.08.002 · 2004 · External reference
Transient hysteresis in CDK4/6 activity underlies passage of the restriction point in G1
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Loss of CDK4/6 activity in S/G2 phase leads to cell cycle reversal
10.1038/s41586-023-06274-3 · 2023 · External reference
Rapid adaptation to CDK2 inhibition exposes intrinsic cell-cycle plasticity
10.1016/j.cell.2023.05.013 · 2023 · External reference
Quantitative analysis of cell cycle phase durations and PC12 differentiation using fluorescent biosensors
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A precise Cdk activity threshold determines passage through the restriction point
10.1016/j.molcel.2017.12.017 · 2018 · External reference
EGF receptor in relation to tumor development: molecular basis of responsiveness of cancer cells to EGFR-targeting tyrosine kinase inhibitors
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Targeting the EGFR signaling pathway in cancer therapy
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Epidermal Growth Factor Receptor Cell Proliferation Signaling Pathways
10.3390/cancers9050052 · 2017 · External reference
Constitutive overexpression of cyclin D1 in human breast epithelial cells does not prevent G1 arrest induced by deprivation of epidermal growth factor
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GPER Mediates Estrogen-Induced Signaling and Proliferation in Human Breast Epithelial Cells and Normal and Malignant Breast
10.1007/s12672-014-0174-1 · 2014 · External reference
Spontaneously slow-cycling subpopulations of human cells originate from activation of stress-response pathways
2019 · External reference
Impact of variability in cell cycle periodicity on cell population dynamics
10.1371/journal.pcbi.1011080 · 2023 · External reference
Physicochemical modelling of cell signalling pathways
10.1038/ncb1497 · 2006 · External reference
Regulation of the cell cycle
10.1016/b978-1-4557-4066-6.00011-1 · 2015 · External reference
Palbociclib—The First of a New Class of Cell Cycle Inhibitors.
10.1007/978-3-319-91442-8_11 · 2018 · External reference
Retinoblastoma-protein-dependent cell-cycle inhibition by the tumour suppressor p16
10.1038/375503a0 · 1995 · External reference
PD 0332991, a selective cyclin D kinase 4/6 inhibitor, preferentially inhibits proliferation of luminal estrogen receptor-positive human breast cancer cell lines in vitro
2009 · External reference
Palbociclib in Hormone-Receptor-Positive Advanced Breast Cancer
10.1056/nejmoa1505270 · 2015 · External reference
The retinoblastoma tumor suppressor inhibits cellular proliferation through two distinct mechanisms: inhibition of cell cycle progression and induction of cell death
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Cyclin E2 overexpression is associated with endocrine resistance but not insensitivity to CDK2 inhibition in human breast cancer cells
10.1158/1535-7163.mct-11-0963 · 2012 · External reference
Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle
10.1073/pnas.0903827106 · 2009 · External reference
A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology
10.1093/bib/bbz014 · 2020 · External reference
Parameter Sensitivity Analysis of Stochastic Models Provides Insights into Cardiac Calcium Sparks
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Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format
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ERK signalling: a master regulator of cell behaviour, life and fate
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Temporal integration of mitogen history in mother cells controls proliferation of daughter cells
10.1126/science.aay8241 · 2020 · External reference
Models of stochastic gene expression
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Analytical distributions for stochastic gene expression
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Vivarium: an interface and engine for integrative multiscale modeling in computational biology
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