(Q34328597)

1 August 2017

Programming biological models in Python using PySB (English)

1 reference

1 August 2017

1 reference

3

John A Bachman

1 reference

1 August 2017

4

Peter K Sorger

1 reference

1 August 2017

2

Jeremy L Muhlich

1 reference

1 August 2017

Carlos F Lopez

1

1 reference

1 August 2017

1 January 2013

1 reference

Molecular Systems Biology

1 August 2017

1 reference

1 August 2017

9

1 reference

1 August 2017

646

1 reference

PubMed ID

23423320

describes a project that uses

1 August 2017

Python

1 reference

maintained by WikiProject

inferred from title

WikiProject Software

0 references

cites work

Stoichiometry of the CD95 death-inducing signaling complex: experimental and modeling evidence for a death effector domain chain model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Predictive Bcl-2 family binding models rooted in experiment or structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

A framework for mapping, visualisation and automatic model creation of signal-transduction networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Proteus: a web-based, context-specific modelling tool for molecular networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Combinatorial complexity and compositional drift in protein interaction networks.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

A modular model of the apoptosis machinery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

A unified model of mammalian BCL-2 protein family interactions at the mitochondria.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Guidelines for visualizing and annotating rule-based models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Glucose metabolism determines resistance of cancer cells to bioenergetic crisis after cytochrome-c release.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

The challenges and scope of theoretical biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

New approaches to modeling complex biochemistry

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

BID, BIM, and PUMA are essential for activation of the BAX- and BAK-dependent cell death program

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Model-based dissection of CD95 signaling dynamics reveals both a pro- and antiapoptotic role of c-FLIPL.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Still embedded together binding to membranes regulates Bcl-2 protein interactions.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Dynamics within the CD95 death-inducing signaling complex decide life and death of cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Stepwise activation of BAX and BAK by tBID, BIM, and PUMA initiates mitochondrial apoptosis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Single-cell quantification of Bax activation and mathematical modelling suggest pore formation on minimal mitochondrial Bax accumulation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

The role of BH3-only protein Bim extends beyond inhibiting Bcl-2-like prosurvival proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Rule-based modeling of biochemical systems with BioNetGen

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Internal coarse-graining of molecular systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Assembly of the mitochondrial apoptosis-induced channel, MAC.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

PROMOT: modular modeling for systems biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Membrane binding by tBid initiates an ordered series of events culminating in membrane permeabilization by Bax

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Modeling a snap-action, variable-delay switch controlling extrinsic cell death

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Programming with models: modularity and abstraction provide powerful capabilities for systems biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Dynamical modeling and multi-experiment fitting with PottersWheel

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Intracellular signaling dynamics during apoptosis execution in the presence or absence of X-linked-inhibitor-of-apoptosis-protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Bcl-XL inhibits membrane permeabilization by competing with Bax.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Quantitative analysis of pathways controlling extrinsic apoptosis in single cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Modular cell biology: retroactivity and insulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Two independent positive feedbacks and bistability in the Bcl-2 apoptotic switch

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

The BCL-2 protein family: opposing activities that mediate cell death

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Robustness analysis identifies the plausible model of the Bcl-2 apoptotic switch

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Apoptosis initiated when BH3 ligands engage multiple Bcl-2 homologs, not Bax or Bak

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

COPASI--a COmplex PAthway SImulator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Systems analysis of effector caspase activation and its control by X-linked inhibitor of apoptosis protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Rules for modeling signal-transduction systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Mitochondria primed by death signals determine cellular addiction to antiapoptotic BCL-2 family members

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Auto-activation of the apoptosis protein Bax increases mitochondrial membrane permeability and is inhibited by Bcl-2

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Minimum information requested in the annotation of biochemical models (MIRIAM)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Proapoptotic Bak is sequestered by Mcl-1 and Bcl-xL, but not Bcl-2, until displaced by BH3-only proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

BH3 domains of BH3-only proteins differentially regulate Bax-mediated mitochondrial membrane permeabilization both directly and indirectly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

6 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

BH3-triggered structural reorganization drives the activation of proapoptotic BAX.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

How to deal with large models?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

A systems-level analysis of perfect adaptation in yeast osmoregulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

Single-cell fluorescence resonance energy transfer analysis demonstrates that caspase activation during apoptosis is a rapid process. Role of caspase-3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

Dynamics of outer mitochondrial membrane permeabilization during apoptosis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

A single cell analysis of apoptosis. Ordering the apoptotic phenotype

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588907

Hierarchical regulation of mitochondrion-dependent apoptosis by BCL-2 subfamilies

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23423320

12 December 2020

inferred from PubMed ID database lookup

The virtual cell: an integrated modeling environment for experimental and computational cell biology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23423320

12 December 2020

inferred from PubMed ID database lookup

Using process diagrams for the graphical representation of biological networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23423320

12 December 2020

inferred from PubMed ID database lookup

Bcl-x L blocks mitochondrial multiple conductance channel activation and inhibits 6-OHDA-induced death in SH-SY5Y cells

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

7 January 2021

inferred from DOI database lookup

Python for Scientific Computing

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.1

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/MSB.2013.1

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

PubMed ID

23423320