Programming with models: modularity and abstraction provide powerful capabilities for systems biology (Q33353920)

26 July 2017

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

1 reference

26 July 2017

Aneil Mallavarapu

1

1 reference

26 July 2017

Matthew Thomson

series ordinal

2

1 reference

26 July 2017

Benjamin Ullian

series ordinal

3

1 reference

26 July 2017

Jeremy Gunawardena

series ordinal

4

1 reference

26 July 2017

language of work or name

English

0 references

publication date

1 March 2009

1 reference

Journal of the Royal Society Interface

26 July 2017

1 reference

26 July 2017

6

1 reference

26 July 2017

32

1 reference

26 July 2017

257-270

1 reference

A mathematical tool for exploring the dynamics of biological networks

26 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

21 June 2018

Executable cell biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Universally sloppy parameter sensitivities in systems biology models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

A systems biology dynamical model of mammalian G1 cell cycle progression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Decreased internalisation of erbB1 mutants in lung cancer is linked with a mechanism conferring sensitivity to gefitinib

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Physicochemical modelling of cell signalling pathways.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The emergence of geometric order in proliferating metazoan epithelia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Rules for modeling signal-transduction systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Molecular interaction maps of bioregulatory networks: a general rubric for systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Mass spectrometric and kinetic analysis of ASF/SF2 phosphorylation by SRPK1 and Clk/Sty

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Multisite protein phosphorylation makes a good threshold but can be a poor switch

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Querying and computing with BioCyc databases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Computational representation of developmental genetic regulatory networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The meaning of systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Automatic generation of cellular reaction networks with Moleculizer 1.0.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

BioLingua: a programmable knowledge environment for biologists

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Topology and robustness in the Drosophila segment polarity network

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

CellML: its future, present and past

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Schizosaccharomyces pombe carboxyl-terminal domain (CTD) phosphatase Fcp1: distributive mechanism, minimal CTD substrate, and active site mapping

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Regulation of MAP Kinase Signaling Modules by Scaffold Proteins in Mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Processive phosphorylation of alternative splicing factor/splicing factor 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Modular modeling of cellular systems with ProMoT/Diva

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Multisite phosphorylation provides sophisticated regulation of transcription factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Computational systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Computational cell biology: spatiotemporal simulation of cellular events

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

21 June 2018

Synthetic cell biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

A new approach to decoding life: systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Regulation of GSK-3: a cellular multiprocessor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Processive phosphorylation of p130Cas by Src depends on SH3-polyproline interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The kinetic mechanism of the dual phosphorylation of the ATF2 transcription factor by p38 mitogen-activated protein (MAP) kinase alpha. Implications for signal/response profiles of MAP kinase pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The segment polarity network is a robust developmental module

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

From molecular to modular cell biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The development and therapeutic potential of protein kinase inhibitors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Robustness in bacterial chemotaxis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Emergent properties of networks of biological signaling pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The activating dual phosphorylation of MAPK by MEK is nonprocessive

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Ultrasensitivity in the mitogen-activated protein kinase cascade

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Multisite and hierarchal protein phosphorylation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture.

21 June 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

The existence and uniqueness of steady states for a class of chemical reaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Rete: A fast algorithm for the many pattern/many object pattern match problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Autophosphorylation of FGFR1 kinase is mediated by a sequential and precisely ordered reaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Novel phosphorylation sites in tau from Alzheimer brain support a role for casein kinase 1 in disease pathogenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Linking data to models: data regression

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

The mechanism of dephosphorylation of extracellular signal-regulated kinase 2 by mitogen-activated protein kinase phosphatase 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0205

Uncovering the design principles of circadian clocks: mathematical analysis of flexibility and evolutionary goals.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

UML as a cell and biochemistry modeling language.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2659579

Dizzy: stochastic simulation of large-scale genetic regulatory networks

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18647734

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Using process diagrams for the graphical representation of biological networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18647734

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Formal molecular biology

1 reference

21 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1098/RSIF.2008.0205

Identifiers

DOI

10.1098/RSIF.2008.0205

1 reference

26 July 2017

1 reference

26 July 2017

1 reference