(Q28652349)

15

0 references

Nicolas Le Novère

26

0 references

Michael Schubert

Michael Schubert

8

0 references

Nicolas Rodriguez

Nicolas Rodriguez

2

0 references

Camille Laibe

Camille Laibe

24

0 references

Martijn P van Iersel

Martijn van Iersel

11

0 references

Claudine Chaouiya

Claudine Chaouiya

21

0 references

Pedro Mendes

Pedro Mendes

19

0 references

Julio Saez-Rodriguez

Julio Saez-Rodriguez

22

0 references

Douglas Kell

Douglas B Kell

17

0 references

Florian Mittag

Florian Mittag

7

0 references

Finja Büchel

Finja Büchel

1

0 references

Clemens Wrzodek

Clemens Wrzodek

4

0 references

Martin Golebiewski

Martin Golebiewski

10

0 references

Michael Wybrow

Michael Wybrow

14

0 references

Sarah M Keating

Sarah Keating

12

0 references

Michael Hucka

Michael Hucka

16

0 references

Andreas Dräger

Andreas Dräger

25

0 references

Neil Swainston

3

Neil Swainston

0 references

Tobias Czauderna

5

Tobias Czauderna

0 references

Mihai Glonț

9

Mihai Glont

0 references

author name string

Roland Keller

6

0 references

Matthias Rall

13

0 references

Wolfgang Müller

18

0 references

Andreas Zell

20

0 references

Falk Schreiber

The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

23

0 references

language of work or name

English

0 references

publication date

1 November 2013

0 references

published in

BMC Systems Biology

0 references

volume

7

0 references

issue

1

0 references

page(s)

116

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Precise generation of systems biology models from KEGG pathways

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The Units Ontology: a tool for integrating units of measurement in science

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Qualitative translation of relations from BioPAX to SBML qual

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The Cell Collective: toward an open and collaborative approach to systems biology.

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A whole-cell computational model predicts phenotype from genotype

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

SABIO-RK--database for biochemical reaction kinetics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Controlled vocabularies and semantics in systems biology

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Systematic integration of experimental data and models in systems biology

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Further developments towards a genome-scale metabolic model of yeast

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The BioPAX community standard for pathway data sharing

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

High-throughput generation, optimization and analysis of genome-scale metabolic models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A protocol for generating a high-quality genome-scale metabolic reconstruction

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

PID: the Pathway Interaction Database

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Presenting and exploring biological pathways with PathVisio

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

WikiPathways: pathway editing for the people

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A model diagram layout extension for SBML

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Reactome: a knowledgebase of biological pathways

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

KEGG: kyoto encyclopedia of genes and genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Metabolic stability and epigenesis in randomly constructed genetic nets

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

KEGG for integration and interpretation of large-scale molecular data sets

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A community-driven global reconstruction of human metabolism.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The Systems Biology Graphical Notation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

An analysis of a 'community-driven' reconstruction of the human metabolic network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Reconciliation of metabolites and biochemical reactions for metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

State-time spectrum of signal transduction logic models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Improving metabolic flux predictions using absolute gene expression data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Software support for SBGN maps: SBGN-ML and LibSBGN.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Sustainable model building the role of standards and biological semantics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

JSBML: a flexible Java library for working with SBML.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Mining metabolites: extracting the yeast metabolome from the literature

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Enzyme kinetics informatics: from instrument to browser

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Editing, validating and translating of SBGN maps

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Event extraction for systems biology by text mining the literature

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Logic-based models for the analysis of cell signaling networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Towards a genome-scale kinetic model of cellular metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A generic algorithm for layout of biological networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

libAnnotationSBML: a library for exploiting SBML annotations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Logic models of pathway biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Using a logical model to predict the growth of yeast

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

LibSBML: an API library for SBML.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Petri net modelling of biological networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

A structure-based anatomy of the E.coli metabolome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The EcoCyc and MetaCyc databases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

Boolean formalization of genetic control circuits.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228421

The CellML Model Repository

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-116

A computational algebra approach to the reverse engineering of gene regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-116

Logical modelling of gene regulatory networks with GINsim

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-116

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-116

The logical analysis of continuous, non-linear biochemical control networks

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24180668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24180668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SBML Level 3 package: Qualitative Models, Version 1, Release 1.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24180668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

12 August 2022

https://opencitations.net/index/coci/api/v1/references/10.1186/1752-0509-7-116

Orthogonal Connector Routing

1 reference

12 August 2022

https://opencitations.net/index/coci/api/v1/references/10.1186/1752-0509-7-116

Identifiers

DOI

10.1186/1752-0509-7-116

1 reference

journals/bmcsb/BuchelRSWCKMSGGIKRWHHK0MZCSSLDN13

0 references

1 reference

DBLP Dataset 2021-01-02

28 January 2021

4835060

1 reference

1 reference

4835060

PubMed publication ID

24180668

1 reference