Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (Q30990372)

15 October 2017

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (English)

1 reference

15 October 2017

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1 reference

Nikolaus Sonnenschein

series ordinal

4

1 reference

15 October 2017

Ali Ebrahim

3

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Andreas Dräger

object named as

Andreas Dräger

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2

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Bernhard Palsson

series ordinal

6

object named as

Bernhard O Palsson

1 reference

15 October 2017

Zachary A King

1

1 reference

PMCID

4552468

15 October 2017

language of work or name

1 reference

27 August 2015

1 reference

PLOS Computational Biology

15 October 2017

1 reference

15 October 2017

11

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15 October 2017

8

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15 October 2017

e1004321

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Creative Commons Attribution 4.0 International

15 October 2017

start time

27 August 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Jupyter notebook file

1 reference

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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PathVisio 3: an extendable pathway analysis toolbox

14 July 2018

1 reference

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Next-generation genome-scale models for metabolic engineering.

14 July 2018

1 reference

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Improving collaboration by standardization efforts in systems biology.

14 July 2018

1 reference

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Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Minimal metabolic pathway structure is consistent with associated biomolecular interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Constraint-based models predict metabolic and associated cellular functions.

14 July 2018

1 reference

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14 July 2018

1 reference

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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

14 July 2018

1 reference

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COBRApy: COnstraints-Based Reconstruction and Analysis for Python

14 July 2018

1 reference

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VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies

14 July 2018

1 reference

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Biographer: web-based editing and rendering of SBGN compliant biochemical networks

14 July 2018

1 reference

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VANTED v2: a framework for systems biology applications

14 July 2018

1 reference

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

WikiPathways: building research communities on biological pathways

14 July 2018

1 reference

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D³: Data-Driven Documents

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

14 July 2018

1 reference

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Biomolecules in the computer: Jmol to the rescue

14 July 2018

1 reference

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Web-based metabolic network visualization with a zooming user interface

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

iPath2.0: interactive pathway explorer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Cytoscape 2.8: new features for data integration and network visualization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Editing, validating and translating of SBGN maps

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

JBrowse: a next-generation genome browser

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Dendroscope: An interactive viewer for large phylogenetic trees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

A model diagram layout extension for SBML

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4552468

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004321

Using process diagrams for the graphical representation of biological networks

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26313928

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004321

1 reference

journals/ploscb/KingDESLP15

15 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 October 2017

1 reference

PMCID

4552468