Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (Q24642068)

22 June 2017

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (English)

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22 June 2017

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22 June 2017

12

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22 June 2017

3

Markus Krummenacker

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22 June 2017

Suzanne M Paley

2

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22 June 2017

Mario Latendresse

4

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22 June 2017

Joseph M Dale

5

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22 June 2017

Thomas J Lee

6

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22 June 2017

Pallavi Kaipa

7

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22 June 2017

Fred Gilham

8

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22 June 2017

Aaron Spaulding

9

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22 June 2017

Liviu Popescu

10

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22 June 2017

Tomer Altman

11

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22 June 2017

Ingrid M Keseler

13

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22 June 2017

Ron Caspi

14

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22 June 2017

language of work or name

English

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publication date

2 December 2009

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Briefings in Bioinformatics

22 June 2017

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22 June 2017

11

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22 June 2017

1

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22 June 2017

40-79

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Presenting and exploring biological pathways with PathVisio

22 June 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

KEGG Atlas mapping for global analysis of metabolic pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The Gene Ontology project in 2008

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Gramene: a bird's eye view of cereal genomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The UCSC Genome Browser Database: update 2006

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

MetaCyc: a multiorganism database of metabolic pathways and enzymes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

dictyBase, the model organism database for Dictyostelium discoideum

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

From genomics to chemical genomics: new developments in KEGG

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The integrated microbial genomes (IMG) system

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Computational prediction of human metabolic pathways from the complete human genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Reactome: a knowledgebase of biological pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

FlyBase: genes and gene models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Cytoscape: a software environment for integrated models of biomolecular interaction networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

AraCyc: a biochemical pathway database for Arabidopsis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The generic genome browser: a building block for a model organism system database

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

PATRIC: the VBI PathoSystems Resource Integration Center

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Querying and computing with BioCyc databases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The Pathway Tools software

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Integrated access to metabolic and genomic data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Reactome: a knowledge base of biologic pathways and processes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The large-scale organization of metabolic networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

BioMart--biological queries made easy

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Reactome knowledgebase of human biological pathways and processes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

PlasmoDB: a functional genomic database for malaria parasites

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Flux balance analysis: interrogating genome-scale metabolic networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Reconstruction of metabolic pathways for the cattle genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

EcoCyc: a comprehensive view of Escherichia coli biology

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Annotation-based inference of transporter function

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The Mouse Genome Database (MGD): mouse biology and model systems

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Multidimensional annotation of the Escherichia coli K-12 genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

GenMAPP 2: new features and resources for pathway analysis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

ApiDB: integrated resources for the apicomplexan bioinformatics resource center

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The Pathway Tools cellular overview diagram and Omics Viewer

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The outcomes of pathway database computations depend on pathway ontology

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Genomic pathways database and biological data management

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

BioWarehouse: a bioinformatics database warehouse toolkit

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

BIOZON: a system for unification, management and analysis of heterogeneous biological data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

VitaPad: visualization tools for the analysis of pathway data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

An evidence ontology for use in pathway/genome databases.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

PathMiner: predicting metabolic pathways by heuristic search

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Pathways database system: an integrated system for biological pathways

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Pathway databases: a case study in computational symbolic theories

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Global properties of the metabolic map of Escherichia coli

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Integrating functional genomic information into the Saccharomyces genome database

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Adapting EcoCyc for use on the World Wide Web.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

30 May 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

MedicCyc: a biochemical pathway database for Medicago truncatula.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

From molecular activities and processes to biological function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

The Comprehensive Microbial Resource.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

Choke point analysis of metabolic pathways in E.histolytica: a computational approach for drug target identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBP043

Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Flux balance analysis of biological systems: applications and challenges.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Using the Generic Genome Browser (GBrowse).

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

MEGU: pathway mapping web-service based on KEGG and SVG

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810111

Integrated pathway–genome databases and their role in drug discovery

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19955237

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIB/BBP043

1 reference

journals/bib/KarpPKLDLKGSPAPKC10

22 June 2017

1 reference

1 reference

DBLP Dataset 2021-01-02

OpenCitations bibliographic resource ID

28 January 2021

197205

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference