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

By Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Mario Latendresse, Joseph M. Dale, Thomas J. Lee, Pallavi Kaipa, F. Gilham, Aaron Spaulding, Liviu Popescu and 4 more. Briefings Bioinform., 2010

652 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6b7b20f3bb416efe35baf3a965f69fadeb11beff

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Insights from 20 years of bacterial genome sequencing (2015, methodology): “MetaCyc and BioCyc provide the basis for developing pathway genome databases (PGDBs) and metabolic models for non-model organisms using the Pathway Tools software (Karp et al. 2010).”
The Sol Genomics Network (SGN)—from genotype to phenotype to breeding (2014, methodology): “SolCyc was created using MetaCyc as a reference database and the Pathologic component of Pathway Tools software (25).”
Efficient comparative phylogenetics on large trees (2018, background): “Further, machine learning algorithms enable the automated inference of metabolic phenotypes for thousands of microbial genomes (Karp et al. , 2010).”
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data (2012, methodology): “This generated set of functional annotations involving enzymatic activities is then the starting point for metabolic pathway reconstructions using the PathoLogic software (10) and the MetaCyc pathway reference database (11).”
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2015, methodology): “In addition to its role as a general reference on metabolism, MetaCyc can be used by the PathoLogic component of the Pathway Tools software (2) as a reference database to computationally predict the metabolic network of any organism that has a sequenced and annotated genome (3).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…Mrvar, 1998 PathDraw http://rospath.ewha.ac.kr/toolbox/PathwayViewerFrm.jsp Paek et al., 2004 Pathway Tools http://bioinformatics.ai.sri.com/ptools Karp et al., 2010 PATIKA http://www.patika.org Dogrusoz et al., 2006 PaVESy http://pavesy.mpimp-golm.mpg.de/PaVESy.htm Ludemann et al., 2004…”
MEMOTE for standardized genome-scale metabolic model testing (2020, background): “Alternatives include Pathway Tools (Karp et al. 2009) which internally stores organism data in the form of a database, and AuReMe (Aite et al.”
Activation and regulation of primary metabolism during seed germination (2014, background): “The b-oxidation and glyoxylate pathways take place mostly in glyoxysomes, which are a specialized form of peroxisome found in seeds (PlantCyc, Karp et al., 2010).”