Suzanne M Paley
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Explore the profile of Suzanne M Paley including associated specialties, affiliations and a list of published articles.
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12
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1323
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Recent Articles
1.
Moore L, Caspi R, Campbell D, Casey J, Crevecoeur S, Lea-Smith D, et al.
Front Microbiol
. 2024 Feb;
15:1340413.
PMID: 38357349
CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the...
2.
Karp P, Midford P, Billington R, Kothari A, Krummenacker M, Latendresse M, et al.
Brief Bioinform
. 2019 Dec;
22(1):109-126.
PMID: 31813964
Motivation: Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to...
3.
Karp P, Billington R, Caspi R, Fulcher C, Latendresse M, Kothari A, et al.
Brief Bioinform
. 2018 Feb;
20(4):1085-1093.
PMID: 29447345
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by...
4.
Karp P, Latendresse M, Paley S, Krummenacker M, Ong Q, Billington R, et al.
Brief Bioinform
. 2015 Oct;
17(5):877-90.
PMID: 26454094
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics...
5.
Travers M, Paley S, Shrager J, Holland T, Karp P
Database (Oxford)
. 2013 Sep;
2013:bat061.
PMID: 24037025
Knowledge spreadsheets (KSs) are a visual tool for interactive data analysis and exploration. They differ from traditional spreadsheets in that rather than being oriented toward numeric data, they work with...
6.
Paley S, Latendresse M, Karp P
BMC Bioinformatics
. 2012 Sep;
13:243.
PMID: 22998532
Background: Biologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data. Results: The Pathway Tools software supports storage and manipulation...
7.
Karp P, Paley S, Krummenacker M, Latendresse M, Dale J, Lee T, et al.
Brief Bioinform
. 2009 Dec;
11(1):40-79.
PMID: 19955237
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the...
8.
Karp P, Keseler I, Shearer A, Latendresse M, Krummenacker M, Paley S, et al.
Nucleic Acids Res
. 2007 Oct;
35(22):7577-90.
PMID: 17940092
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc...
9.
Paley S, Karp P
Nucleic Acids Res
. 2006 Aug;
34(13):3771-8.
PMID: 16893960
The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The...
10.
Paley S, Karp P
Bioinformatics
. 2002 Jun;
18(5):715-24.
PMID: 12050068
Motivation: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference...