Zobrazeno 1 - 10
of 23
pro vyhledávání: '"Suzanne Paley"'
Publikováno v:
Frontiers in Bioinformatics, Vol 4 (2024)
We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions
Externí odkaz:
https://doaj.org/article/c8745e51f43e4950b5792b1454bd4ec0
Publikováno v:
Frontiers in Microbiology, Vol 15 (2024)
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms. It provides a high-level graphical survey of cellular functions, and enables the user t
Externí odkaz:
https://doaj.org/article/9a1f0cb9d75c41b782d3650ce1289061
Autor:
Suzanne Paley, Peter D. Karp
Publikováno v:
Metabolites, Vol 14, Iss 1, p 65 (2024)
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets. Organized as a hierarchy of cellular systems, the Dashboard at its highest level contains graphica
Externí odkaz:
https://doaj.org/article/d235d37249db40bfa90d54f06d4f799a
Autor:
Alexandra Proctor, Shadi Parvinroo, Tanner Richie, Xinglin Jia, Sonny T. M. Lee, Peter D. Karp, Suzanne Paley, Aleksandar D. Kostic, Joseph F. Pierre, Michael J. Wannemuehler, Gregory J. Phillips
Publikováno v:
mSystems, Vol 8, Iss 2 (2023)
Externí odkaz:
https://doaj.org/article/07b969dd36d5484d8765f0a41370e75a
Autor:
Alexandra Proctor, Shadi Parvinroo, Tanner Richie, Xinglin Jia, Sonny T. M. Lee, Peter D. Karp, Suzanne Paley, Aleksandar D. Kostic, Joseph F. Pierre, Michael J. Wannemuehler, Gregory J. Phillips
Publikováno v:
mSystems, Vol 7, Iss 5 (2022)
ABSTRACT Animals colonized with a defined microbiota represent useful experimental systems to investigate microbiome function. The altered Schaedler flora (ASF) represents a consortium of eight murine bacterial species that have been used for more th
Externí odkaz:
https://doaj.org/article/f2ac8f4ddec5422cb279d74b55f0ef68
Autor:
Suzanne Paley, Peter D. Karp
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-6 (2021)
Abstract Background The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by nece
Externí odkaz:
https://doaj.org/article/3f14c4b26b114c32a5de3caa3a86a1e9
Autor:
Peter D. Karp, Suzanne Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips
Publikováno v:
Frontiers in Bioinformatics, Vol 2 (2022)
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is rep
Externí odkaz:
https://doaj.org/article/21713a7936ad442f810fe1e662f049e1
Autor:
Ingrid M. Keseler, Socorro Gama-Castro, Amanda Mackie, Richard Billington, César Bonavides-Martínez, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Luis Muñiz-Rascado, Wai Kit Ong, Suzanne Paley, Alberto Santos-Zavaleta, Pallavi Subhraveti, Víctor H. Tierrafría, Alan J. Wolfe, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp
Publikováno v:
Frontiers in Microbiology, Vol 12 (2021)
The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the pro
Externí odkaz:
https://doaj.org/article/3e5385087dd74fe2b99b461d7b140fcf
Autor:
Suzanne Paley, Peter D. Karp
Publikováno v:
BMC Bioinformatics, Vol 20, Iss 1, Pp 1-13 (2019)
Abstract Background High-throughput experiments can bring to light associations between genes, proteins and/or metabolites, many of which will be explainable by existing knowledge. Our aim is to speed elucidation of such explanations and, in some cas
Externí odkaz:
https://doaj.org/article/7b0a493219c14780baf818c81a49cc19
Publikováno v:
Frontiers in Microbiology, Vol 12 (2021)
Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge
Externí odkaz:
https://doaj.org/article/95bcd9ad22d14ee2986c76ea63c7d5c9