Zobrazeno 1 - 10
of 197
pro vyhledávání: '"Peter D. Karp"'
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
Publikováno v:
mSystems, Vol 9, Iss 7 (2024)
ABSTRACT Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions su
Externí odkaz:
https://doaj.org/article/1abc784a1d8d477388f2c8b3409a0c37
Autor:
Lisa R. Moore, Ron Caspi, Douglas A. Campbell, John R. Casey, Sophie Crevecoeur, David J. Lea-Smith, Bin Long, Naaman M. Omar, Suzanne M. Paley, Nicolas M. Schmelling, Alejandro Torrado, Jonathan P. Zehr, Peter D. Karp
Publikováno v:
Frontiers in Microbiology, Vol 15 (2024)
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 needs of the cyanobacterial research and b
Externí odkaz:
https://doaj.org/article/9d9a660bb9a24a14af33a398e0dbb1fb
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
Publikováno v:
BMC Genomics, Vol 22, Iss 1, Pp 1-11 (2021)
Abstract Background Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expre
Externí odkaz:
https://doaj.org/article/2d9bd4ebc1624d689a01172f053f63dc
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