Ron Caspi
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Explore the profile of Ron Caspi including associated specialties, affiliations and a list of published articles.
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33
Citations
4592
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Recent Articles
1.
Moore L, Caspi R, Boyd D, Berkmen M, Mackie A, Paley S, et al.
Nucleic Acids Res
. 2024 Oct;
52(20):12201-12207.
PMID: 39373482
The model organism Escherichia coli K-12 has one of the most extensively annotated genomes in terms of functional characterization, yet a significant number of genes, ∼35%, are still considered poorly...
2.
Swart A, Caspi R, Paley S, Karp P
Front Bioinform
. 2024 Sep;
4:1395981.
PMID: 39318761
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...
3.
Paley S, Caspi R, OMaille P, Karp P
Front Microbiol
. 2024 Aug;
15:1447632.
PMID: 39144229
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...
4.
Caspi R, Karp P
Access Microbiol
. 2024 Jul;
6(6).
PMID: 39045247
ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations...
5.
Paley S, Caspi R, OMaille P, Karp P
bioRxiv
. 2024 Jun;
PMID: 38915637
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...
6.
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...
7.
Karp P, Paley S, Caspi R, Kothari A, Krummenacker M, Midford P, et al.
EcoSal Plus
. 2023 May;
11(1):eesp00022023.
PMID: 37220074
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the...
8.
Keseler I, Gama-Castro S, Mackie A, Billington R, Bonavides-Martinez C, Caspi R, et al.
Front Microbiol
. 2021 Aug;
12:711077.
PMID: 34394059
The EcoCyc model-organism database collects and summarizes experimental data for K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways,...
9.
Swietnicki W, Caspi R
Pathogens
. 2021 Apr;
10(3).
PMID: 33804654
is an oral human pathogen. The bacterium destroys dental tissue and is a serious health problem worldwide. Experimental data and bioinformatic analysis revealed that the pathogen produces three types of...
10.
Karp P, Midford P, Caspi R, Khodursky A
BMC Genomics
. 2021 Mar;
22(1):191.
PMID: 33726670
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...