Matthew Nethery

Works (10)

Updated: April 19th, 2025 05:02

2025 article

Characterization of diverse Cas9 orthologs for genome and epigenome editing

Butterfield, G. L., Rohm, D., Roberts, A., Nethery, M. A., Rizzo, A. J., Morone, D. J., … Gersbach, C. A. (2025, March 12). Proceedings of the National Academy of Sciences, Vol. 122.

By: G. Butterfield *, D. Rohm*, A. Roberts n, M. Nethery n, A. Rizzo *, D. Morone*, L. Garnier*, N. Iglesias *, R. Barrangou n , C. Gersbach*

author keywords: CRISPR; genome editing; Cas9
MeSH headings : Gene Editing / methods; CRISPR-Cas Systems; Humans; CRISPR-Associated Protein 9 / metabolism; CRISPR-Associated Protein 9 / genetics; Epigenome; Streptococcus pyogenes / genetics; Staphylococcus aureus / genetics; HEK293 Cells; Genome, Human
topics (OpenAlex): CRISPR and Genetic Engineering; Insect symbiosis and bacterial influences; Mosquito-borne diseases and control
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: March 12, 2025

2024 article

Characterization of Ligilactobacillus salivarius CRISPR-Cas systems

Roberts, A., Spang, D., Sanozky-Dawes, R., Nethery, M. A., & Barrangou, R. (2024, July 11). (C. D. Ellermeier, Ed.). MSphere, Vol. 7.

By: A. Roberts n, D. Spang n, R. Sanozky-Dawes n, M. Nethery n & R. Barrangou n 

Ed(s): C. Ellermeier

author keywords: Ligilactobacillus; salivarius; CRISPR; Cas
MeSH headings : CRISPR-Cas Systems; Genome, Bacterial; Ligilactobacillus salivarius / genetics; Ligilactobacillus salivarius / physiology; Clustered Regularly Interspaced Short Palindromic Repeats
topics (OpenAlex): CRISPR and Genetic Engineering; Bacteriophages and microbial interactions; RNA and protein synthesis mechanisms
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 15, 2024

2022 article

CRISPR-based engineering of phages for in situ bacterial base editing

Nethery, M. A., Hidalgo-Cantabrana, C., Roberts, A., & Barrangou, R. (2022, November 7). Proceedings of the National Academy of Sciences, Vol. 119.

By: M. Nethery n, C. Hidalgo-Cantabrana  n, A. Roberts n & R. Barrangou n 

author keywords: phage engineering; CRISPR; base editing; soil microbiome
MeSH headings : Gene Editing; CRISPR-Cas Systems / genetics; Bacteriophages / genetics; Ecosystem; Soil
topics (OpenAlex): CRISPR and Genetic Engineering; Bacteriophages and microbial interactions; Transgenic Plants and Applications
TL;DR: Phage-assisted delivery, together with base editing, offers an important in situ editing approach for the genetic interrogation of microbial community members. (via Semantic Scholar)
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15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 8, 2022

2022 article

Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil

Monte, D. F. M., Nethery, M. A., Berman, H., Keelara, S., Lincopan, N., Fedorka-Cray, P. J., … Landgraf, M. (2022, June 17). Frontiers in Microbiology, Vol. 6.

By: D. Monte *, M. Nethery n, H. Berman n, S. Keelara n, N. Lincopan *, P. Fedorka-Cray n, R. Barrangou n , M. Landgraf *

author keywords: antibiotic resistance; CRISPR; phylogeny; Salmonella Heidelberg; foodborne disease; WGS
topics (OpenAlex): Salmonella and Campylobacter epidemiology; Antibiotic Resistance in Bacteria; Bacteriophages and microbial interactions; Vibrio bacteria research studies; Listeria monocytogenes in Food Safety
TL;DR: The findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae and emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: July 11, 2022

2022 article

Functional characterization of diverse type I-F CRISPR-associated transposons

Roberts, A., Nethery, M. A., & Barrangou, R. (2022, November 11). Nucleic Acids Research, Vol. 11.

By: A. Roberts n, M. Nethery n & R. Barrangou n 

MeSH headings : CRISPR-Cas Systems; Plasmids; Endonucleases / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; DNA; RNA; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism
topics (OpenAlex): CRISPR and Genetic Engineering; Chromosomal and Genetic Variations; Bacterial Genetics and Biotechnology
TL;DR: This work selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli, demonstrating that these systems possess a significant range of integration efficiencies with regards to temperature, transposition size, and flexible PAM requirements. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 19, 2022

2021 article

CRISPRclassify: Repeat-Based Classification of CRISPR Loci

Nethery, M. A., Korvink, M., Makarova, K. S., Wolf, Y. I., Koonin, E. V., & Barrangou, R. (2021, August 1). The CRISPR Journal, Vol. 8.

By: M. Nethery n, M. Korvink *, K. Makarova *, Y. Wolf *, E. Koonin * & R. Barrangou n 

MeSH headings : Algorithms; Area Under Curve; Base Sequence; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computational Biology / methods; Databases, Genetic; Gene Editing; Genetic Loci; Genome, Bacterial; Genomics / methods; Reproducibility of Results
topics (OpenAlex): CRISPR and Genetic Engineering; RNA and protein synthesis mechanisms; Genomics and Phylogenetic Studies
TL;DR: Although the performance of cas-based identification will exceed that of a repeat-based approach in many cases, CRISprclassify provides an efficient approach to classification of CRISPR loci for cases in which cas gene information is unavailable, such as metagenomes and fragmented genome assemblies. (via Semantic Scholar)
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4. Quality Education (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: September 7, 2021

2020 article

Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources

Monte, D. F. M., Nethery, M. A., Barrangou, R., Landgraf, M., & Fedorka-Cray, P. J. (2020, August 4). Food Microbiology, Vol. 93.

By: D. Monte  n, M. Nethery n, R. Barrangou n , M. Landgraf * & P. Fedorka-Cray  n

author keywords: Antibiotic resistance; CRISPR; Phylogeny; Salmonella serovars; Whole genome sequencing
MeSH headings : Anti-Bacterial Agents / pharmacology; Brazil; Clustered Regularly Interspaced Short Palindromic Repeats; Drug Resistance, Multiple, Bacterial / genetics; Food Microbiology; Genome, Bacterial; Genotype; Genotyping Techniques; Microbial Sensitivity Tests; Salmonella / classification; Salmonella / genetics; Salmonella / isolation & purification; Salmonella Food Poisoning; Salmonella enterica / classification; Salmonella enterica / drug effects; Salmonella enterica / genetics; Salmonella enterica / isolation & purification; Serogroup; Serotyping; Whole Genome Sequencing
topics (OpenAlex): Salmonella and Campylobacter epidemiology; Vibrio bacteria research studies; Antibiotic Resistance in Bacteria
TL;DR: CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 5, 2020

2019 article

Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

Nethery, M. A., Henriksen, E. D. C., Daughtry, K. V., Johanningsmeier, S. D., & Barrangou, R. (2019, November 27). BMC Genomics, Vol. 20.

By: M. Nethery n, E. Henriksen n, K. Daughtry n, S. Johanningsmeier n & R. Barrangou n 

author keywords: Lactobacillus buchneri; Comparative genomics; Lactic acid bacteria; CRISPR-Cas systems; Fermentation; Spoilage; Food microbiology
MeSH headings : Computational Biology / methods; Evolution, Molecular; Fermentation; Food Microbiology; Genome, Bacterial; Genomics / methods; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Molecular Sequence Annotation; Phylogeny; Whole Genome Sequencing
topics (OpenAlex): Probiotics and Fermented Foods; Genomics and Phylogenetic Studies; Bacteriophages and microbial interactions
TL;DR: The findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes provide new insights into the genomics of L. buchneri, building a platform for future studies and identifying elements for potential strain manipulation or engineering. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 16, 2019

2018 article

CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline

Nethery, M. A., & Barrangou, R. (2018, August 21). RNA Biology, Vol. 16, pp. 577–584.

By: M. Nethery n & R. Barrangou n 

author keywords: CRISPR-Cas; repeat detection; software; CRISPR spacer; crRNA
MeSH headings : Bacteria / genetics; Base Sequence; CRISPR-Cas Systems / genetics; Computational Biology; Genetic Loci; High-Throughput Nucleotide Sequencing / methods; Time Factors
topics (OpenAlex): CRISPR and Genetic Engineering; Genomics and Phylogenetic Studies; Insect symbiosis and bacterial influences
TL;DR: A high-throughput extraction pipeline coupled with a local web-based visualization tool is constructed which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment and supports accelerated analysis of genomic data sets. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 20, 2019

2018 article

Predicting and visualizing features of CRISPR–Cas systems

Nethery, M. A., & Barrangou, R. (2018, December 19). Methods in Enzymology on CD-ROM/Methods in Enzymology, Vol. 616, pp. 1–25.

By: M. Nethery n & R. Barrangou n 

MeSH headings : Animals; Bacteria / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Simulation; Gene Editing / methods; Genomics / methods; Humans; RNA, Guide, Kinetoplastida / genetics; Software
topics (OpenAlex): CRISPR and Genetic Engineering; RNA and protein synthesis mechanisms; Genomics and Phylogenetic Studies
TL;DR: In silico methods for predicting and visualizing notable features of CRISPR-Cas systems, including Cas domain determination,CRISPR array visualization, and inference of the protospacer-adjacent motif are described. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: December 30, 2019

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