Publications

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2026

Modular determinants of cleavage preference in GIY-YIG nucleases revealed by block-based DNA shuffling and directed evolution

Loedige KW, Hall MA, Ghimirey S, Stead BE, Edgell DR

Nucleic Acids Research
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Machine learning reveals sequence and methylation determinants of SaCas9-PAM interactions in bacteria

Ham DT, Browne TS, Zhang CQ, Foo GW, Uruthirapathy AS, Gloor GB, Edgell DR

Nucleic Acids Research
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Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction

Browne TS, Edgell DR, Gloor GB

PeerJ
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PHYCUT: Scalable Multiplex CRISPR/Cas9 editing for Genome Engineering in the Diatom Phaeodactylum tricornutum

Stuckless EE, Gai LS, Slattery SS, Dempsey KH, Browne TS, Gloor GB, Edgell DR

ACS Synthetic Biology
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2025

Ku limits RNA-induced innate immunity to allow Alu expansion in primates

Zhu Y, Li A, Maji S, Lee BJ, Korn SM, Gertie JA, Dorrity TJ, Wang J, Wang KJ, Pelletier A, Moakley DF, Kelly RD, Holmes AB, Rabadan R, Edgell DR, Schild-Poulter C, Modesti M, Steckelberg AL, Hendrickson EA, Chung H, Zhang C, Zha S

Nature
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Genetic Entanglement Enables Ultrastable Biocontainment in the Mammalian Gut

Foo GW, Uruthirapathy AS, Zhang CQ, Batko IZ, Heinrichs DE, Edgell DR

ACS Synthetic Biology
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A buffer-tuning strategy to profile domain-specific activity of chimeric I-TevI/CRISPR gene editors in vitro

Loedige KW, White AL, McMurrough TA, Stead BE, Edgell DR

Scientific Reports
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2024

Intein-based thermoregulated meganucleases for containment of genetic material

Foo GW, Leichthammer CD, Saita IM, Lukas ND, Batko IZ, Heinrichs DE, Edgell DR

Nucleic Acids Research
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2023

Metabolically-targeted dCas9 expression in bacteria

Pellegrino GM, Browne TS, Sharath K, Bari KA, Vancuren SJ, Allen-Vercoe E, Gloor GB, Edgell DR

Nucleic Acids Research
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Noncanonical functions of Ku may underlie essentiality in human cells

Kelly RD, Parmar G, Bayat L, Maitland MER, Lajoie GA, Edgell DR, Schild-Poulter C

Scientific Reports
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A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets

Ham DT, Browne TS, Banglorewala PN, Wilson TL, Michael RK, Gloor GB, Edgell DR

Nature Communications
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De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials

Hamilton TA, Joris BR, Shrestha A, Browne TS, Rodrigue S, Karas BJ, Gloor GB, Edgell DR

ACS Synthetic Biology
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2022

Conjugation-Based Genome Engineering in Deinococcus radiodurans

Brumwell SL, Van Belois KD, Giguere DJ, Edgell DR, Karas BJ

ACS Synthetic Biology
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Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics

Slattery SS, Giguere DJ, Stuckless EE, Shrestha A, Briere LK, Galbraith A, Reaume S, Boyko X, Say HH, Browne TS, Frederick MI, Lant JT, Heinemann IU, O'Donoghue P, Dsouza L, Martin S, Howard P, Jedeszko C, Ali K, Styba G, Flatley M, Karas BJ, Gloor GB, Edgell DR

Scientific Reports
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Telomere-to-telomere genome assembly of Phaeodactylum tricornutum

Giguere DJ, Bahcheli AT, Slattery SS, Patel RR, Browne TS, Flatley M, Karas BJ, Edgell DR, Gloor GB

PeerJ
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Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi

Cochrane RR, Shrestha A, Severo de Almeida MM, Agyare-Tabbi M, Brumwell SL, Hamadache S, Meaney JS, Nucifora DP, Say HH, Sharma J, Soltysiak MPM, Tong C, Van Belois K, Walker EJL, Lachance MA, Gloor GB, Edgell DR, Shapiro RS, Karas BJ

BioDesign Research
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Editorial: Genetically mobile elements repurposed by nature and biotechnologists

Lennon CW, Callahan BP, Cousineau B, Edgell DR, Belfort M

Frontiers in Molecular Biosciences
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2020

Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing

Slattery SS, Wang H, Giguere DJ, Kocsis C, Urquhart BL, Karas BJ, Edgell DR

Scientific Reports
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Cloning of Thalassiosira pseudonana's Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli

Cochrane RR, Brumwell SL, Shrestha A, Giguere DJ, Hamadache S, Gloor GB, Edgell DR, Karas BJ

Biology
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2019

Designer Sinorhizobium meliloti strains and multi-functional vectors enable direct inter-kingdom DNA transfer

Brumwell SL, MacLeod MR, Huang T, Cochrane RR, Meaney RS, Zamani M, Matysiakiewicz O, Dan KN, Janakirama P, Edgell DR, Charles TC, Finan TM, Karas BJ

PLOS ONE
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Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing

Hamilton TA, Pellegrino GM, Therrien JA, Ham DT, Bartlett PC, Karas BJ, Gloor GB, Edgell DR

Nature Communications
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Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease

Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR

Nucleic Acids Research
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Trans-Kingdom Conjugation within Solid Media from Escherichia coli to Saccharomyces cerevisiae

Soltysiak MPM, Meaney RS, Hamadache S, Janakirama P, Edgell DR, Karas BJ

International Journal of Molecular Sciences
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2018

An Expanded Plasmid-Based Genetic Toolbox Enables Cas9 Genome Editing and Stable Maintenance of Synthetic Pathways in Phaeodactylum tricornutum

Slattery SS, Diamond A, Wang H, Therrien JA, Lant JT, Jazey T, Lee K, Klassen Z, Desgagné-Penix I, Karas BJ, Edgell DR

ACS Synthetic Biology
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Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

Kaiser JC, King AN, Grigg JC, Sheldon JR, Edgell DR, Murphy MEP, Brinsmade SR, Heinrichs DE

PLOS Genetics
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mitoTev-TALE: a monomeric DNA editing enzyme to reduce mutant mitochondrial DNA levels

Pereira CV, Bacman SR, Arguello T, Zekonyte U, Williams SL, Edgell DR, Moraes CT

EMBO Molecular Medicine
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Delivery of the Cas9 or TevCas9 system into Phaeodactylum tricornutum via conjugation of plasmids from a bacterial donor

Wang H, Slattery SS, Karas BJ, Edgell DR

Bio-Protocol
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Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases

McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR

Nucleic Acids Research
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2017

Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia)

Celis JS, Edgell DR, Stelbrink B, Wibberg D, Hauffe T, Blom J, Kalinowski J, Wilke T

PLOS ONE
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Applications of Alternative Nucleases in the Age of CRISPR/Cas9

Guha TK, Edgell DR

International Journal of Molecular Sciences
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2016

Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference

Roy AC, Wilson GG, Edgell DR

Nucleic Acids Research
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Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease

Wolfs JM, Hamilton TA, Lant JT, Laforet M, Zhang J, Salemi LM, Gloor GB, Schild-Poulter C, Edgell DR

Proceedings of the National Academy of Sciences USA
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2014

Rapid screening of endonuclease target site preference using a modified bacterial two-plasmid selection

Wolfs JM, Kleinstiver BP, Edgell DR

Methods in Molecular Biology
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Bacterial group I introns: mobile RNA catalysts

Hausner G, Hafez M, Edgell DR

Mobile DNA
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The I-TevI nuclease and linker domains contribute to the specificity of monomeric TALENs

Kleinstiver BP, Wang L, Wolfs JM, Kolaczyk T, McDowell B, Wang X, Schild-Poulter C, Bogdanove AJ, Edgell DR

G3: Genes, Genomes, Genetics
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Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB

Microbiome
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Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues

McMurrough TA, Dickson RJ, Thibert SM, Gloor GB, Edgell DR

Proceedings of the National Academy of Sciences USA
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MegaTevs: single-chain dual nucleases for efficient gene disruption

Wolfs JM, DaSilva M, Meister SE, Wang X, Schild-Poulter C, Edgell DR

Nucleic Acids Research
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2013

The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA

Kleinstiver BP, Wolfs JM, Edgell DR

Nucleic Acids Research
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2012

Monomeric site-specific nucleases for genome editing

Kleinstiver BP, Wolfs JM, Kolaczyk T, Roberts AK, Hu SX, Edgell DR

Proceedings of the National Academy of Sciences USA
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2011

Assembly of a fragmented ribonucleotide reductase by protein interaction domains derived from a mobile genetic element

Crona M, Moffatt C, Friedrich NC, Hofer A, Sjöberg BM, Edgell DR

Nucleic Acids Research
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Learning to live together: mutualism between self-splicing introns and their hosts

Edgell DR, Chalamcharla VR, Belfort M

BMC Biology
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Tapping natural reservoirs of homing endonucleases for targeted gene modification

Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL

Proceedings of the National Academy of Sciences USA
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Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI

Kleinstiver BP, Bérubé-Janzen W, Fernandes AD, Edgell DR

PLOS ONE
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2010

A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI

Kleinstiver BP, Fernandes AD, Gloor GB, Edgell DR

Nucleic Acids Research
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Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron

Gibb EA, Edgell DR

Molecular Microbiology
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Subunit and small-molecule interaction of ribonucleotide reductases via surface plasmon resonance biosensor analyses

Crona M, Furrer E, Torrents E, Edgell DR, Sjöberg BM

Protein Engineering, Design and Selection
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Mobile DNA elements in T4 and related phages

Edgell DR, Gibb EA, Belfort M

Virology Journal
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Estimating the evidence of selection and the reliability of inference in unigenic evolution

Fernandes AD, Kleinstiver BP, Edgell DR, Wahl LM, Gloor GB

Algorithms for Molecular Biology
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2009

An RNA hairpin sequesters the ribosome binding site of the homing endonuclease mobE gene

Gibb EA, Edgell DR

Journal of Bacteriology
Selfish DNA: homing endonucleases find a home

Edgell DR

Current Biology
Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene

Sethuraman J, Majer A, Friedrich NC, Edgell DR, Hausner G

Molecular Biology and Evolution
Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII

Wilson GW, Edgell DR

Nucleic Acids Research
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2007

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase

Friedrich NC, Torrents E, Gibb EA, Sahlin M, Sjöberg BM, Edgell DR

Proceedings of the National Academy of Sciences USA
Multiple controls regulate the expression of mobE, an HNH homing endonuclease gene

Gibb EA, Edgell DR

Journal of Bacteriology
Strand-specific contacts and divalent metal ion regulate double-strand break formation by the GIY-YIG homing endonuclease I-BmoI

Carter JM, Friedrich NC, Kleinstiver B, Edgell DR

Journal of Molecular Biology

2006

Distance determination by GIY-YIG intron endonucleases

Liu Q, Derbyshire V, Belfort M, Edgell DR

Nucleic Acids Research

2004

Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor

Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M

Nature Structural & Molecular Biology
FhuD1, a ferric hydroxamate-binding lipoprotein in Staphylococcus aureus

Sebulsky MT, Speziali CD, Shilton BH, Edgell DR, Heinrichs DE

Journal of Biological Chemistry
Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host group I intron

Edgell DR, Stanger MJ, Belfort M

Journal of Molecular Biology

2003

Importance of a single base pair for discrimination between intron-containing and intronless alleles by the homing endonuclease I-BmoI

Edgell DR, Stanger MJ, Belfort M

Current Biology
SegG endonuclease promotes marker exclusion and mediates co-conversion from the phage T4 genome

Liu Q, Belle A, Shub DA, Belfort M, Edgell DR

Journal of Molecular Biology

2002

Selfish DNA: new abode for homing endonucleases

Edgell DR

Current Biology

2001

Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites

Edgell DR, Shub DA

Proceedings of the National Academy of Sciences USA

2000

Barriers to intron promiscuity in bacteria

Edgell DR, Belfort M, Shub DA

Journal of Bacteriology

1998

Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases

Edgell DR, Malik SB, Doolittle WF

Molecular Biology and Evolution

1997

Gene duplications in evolution of archaeal family B DNA polymerases

Edgell DR, Klenk HP, Doolittle WF

Journal of Bacteriology
Archaea and the origin(s) of DNA replication proteins

Edgell DR, Doolittle WF

Cell

1996

Selfish DNA: the best defense is a good offense

Edgell DR, Fast NM, Doolittle WF

Current Biology