Author

J. Monk

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 7 Bioengineering· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Assay:whole-genome sequencing· 4 Assay:bulk RNA-seq· 3 Research Focus:chromatin & epigenetic regulation· 3 Research Focus:drug response / drug discovery· 3 Organism:E. coli· 3 Organism:human· 3 Approach:statistical model· 3

Frequent Co-Authors

A. Rajput· 4 shared B. O. Palsson· 4 shared R. Szubin· 4 shared S. Poudel· 4 shared Y. Seif· 4 shared A. Feist· 3 shared A. Lamsa· 3 shared A. Vrbanac· 3 shared

Activity by Year

2018-2022 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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4 shared papersMicrobiology

A. Rajput

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Author profile →

8 papers

Recent·Most cited

Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

E. A. Catoiu, P. V. Phaneuf, J. Monk, B. Palsson

The paper compares laboratory-acquired mutations to the wild-type alleleome of E. coli, finding that lab mutations rarely exist in the wild-type alleleome and are less likely to be synonymous.

bioRxiv · Apr 4, 2022 · PreprintBioengineering

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

J. Hawkey, B. Vezina, J. Monk, L. M. Judd, T. Harshegyi, S. Lopez-Fernandez, C. Rodrigues, S. Brisse, K. E. Holt, K. L. Wyres

The paper curates 37 strain-specific genome-scale metabolic models for Klebsiella pneumoniae species complex isolates, revealing strain-specific metabolic differences and gene essentiality.

bioRxiv · Oct 10, 2021Microbiology

Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

N. A. Dillon, Y. Seif, H. Tsunemoto, S. Poudel, M. Meehan, R. Szubin, C. Olson, A. Rajput, G. Alarcon, A. Lamsa, A. Vrbanac, J. Sugie, S. Dahesh, J. Monk, P. Dorrestein, , V. Nizet

This study examines how MDR A. baumannii responds to azithromycin in different growth conditions using multiple analytical techniques.

bioRxiv · May 19, 2020 · PreprintMicrobiology

Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

A. Rajput, S. Poudel, H. Tsunemoto, M. Meehan, R. Szubin, C. Olson, Y. Seif, A. Lamsa, N. Dillon, A. Vrbanac, J. Sugie, S. Dahesh, J. Monk, P. Dorrestein, J. Pogliano, , B. O. Palsson

The paper examines vancomycin's effect on HA-MRSA USA100 strains using bacteriological and physiological media through growth curves, RNA sequencing, and exo-metabolomics.

bioRxiv · May 6, 2020 · PreprintMicrobiology

Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

Y. Seif, S. Poudel, H. Tsunemoto, R. Szubin, M. J. Meehan, C. Olson, A. Rajput, G. Alarcon, A. Lamsa, N. Dillon, A. Vrbanac, J. Sugie, S. Daesh, J. Monk, P. Dorrestein, , V. Nizet

This study investigates how nafcillin affects HA-MRSA D592 in different media types, revealing media-dependent antibiotic activity through multi-dimensional analysis.

bioRxiv · Apr 30, 2020 · PreprintMicrobiology

PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization

I. A. Rodionova, Y. Gao, A. V. Sastry, J. Monk, n. wong, R. Szubin, H. Lim, Z. Zhang, M. H. Saier, B. O. Palsson

This paper identifies PtrR as a dual activator/repressor in E. coli that regulates putrescine stress response and glutamate utilization through transcriptional control of multiple genes.

bioRxiv · Apr 27, 2020 · PreprintMicrobiology

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

A. Rajput, Y. Seif, K. S. Choudhary, C. Dalldorf, S. Poudel, J. Monk, B. O. Palsson

This study uses pangenome analytics to analyze two-component systems in ESKAPEE pathogens, revealing their phylogenetic distribution and sequence variation, and highlights their potential as targets for antibiotic resistance.

bioRxiv · Apr 25, 2020Microbiology

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

K. S. Choudhary, N. Mih, J. Monk, E. Kavvas, J. T. Yurkovich, G. Sakoulas, B. O. Palsson

The paper classifies S. aureus strains based on AgrAC TCS genomic arrangements, linking agr types to virulence factor presence and protein structural properties.

bioRxiv · Mar 6, 2018Microbiology