Jonathan M. Monk

Also affiliated with La Jolla Bioengineering Institute

Biochemistry, Genetics and Molecular BiologyEngineering

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.601Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2218835120

Top 33%

0.601DataRank

Top 33%22 citations

Patrick V. Phaneuf, Jonathan M. Monk, Bernhard Ø. Palsson, Edward Catoiu

Papers

Driven by 36 papers — median percentile 0. Top paper: “Systems biology of the structural proteome”.

Systems biology of the structural proteome

BMC Systems Biology(2016)10.1186/s12918-016-0271-6

N/A

1.9DataRank · unranked

60 citations

Nathan Mih, Zhen Zhang, Edward J. O’Brien, Ke Chen, Roger L. Chang +5 more

Impact of insertion sequences on convergent evolution of Shigella species

PLoS Genetics(2020)10.1371/journal.pgen.1008931

N/A

1.7DataRank · unranked

67 citations

Jonathan M. Monk, Helen Billman‐Jacobe, Bernhard Ø. Palsson, Kathryn E. Holt, Jane Hawkey

Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2218835120

Top 33%

0.601DataRank

Top 33%22 citations

Patrick V. Phaneuf, Jonathan M. Monk, Bernhard Ø. Palsson, Edward Catoiu

Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media

GigaScience(2021)10.1093/gigascience/giaa156

N/A

0.548DataRank · unranked

15 citations

Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson +14 more

Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Current Research in Microbial Sciences(2023)10.1016/j.crmicr.2023.100180

N/A

0.241DataRank · unranked

4 citations

Alison Coady, Richard Szubin, Thomas Martin, Bernhard Ø. Palsson, Victor Nizet +2 more

CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli

Communications Biology(2024)10.1038/s42003-024-06831-0

N/A

0.184DataRank · unranked

2 citations

Hyun Gyu Lim, Ye Gao, Dmitry A. Rodionov, Ying Hutchison, Richard Szubin +4 more

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

Frontiers in Microbiology(2020)10.3389/fmicb.2020.596626

N/A

0DataRank · unranked

4 citations

Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard Ø. Palsson, Mary N. Parenteau +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.27.065417

N/A

0DataRank · unranked

7 citations

Ye Gao, Anand V. Sastry, Jonathan M. Monk, Nicholas Wong, Richard Szubin +5 more

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.23.003236

N/A

0DataRank · unranked

3 citations

Jonathan M. Monk, Laurence Yang, Ali Ebrahim, Bernhard Ø. Palsson, Colton J. Lloyd

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.30.070904

N/A

0DataRank · unranked

3 citations

Saugat Poudel, Hannah Tsunemoto, Richard Szubin, Michael J. Meehan, Connor A. Olson +15 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.19.079962

N/A

0DataRank · unranked

2 citations

Yara Seif, Hannah Tsunemoto, Saugat Poudel, Michael J. Meehan, Richard Szubin +15 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.25.061994

N/A

0DataRank · unranked

0 citations

Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.06.079640

N/A

0DataRank · unranked

0 citations

Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson +14 more

Metabolic and Behavioral Features of Acute Hyperpurinergia and the Connection to Autism Spectrum Disorder

Research Square(2020)10.21203/rs.3.rs-63567/v1

N/A

0DataRank · unranked

0 citations

Jane C. Naviaux, Tomohiro Nakayama, Charlotte M. Hirsch, Jonathan M. Monk, Kefeng Li +6 more

Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

mSystems(2021)10.1128/msystems.00981-20

N/A

0DataRank · unranked

45 citations

Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk +2 more

Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder

PLoS ONE(2021)10.1371/journal.pone.0248771

N/A

0DataRank · unranked

26 citations

Jane C. Naviaux, Tomohiro Nakayama, Charlotte M. Hirsch, Jonathan M. Monk, Kefeng Li +6 more

Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia

PLoS ONE(2021)10.1371/journal.pone.0258592

N/A

0DataRank · unranked

14 citations

Jonathan M. Monk, Richard Szubin, Andrew D. Berti, Christopher R. Miller

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

PLoS Computational Biology(2021)10.1371/journal.pcbi.1007817

N/A

0DataRank · unranked

11 citations

Jonathan M. Monk, Laurence Yang, Ali Ebrahim, Bernhard Ø. Palsson, Colton J. Lloyd

Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.20.473592

N/A

0DataRank · unranked

0 citations

Henrik Westh, Michael Kemp, Svend Ellermann‐Eriksen, Bernhard Ø. Palsson, Helle Krogh Johansen +2 more

Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

BMC Genomics(2022)10.1186/s12864-021-08223-8

N/A

0DataRank · unranked

87 citations

Jonathan M. Monk, Bernhard Ø. Palsson, Jason C. Hyun

Mathematical models to study the biology of pathogens and the infectious diseases they cause

iScience(2022)10.1016/j.isci.2022.104079

N/A

0DataRank · unranked

22 citations

Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao +15 more

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Scientific Reports(2022)10.1038/s41598-022-11134-7

N/A

0DataRank · unranked

22 citations

Ye Gao, Jonathan M. Monk, Ying Hefner, Nicholas Wong, Richard Szubin +6 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.487056

N/A

0DataRank · unranked

4 citations

Patrick V. Phaneuf, Jonathan M. Monk, Bernhard Ø. Palsson, Edward Catoiu

Metabolic features of treatment-refractory major depressive disorder with suicidal ideation

Translational Psychiatry(2023)10.1038/s41398-023-02696-9

N/A

0DataRank · unranked

34 citations

Jane C. Naviaux, Lin Wang, Kefeng Li, Jonathan M. Monk, Sai Sachin Lingampelly +8 more

Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

Nature Communications(2023)10.1038/s41467-023-43549-9

N/A

0DataRank · unranked

20 citations

Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard Ø. Palsson, Jason C. Hyun

Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD+ precursor nicotinamide riboside

Heliyon(2023)10.1016/j.heliyon.2023.e17392

N/A

0DataRank · unranked

2 citations

Zhiquan Li, Yuan Li, Alexander Hendriksen, Peter Bjarn Christensen, Lin Wang +7 more

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.16.541025

N/A

0DataRank · unranked

1 citations

Hyun Gyu Lim, Dmitry A. Rodionov, Ying Hutchison, Christopher Dalldorf, Ye Gao +3 more

Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.26.542542

N/A

0DataRank · unranked

1 citations

Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard Ø. Palsson, Jason C. Hyun

Colistin exerts potent activity against mcr+ Enterobacteriaceae via synergistic interactions with the host defense

Journal of Clinical Investigation(2025)10.1172/jci170690

N/A

0DataRank · unranked

4 citations

Angelica M. Riestra, Anabel Flores, Samira Dahesh, Fatemeh Askarian, Satoshi Uchiyama +15 more

Investigating Azithromycin Activity Against ESBL-Producing Escherichia coli Under Physiologically Relevant Conditions

The Journal of Infectious Diseases(2025)10.1093/infdis/jiaf480

N/A

0DataRank · unranked

2 citations

Samira Dahesh, Elisabet Bjånes, Jonathan M. Monk, Natalie Chavarria, Sachiko Correa +5 more

PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data

Microbiology Spectrum(2025)10.1128/spectrum.03279-24

N/A

0DataRank · unranked

3 citations

Ying Hefner, Richard Szubin, Jonathan M. Monk, David T. Pride, Bernhard Ø. Palsson +1 more

Additional File 2: Database S2:

Figshare(2016)10.6084/m9.figshare.c.3634922_d2

Top 100%

0DataRank

Top 100%0 citations

Nathan Mih, Jonathan M. Monk, Zhen Zhang, Edward OâBrien, Spencer E. Bliven +5 more

Additional File 3: Database S1:

Figshare(2016)10.6084/m9.figshare.c.3634922_d3

Top 100%

0DataRank

Top 100%0 citations

Nathan Mih, Jonathan M. Monk, Zhen Zhang, Edward OâBrien, Spencer E. Bliven +5 more

MEMOTE for standardized genome-scale metabolic model testing

Nature Biotechnology(2020)10.1038/s41587-020-0446-y

N/A

0DataRank · unranked

558 citations

Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meriç Ataman, Parizad Babaei +64 more

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007608

N/A

0DataRank · unranked

90 citations

Erol Kavvas, Jonathan M. Monk, Bernhard Ø. Palsson, Jason C. Hyun

Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

npj Systems Biology and Applications(2020)10.1038/s41540-020-00151-9

N/A

0DataRank · unranked

30 citations

Heather A. Danhof, Colleen K. Brand, Numan Oezguen, Firas S. Midani, Bernhard Ø. Palsson +5 more

Jonathan M. Monk

Indexed papers

Top data-sharing exemplar

Papers