Vaughn S. Cooper

Biochemistry, Genetics and Molecular BiologyAgricultural and Biological Sciences

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 47 papers. Top paper: “The roles of history, chance, and natural selection in the evolution of antibiotic resistance”.

The roles of history, chance, and natural selection in the evolution of antibiotic resistance

eLife(2021)10.7554/elife.70676

N/A

1.5DataRank · unranked

66 citations

C. W. Marshall, Allison L Haas, Caroline B. Turner, Javier Rasero, Vaughn S. Cooper +1 more

Outbreak of Pseudomonas aeruginosa Infections from a Contaminated Gastroscope Detected by Whole Genome Sequencing Surveillance

Clinical Infectious Diseases(2020)10.1093/cid/ciaa1887

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0DataRank · unranked

48 citations

Jieshi Chen, James Miller, Melissa Saul, Kathleen A. Shutt, M. Patrick Griffith +14 more

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

Frontiers in Microbiology(2020)10.3389/fmicb.2020.574626

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0DataRank · unranked

17 citations

Sandra C. dos Santos, Vaughn S. Cooper, Isabel Sá‐Correia, A. Amir Hassan

Adaptation and Survival of Burkholderia cepacia and B. contaminans During Long-Term Incubation in Saline Solutions Containing Benzalkonium Chloride

Frontiers in Bioengineering and Biotechnology(2020)10.3389/fbioe.2020.00630

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0DataRank · unranked

25 citations

Mariya Kozak, Alexandra Balola, Carla P. Coutinho, Cláudia P. Godinho, A. Amir Hassan +3 more

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.16.155515

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0DataRank · unranked

3 citations

Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, C. Joel McManus +1 more

The roles of history, chance, and natural selection in the evolution of antibiotic resistance

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.22.216465

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0DataRank · unranked

3 citations

C. W. Marshall, Allison L. Welp, Caroline B. Turner, Javier Rasero, Vaughn S. Cooper +1 more

One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.02.074534

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0DataRank · unranked

2 citations

Daniel J. Snyder, Emily Sileo, Caroline B. Turner, Sean W Buskirk, Nico Fernandez +4 more

Experimental evolution to identify undescribed mechanisms of resistance to a novel cationic peptide antibiotic

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.16.423161

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0DataRank · unranked

2 citations

MJ Fritz, JB Lombardo, AHP Burr, VA Heinrich, C. W. Marshall +2 more

Host adaptations in the fixLJ pathway of the Burkholderia cepacia complex increase virulence

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.04.070367

N/A

0DataRank · unranked

0 citations

Benjamin Wang, Nicole M. Boisvert, Sarah Martini, Sarah Bonney, C. W. Marshall +4 more

Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection

Clinical Infectious Diseases(2021)10.1093/cid/ciab946

N/A

0DataRank · unranked

133 citations

Jieshi Chen, Praveen Kumar, Ashley Ayres, Shu‐Ting Cho, Chinelo Ezeonwuka +17 more

Emergence of an early SARS-CoV-2 epidemic in the United States

Cell(2021)10.1016/j.cell.2021.07.030

N/A

0DataRank · unranked

52 citations

Karthik Gangavarapu, Catelyn Anderson, Allison R. Smither, John A. Vanchiere, Rebecca Rose +47 more

Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis

Cell Reports(2021)10.1016/j.celrep.2021.109829

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0DataRank · unranked

44 citations

C. W. Marshall, Arkadiy I. Garber, Jeffrey A. Melvin, Anna C. Zemke, John Allphin Moore +13 more

Rampant prophage movement among transient competitors drives rapid adaptation during infection

Science Advances(2021)10.1126/sciadv.abh1489

N/A

0DataRank · unranked

32 citations

Erin S. Gloag, Christina Lim, Daniel J. Wozniak, Vaughn S. Cooper, C. W. Marshall

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin

PLoS Genetics(2021)10.1371/journal.pgen.1009634

N/A

0DataRank · unranked

15 citations

Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, C. Joel McManus +1 more

Evolution towards Virulence in a Burkholderia Two-Component System

mBio(2021)10.1128/mbio.01823-21

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0DataRank · unranked

9 citations

Benjamin Wang, Nicole M. Boisvert, Sarah Martini, Sarah Bonney, C. W. Marshall +4 more

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

medRxiv(2021)10.1101/2021.02.12.21251658

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0DataRank · unranked

132 citations

Daryl Domman, Daniel J. Snyder, Kasopefoluwa Y. Oguntuyo, Maarten Van Diest, Kenneth Densmore +14 more

Emergence of an early SARS-CoV-2 epidemic in the United States

medRxiv(2021)10.1101/2021.02.05.21251235

N/A

0DataRank · unranked

10 citations

Karthik Gangavarapu, Catelyn Anderson, Allison R. Smither, John A. Vanchiere, Rebecca Rose +47 more

SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.17.452725

N/A

0DataRank · unranked

4 citations

Catherine R. Armbruster, Stella E. Lee, Vaughn S. Cooper, Jennifer M. Bomberger, Sean M. McAllister +1 more

Immunosuppression broadens evolutionary pathways to treatment failure during Acinetobacter baumannii pneumonia

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.07.438861

N/A

0DataRank · unranked

3 citations

Lindsay M. Busch, Juan Hernandez-Bird, Efrat Hamami, C. W. Marshall, Edward Geisinger +5 more

Rampant prophage movement among transient competitors drives rapid adaptation during infection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.01.429245

N/A

0DataRank · unranked

1 citations

Erin S. Gloag, Christina Lim, Daniel J. Wozniak, Vaughn S. Cooper, C. W. Marshall

Excess dietary sugar impairs colonic epithelial regeneration in response to damage

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.18.456840

N/A

0DataRank · unranked

1 citations

Junyi Ji, Kadir Ozler, Onur Eskiocak, Brian Yueh, Ashley V. Menk +12 more

Evolutionary divergence of the Wsp signal transduction system in β- and γ-proteobacteria

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.02.450980

N/A

0DataRank · unranked

0 citations

Eisha Mhatre, Vaughn S. Cooper, Wook Kim, Collin Kessler

Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance

mBio(2022)10.1128/mbio.02759-21

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0DataRank · unranked

98 citations

Mustapha M. Mustapha, M. Patrick Griffith, Lauren Komarow, Courtney Luterbach, Daniel R. Evans +14 more

Immunosuppression broadens evolutionary pathways to drug resistance and treatment failure during Acinetobacter baumannii pneumonia in mice

Nature Microbiology(2022)10.1038/s41564-022-01126-8

N/A

0DataRank · unranked

52 citations

Lindsay M. Busch, Juan Hernandez-Bird, Efrat Hamami, C. W. Marshall, Edward Geisinger +5 more

Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply

Evolution Medicine and Public Health(2022)10.1093/emph/eoac022

N/A

0DataRank · unranked

13 citations

Melissa J. Fritz, J Lombardo, Ansen B.P. Burr, Victoria A. Heinrich, C. W. Marshall +2 more

SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

BMC Genomics(2022)10.1186/s12864-022-08382-2

N/A

0DataRank · unranked

12 citations

Catherine R. Armbruster, Stella E. Lee, Vaughn S. Cooper, Jennifer M. Bomberger, Sean M. McAllister +1 more

Novel Requirement for Staphylococcal Cell Wall-Anchored Protein SasD in Pulmonary Infection

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.01.486802

N/A

0DataRank · unranked

1 citations

Abigail M. Riesmeyer, Vaughn S. Cooper, Jennifer M. Bomberger, Anthony R. Richardson, John F. Alcorn +1 more

Phage therapy in a lung transplant recipient with cystic fibrosis infected with multidrug‐resistant Burkholderia multivorans

Transplant Infectious Disease(2023)10.1111/tid.14041

N/A

0DataRank · unranked

40 citations

Benjamin K. Chan, Shu‐Ting Cho, Kailey Hughes Kramer, Hayley R. Nordstrom, Nathan R. Wallace +11 more

Excess Dietary Sugar Alters Colonocyte Metabolism and Impairs the Proliferative Response to Damage

Cellular and Molecular Gastroenterology and Hepatology(2023)10.1016/j.jcmgh.2023.05.001

N/A

0DataRank · unranked

25 citations

Junyi Ji, Kadir Ozler, Heather Mentrup, Onur Eskiocak, Brian Yueh +15 more

Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens

EBioMedicine(2023)10.1016/j.ebiom.2023.104681

N/A

0DataRank · unranked

17 citations

Alexander Sundermann, M. Patrick Griffith, Vatsala Rangachar Srinivasa, Mustapha M. Mustapha, Jieshi Chen +5 more

The contribution of DNA repair pathways to Staphylococcus aureus fitness and fidelity during nitric oxide stress

mBio(2023)10.1128/mbio.02156-23

N/A

0DataRank · unranked

5 citations

Srijon K. Banerjee, Amelia C. Stephens, Michelle R. Scribner, Vaughn S. Cooper, Anthony R. Richardson +1 more

A Prospective Cohort Protocol for the Remnant Investigation in Sepsis Study

Critical Care Explorations(2023)10.1097/cce.0000000000000974

N/A

0DataRank · unranked

2 citations

Kelly Urbanek, Anna Nakayama, Jason Kennedy, Rachel E. Powell, Renã A. S. Robinson +14 more

eLife Assessment: Extensive re-modelling of the cell wall during the development of Staphylococcus aureus bacteraemia

(2023)10.7554/elife.87026.2.sa4

N/A

0DataRank · unranked

0 citations

Vaughn S. Cooper

90 Initiation of elexacaftor-tezacaftor-ivacaftor treatment lowers total bacterial load in airways but does not increase microbial diversity or lead to eradication of known pathogens

Journal of Cystic Fibrosis(2023)10.1016/s1569-1993(23)01025-1

N/A

0DataRank · unranked

0 citations

Catherine R. Armbruster, Anna C. Zemke, S. Atteih, C. W. Marshall, John Allphin Moore +7 more

Persistence and evolution of Pseudomonas aeruginosa following initiation of highly effective modulator therapy in cystic fibrosis

mBio(2024)10.1128/mbio.00519-24

N/A

0DataRank · unranked

45 citations

Yasmin Hilliam, Anna C. Zemke, S. Atteih, C. W. Marshall, John Allphin Moore +7 more

Effects of highly effective modulator therapy on the dynamics of the respiratory mucosal environment and inflammatory response in cystic fibrosis

Pediatric Pulmonology(2024)10.1002/ppul.26898

N/A

0DataRank · unranked

16 citations

Catherine R. Armbruster, Yasmin Hilliam, Glenn J. Rapsinski, Junu Koirala Bhusal, Leah Krainz +10 more

Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones

mBio(2024)10.1128/mbio.02828-23

N/A

0DataRank · unranked

9 citations

Haley Echlin, Abigail McKnight, Enolia Marr, Julia Junker, Qidong Jia +6 more

Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting

medRxiv(2024)10.1101/2024.02.16.24302955

N/A

0DataRank · unranked

6 citations

Marissa Pacey Griffith, Alecia B Rokes, Vatsala Rangachar Srinivasa, Erin M. Nawrocki, Deena Ereifej +10 more

Mutations Leading to Ceftolozane/Tazobactam and Imipenem/Cilastatin/Relebactam Resistance During in vivo exposure to Ceftazidime/Avibactam in Pseudomonas aeruginosa

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.10.612322

N/A

0DataRank · unranked

0 citations

Alecia B Rokes, Daria Van Tyne, Vaughn S. Cooper, Glenn J. Rapsinski

Mutations leading to ceftolozane/tazobactam and imipenem/cilastatin/relebactam resistance during in vivo exposure to ceftazidime/avibactam in Pseudomonas aeruginosa

Microbiology Spectrum(2025)10.1128/spectrum.02312-24

N/A

0DataRank · unranked

8 citations

Alecia B Rokes, Daria Van Tyne, Vaughn S. Cooper, Glenn J. Rapsinski

Evaluation of V3–V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates

mSphere(2025)10.1128/msphere.00388-25

N/A

0DataRank · unranked

6 citations

Vaughn S. Cooper, Anna C. Zemke, Ankit Gupta

Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms

npj Biofilms and Microbiomes(2025)10.1038/s41522-025-00863-y

N/A

0DataRank · unranked

1 citations

Isabel-Sophie Kramer, Cristina I. Amador, Lorrie Maccario, Asmus Kalckar Olesen, Vaughn S. Cooper +2 more

Filamentous cheater phages drive bacterial and phage populations to lower fitness

Current Biology(2025)10.1016/j.cub.2025.09.029

N/A

0DataRank · unranked

1 citations

Michelle R. Scribner, Vaughn S. Cooper, Nanami Kubota

Student-led experimental evolution reveals novel biofilm regulators of adaptation to multiple niches

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.06.658356

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0DataRank · unranked

1 citations

Colton W. Siatkowski, Changhua Yan, Sachin Thiagarajan, Vaughn S. Cooper, Abigail M. Matela

Respiratory viral infection is associated with increased Pseudomonas abundance in cystic fibrosis airways

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.08.663034

N/A

0DataRank · unranked

1 citations

Catherine R. Armbruster, S. Atteih, Glenn J. Rapsinski, John Allphin Moore, Junu Koirala +7 more

Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network

Cell Reports(2020)10.1016/j.celrep.2020.107823

N/A

0DataRank · unranked

73 citations

Jack P. Kanarek, Dan Snyder, Vaughn S. Cooper, Seema S. Lakdawala, Nara Lee +1 more

Pseudomonas aeruginosa biofilm-deficient mutants undergo parallel adaptation during chronic infection

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.20.677542

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0DataRank · unranked

1 citations

C. W. Marshall, Nanami Kubota, Stacie E. Deaver, Brennan Deshote, Vaughn S. Cooper +2 more