Ashlee M. Earl

Also affiliated with Vanderbilt University Medical Center

Biochemistry, Genetics and Molecular BiologyMedicine

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 1%percentile

10.9Author 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.

A framework for human microbiome research

Nature(2012)10.1038/nature11209

Top 2%

8.4DataRank

Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Papers

Driven by 60 papers — median percentile 90. Top paper: “A framework for human microbiome research”.

A framework for human microbiome research

Nature(2012)10.1038/nature11209

Top 2%

8.4DataRank

Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

Nature Communications(2021)10.1038/s41467-021-25484-9

Top 10%

2.2DataRank

Top 10%49 citations

Chhavi Gupta, Abigail L. Manson, Jan A. Nguyen, Asli Bahadirli-Talbott, Nicole Parrish +3 more

Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies

Nature Communications(2022)10.1038/s41467-022-30272-0

N/A

2.0DataRank · unranked

70 citations

Ian W. Andrews, Alexandra Grote, Abigail L. Manson, Miguel A. Alcantar, Ashlee M. Earl +2 more

Structure, function and diversity of the healthy human microbiome

Nature(2012)10.1038/nature11234

N/A

1.4DataRank · unranked

10088 citations

Curtis Huttenhower, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger +235 more

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

PLoS ONE(2014)10.1371/journal.pone.0112963

N/A

1.4DataRank · unranked

10052 citations

Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar +7 more

Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections

BMC Microbiology(2021)10.1186/s12866-021-02106-4

N/A

1.2DataRank · unranked

31 citations

Wen‐Chi Chou, Abigail L. Manson, Henry L. Schreiber, Bruce J. Walker, Christopher A. Desjardins +10 more

Discovery of a structural class of antibiotics with explainable deep learning

Nature(2023)10.1038/s41586-023-06887-8

N/A

0.912DataRank · unranked

435 citations

Erica J. Zheng, Jacqueline A. Valeri, Nina M. Donghia, Melis N. Anahtar, Satotaka Omori +16 more

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Nature(2023)10.1038/s41586-022-05546-8

N/A

0.885DataRank · unranked

364 citations

Marcus C. de Goffau, María Elisa Pérez-Muñoz, Marie‐Claire Arrieta, Fredrik Bäckhed, Peer Bork +41 more

Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes

Briefings in Bioinformatics(2023)10.1093/bib/bbad050

N/A

0.870DataRank · unranked

30 citations

Terrance Shea, Christina A. Cuomo, Bruce J. Walker, Regina C. LaRocque, Abigail L. Manson +3 more

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

Nature Microbiology(2022)10.1038/s41564-022-01107-x

N/A

0.783DataRank · unranked

184 citations

Henry L. Schreiber, Timothy J. Straub, Lucas R. van Dijk, Ryan A. Bronson, Benjamin Olson +20 more

StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Genome biology(2022)10.1186/s13059-022-02630-0

N/A

0.710DataRank · unranked

113 citations

Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber +7 more

Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice

Nature Microbiology(2020)10.1038/s41564-020-0683-3

N/A

0.697DataRank · unranked

103 citations

Wen‐Chi Chou, Abigail L. Manson, Peter Rogov, Thomas Abeel, James Bochicchio +8 more

Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway

Cell Host & Microbe(2024)10.1016/j.chom.2023.12.001

N/A

0.696DataRank · unranked

21 citations

Bar Piscon, Abigail L. Manson, Boaz Adani, Helit Cohen, Jonathan Livny +3 more

Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis

mBio(2020)10.1128/mbio.02962-20

N/A

0.584DataRank · unranked

48 citations

Rauf Salamzade, Elizabeth M. Selleck, Noelle C. Bryan, Suelen Scarpa de Mello, Abigail L. Manson +2 more

QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

BMC Genomics(2020)10.1186/s12864-020-6486-3

N/A

0.584DataRank · unranked

48 citations

Arlin Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl +2 more

Acquisition of Antibiotic-Resistant Bacteria by U.S. International Travelers

New England Journal of Medicine(2020)10.1056/nejmc1912464

N/A

0.533DataRank · unranked

34 citations

Sarah E. Turbett, Colin J. Worby, Elizabeth Oliver, Allison Taylor Walker, Maroya Spalding Walters +8 more

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children

Nature Microbiology(2022)10.1038/s41564-022-01101-3

N/A

0.529DataRank · unranked

33 citations

Val F. Lanza, María Camila Montealegre, Sonia Sultana, Erica R. Fuhrmeister, Colin J. Worby +11 more

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters

Nucleic Acids Research(2025)10.1093/nar/gkaf045

N/A

0.522DataRank · unranked

13 citations

Patricia Q. Tran, Cody Martin, Abigail L. Manson, Michael S. Gilmore, Ashlee M. Earl +3 more

Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter

ACS Infectious Diseases(2022)10.1021/acsinfecdis.2c00446

N/A

0.464DataRank · unranked

21 citations

Monica Patiño, Hader E. Elashal, Alexis Jaramillo Cartagena, Yi Zhang, Megan E. Whitley +6 more

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Nature Communications(2024)10.1038/s41467-024-53829-7

N/A

0.414DataRank · unranked

9 citations

Timothy J. Straub, Colin J. Worby, Hayden C. Metsky, Andreas Gnirke, Ryan A. Bronson +13 more

Development of a prediction model for the acquisition of extended spectrum beta-lactam-resistant organisms in U.S. international travellers

Journal of Travel Medicine(2023)10.1093/jtm/taad028

N/A

0.396DataRank · unranked

13 citations

Colin J. Worby, Melissa Pender, Ben J. Brintz, Edward T. Ryan, Sushmita Sridhar +8 more

Dynamics of microbiome and resistome in a poultry burger processing line

Food Research International(2024)10.1016/j.foodres.2024.114842

N/A

0.292DataRank · unranked

6 citations

Elisa Pagán, Daniel Berdejo, Colin J. Worby, Mark Young, Abigail L. Manson +4 more

Clinical and genomic characterization of Klebsiella pneumoniae infections in Dhaka, Bangladesh

Journal of Global Antimicrobial Resistance(2024)10.1016/j.jgar.2024.12.016

Top 58%

0.267DataRank

Top 58%4 citations

Sushmita Sridhar, Sanchita Kar, Tanbir Habib, Sharmin Akter Mukta, Kasrina Azad +14 more

Fast and exact gap-affine partial order alignment with POASTA

Bioinformatics(2024)10.1093/bioinformatics/btae757

N/A

0.259DataRank · unranked

4 citations

Abigail L. Manson, Ashlee M. Earl, Kiran Garimella, Thomas Abeel, Lucas R. van Dijk

Gut-bladder axis syndrome associated with recurrent UTIs in humans

medRxiv(2021)10.1101/2021.11.15.21266268

N/A

0.241DataRank · unranked

4 citations

Henry L. Schreiber, Timothy J. Straub, Lucas R. van Dijk, Ryan A. Bronson, Benjamin Olson +19 more

Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children

Gut Microbes(2025)10.1080/19490976.2025.2541029

N/A

0.208DataRank · unranked

3 citations

Neha Sehgal, Luismarcelo Rojas-Salvatierra, Robert H. Gilman, Ashlee M. Earl, Colin J. Worby +4 more

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.08.471225

N/A

0.165DataRank · unranked

2 citations

Abigail L. Manson, Bruce J. Walker, Thea Brennan-Krohn, Colin J. Worby, Peijun Ma +27 more

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.29.582780

N/A

0.119DataRank · unranked

1 citations

Timothy J. Straub, Colin J. Worby, Hayden C. Metsky, Andreas Gnirke, Ryan A. Bronson +13 more

Effects of commonly used antibiotics on children’s developing gut microbiomes and resistomes in peri-urban Lima, Peru

Journal of Antimicrobial Chemotherapy(2025)10.1093/jac/dkaf358

N/A

0.104DataRank · unranked

1 citations

Mónica J. Pajuelo, Robert H. Gilman, Amy J. Pickering, Ashlee M. Earl, Colin J. Worby +2 more

Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.21.496976

N/A

0.104DataRank · unranked

1 citations

Bar Piscon, Abigail L. Manson, Jonathan Livny, Ashlee M. Earl, Ohad Gal‐Mor +1 more

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.11.430761

N/A

0.104DataRank · unranked

1 citations

Lorrie L. He, Alejandro Pironti, Hannah H. Laibinis, Christoph M. Ernst, Abigail L. Manson +5 more

SAP: Synteny-aware gene function prediction for bacteria using protein embeddings

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.02.539034

N/A

0DataRank · unranked

1 citations

Bianca-Maria Cosma, Ashlee M. Earl, Abigail L. Manson, Thomas Abeel, Aysun Urhan

Strain tracking with uncertainty quantification

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.25.525531

N/A

0DataRank · unranked

0 citations

Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko +8 more

Intrinsic Resistance to Colistin in the Genus Hafnia

Journal of Clinical Microbiology(2023)10.1128/jcm.01326-22

N/A

0DataRank · unranked

0 citations

Ryan A. Bronson, Colin J. Worby, Graham McGrath, Emily Hodgkins, Margaret Becker +8 more

Global diversity of enterococci and description of 18 previously unknown species

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2310852121

N/A

0DataRank · unranked

45 citations

François Lebreton, Rauf Salamzade, Terrance Shea, Melissa J. Martin, Katharina Schaufler +16 more

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

Science(2021)10.1126/science.aba0862

N/A

0DataRank · unranked

362 citations

Sarah C. Bening, Abigail L. Manson, Jonathan Stokes, Michael A. Kohanski, Ahmed H. Badran +5 more

Colon Cancer-Associated Fusobacterium nucleatum May Originate From the Oral Cavity and Reach Colon Tumors via the Circulatory System

Frontiers in Cellular and Infection Microbiology(2020)10.3389/fcimb.2020.00400

N/A

0DataRank · unranked

269 citations

Naseem Maalouf, Abigail L. Manson, Ashlee M. Earl, Lishay Parhi, Johanna Emgård +10 more

SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings

Bioinformatics(2024)10.1093/bioinformatics/btae328

N/A

0DataRank · unranked

6 citations

Bianca-Maria Cosma, Ashlee M. Earl, Abigail L. Manson, Thomas Abeel, Aysun Urhan

High Prevalence of Carbapenem-resistant Klebsiella Pneumoniae in Fecal and Water Samples in Dhaka, Bangladesh

Open Forum Infectious Diseases(2024)10.1093/ofid/ofae612

N/A

0DataRank · unranked

3 citations

Zannat Kawser, Sushmita Sridhar, Sharmin Aktar Mukta, Neamul Hasan, Abu Bakar Siddik +13 more

Bacterial strain sharing between humans, animals, and the environment among urban households

medRxiv(2024)10.1101/2024.08.05.24311509

N/A

0DataRank · unranked

2 citations

Jenna M. Swarthout, Colin J. Worby, Benard Chieng, John Mboya, Ashlee M. Earl +3 more

Rapid Emergence of Resistance to Broad-Spectrum Direct Antimicrobial Activity of Avibactam

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.25.615047

N/A

0DataRank · unranked

1 citations

Shade Rodriguez, Abigail L. Manson, Ashlee M. Earl, Thea Brennan-Krohn, Michelle Nägeli

Effects of commonly used antibiotics on children’s developing gut microbiomes and resistomes in peri-urban Lima, Peru

medRxiv(2024)10.1101/2024.12.13.24317790

N/A

0DataRank · unranked

0 citations

Mónica J. Pajuelo, Robert H. Gilman, Amy J. Pickering, Ashlee M. Earl, Colin J. Worby +2 more

Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

Nature Microbiology(2025)10.1038/s41564-025-01986-w

N/A

0DataRank · unranked

22 citations

Jenna M. Swarthout, Colin J. Worby, Benard Chieng, John Mboya, Ashlee M. Earl +3 more

Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae

Nature Medicine(2020)10.1038/s41591-020-0825-4

N/A

0DataRank · unranked

323 citations

Julian R. Braxton, Carlos A. Rodríguez-Osorio, Anna P. Zagieboylo, Li Li, Alejandro Pironti +9 more

Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain

Nature Microbiology(2025)10.1038/s41564-025-01983-z

N/A

0DataRank · unranked

5 citations

Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko +8 more

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

Briefings in Bioinformatics(2025)10.1093/bib/bbaf589

N/A

0DataRank · unranked

5 citations

Célia Souque, Colin J. Worby, Terrance Shea, Nicoletta Commins, Joshua T. Smith +5 more

Genetic diversity of Salmonella enterica during acute human infections

Gut Microbes(2025)10.1080/19490976.2025.2491666

N/A

0DataRank · unranked

2 citations

Natav Hendin, Sharon Amit, Boaz Adani, Galia Rahav, Amos Adler +4 more

Loss of LafB activity reverses daptomycin resistance in E. faecium

mBio(2025)10.1128/mbio.00715-25

N/A

0DataRank · unranked

1 citations

Bailey J. Schultz, Byoungsook Goh, Alexandra Grote, Terrance Shea, Jacob D. Muscato +7 more

Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis

Research Square(2025)10.21203/rs.3.rs-6976359/v1

N/A

0DataRank · unranked

0 citations

Teri N. Hreha, Abigail L. Manson, Christina A. Collins, Hao Wu, C Georgescu +3 more

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Genome Medicine(2022)10.1186/s13073-022-01040-y

N/A

0DataRank · unranked

44 citations

Abigail L. Manson, Bruce J. Walker, Thea Brennan-Krohn, Colin J. Worby, Peijun Ma +25 more

Efagins – engineerable agents that evolved independently to target the enterococcal cell wall

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.13.693970

N/A

0DataRank · unranked

0 citations

Abigail L. Manson, Joshua T. Smith, Natia Karumidze, Gracie Richards, Suelen Scarpa de Mello +5 more

Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections

Journal of Clinical Investigation(2022)10.1172/jci158497

N/A

0DataRank · unranked

54 citations

Benjamin Olson, Karen Dodson, Ashlee M. Earl, Scott J. Hultgren, Colin J. Worby

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

Molecular Systems Biology(2022)10.15252/msb.202211081

N/A

0DataRank · unranked

271 citations

Aarti Krishnan, Erica J. Zheng, H. Stärk, Abigail L. Manson, Ashlee M. Earl +3 more

Evaluating the relationship between community water and sanitation access and the global burden of antibiotic resistance: an ecological study

The Lancet Microbe(2023)10.1016/s2666-5247(23)00137-4

N/A

0DataRank · unranked

76 citations

Abigail P. Harvey, Maya Nadimpalli, Karin Gallandat, Argaw Ambelu, Benjamin F. Arnold +13 more

Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection

Clinical Infectious Diseases(2023)10.1093/cid/ciad507

N/A

0DataRank · unranked

28 citations

Sushmita Sridhar, Elizabeth Oliver, Sowmya R. Rao, Damien Slater, Wontae Hwang +12 more

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.14.431013

N/A

0DataRank · unranked

10 citations

Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber +7 more

Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States

mSphere(2023)10.1128/msphere.00184-23

N/A

0DataRank · unranked

5 citations

Christi L. McElheny, Abigail L. Manson, Ashlee M. Earl, Nader Shaikh, Yohei Doi +1 more

Utility of Mycobacterium tuberculosis Genome Sequencing Snapshots to Assess Transmission Dynamics Over Time

The Journal of Infectious Diseases(2023)10.1093/infdis/jiad515

N/A

0DataRank · unranked

1 citations

Chuan-Chin Huang, Ana Karina Millones, Róger Calderón, Abigail L. Manson, Judith Jiménez +6 more

Global diversity of enterococci and description of 18 novel species

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.18.540996

N/A

0DataRank · unranked

11 citations

François Lebreton, Rauf Salamzade, Melissa J. Martin, Katharina Schaufler, Aysun Urhan +14 more

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.23.541813

N/A

0DataRank · unranked

6 citations

Kyra Taylor, Leslie C. Lopez, Jian Su, Joshua T. Smith, Abigail L. Manson +5 more

Ashlee M. Earl

Indexed papers

Top data-sharing exemplar

Papers