Ashlee M. Earl

Research interests

Publications

• Discovery of a structural class of antibiotics with explainable deep learning

  Nature · 2023 · https://doi.org/10.1038/s41586-023-06887-8

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

  Nature · 2023 · https://doi.org/10.1038/s41586-022-05546-8

• Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

  Molecular Systems Biology · 2022 · https://doi.org/10.15252/msb.202211081

• Clinically relevant mutations in core metabolic genes confer antibiotic resistance

  Science · 2021 · https://doi.org/10.1126/science.aba0862

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

  Nature Medicine · 2020 · https://doi.org/10.1038/s41591-020-0825-4

• Gut microbiota utilize immunoglobulin A for mucosal colonization

  Science · 2018 · https://doi.org/10.1126/science.aaq0926

• Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

  Nature Genetics · 2017 · https://doi.org/10.1038/ng.3767

• Tracing the Enterococci from Paleozoic Origins to the Hospital

  Cell · 2017 · https://doi.org/10.1016/j.cell.2017.04.027

• Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc

  Cell Host & Microbe · 2016 · https://doi.org/10.1016/j.chom.2016.07.006

• Individual intestinal symbionts induce a distinct population of RORγ + regulatory T cells

  Science · 2015 · https://doi.org/10.1126/science.aaa9420

• Relating the metatranscriptome and metagenome of the human gut

  Proceedings of the National Academy of Sciences · 2014 · https://doi.org/10.1073/pnas.1319284111

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

  PLoS ONE · 2014 · https://doi.org/10.1371/journal.pone.0112963

• Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

  mBio · 2013 · https://doi.org/10.1128/mbio.00534-13

• Structure, function and diversity of the healthy human microbiome

  Nature · 2012 · https://doi.org/10.1038/nature11234

• A framework for human microbiome research

  Nature · 2012 · https://doi.org/10.1038/nature11209

• Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

  Genome Research · 2011 · https://doi.org/10.1101/gr.126573.111

• Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

  Genome Research · 2011 · https://doi.org/10.1101/gr.112730.110

• A Catalog of Reference Genomes from the Human Microbiome

  Science · 2010 · https://doi.org/10.1126/science.1183605

• Ecology and genomics of Bacillus subtilis

  Trends in Microbiology · 2008 · https://doi.org/10.1016/j.tim.2008.03.004

• Extensive Diversity of Ionizing-Radiation-Resistant Bacteria Recovered from Sonoran Desert Soil and Description of Nine New Species of the GenusDeinococcusObtained from a Single Soil Sample

  Applied and Environmental Microbiology · 2005 · https://doi.org/10.1128/aem.71.9.5225-5235.2005

• Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance

  Genetics · 2004 · https://doi.org/10.1534/genetics.104.029249

Current projects

No projects listed.