List of works by Ashlee Earl

A catalog of reference genomes from the human microbiome

scientific article

A framework for human microbiome research

scientific article

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

scientific article published on 13 April 2020

Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance

scientific journal article

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

scientific article published on 25 June 2020

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections

scientific article published on March 2017

Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors

scientific article published on 14 June 2016

Biofilm development with an emphasis on Bacillus subtilis

scientific article published on January 2008

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

scientific article (publication date: March 2011)

Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2

scientific article published on 3 November 2015

Correction: Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1.

scientific article published on 14 November 2006

Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

scientific article published on 25 July 2019

Deinococcus peraridilitoris sp. nov., isolated from a coastal desert

scientific article

Developing a genetic system in Deinococcus radiodurans for analyzing mutations.

scientific article

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage

scientific article published on 3 March 2016

Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques

scientific article

Ecology and genomics of Bacillus subtilis

scientific article

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

scientific article

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes.

scientific article published on 11 October 2010

Evidence of extensive DNA transfer between bacteroidales species within the human gut

scientific article

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

scientific article (publication date: September 2015)

Evolution of invasion in a diverse set of Fusobacterium species ⬇️

scientific article

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

scientific article published in 2005

Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample

scientific article

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

scientific article published on August 2016

Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing

scientific article published on June 2015

Genetic evidence that the uvsE gene product of Deinococcus radiodurans R1 is a UV damage endonuclease

scientific article

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

scientific article

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

scientific article published on 11 April 2016

Gut microbiota utilize immunoglobulin A for mucosal colonization

scientific article published in Science

High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).

scientific article published on 30 December 2011

High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides

scientific article published on 26 December 2013

High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae

scientific article

Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream

scientific article published on 01 April 2019

MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells.

scientific article published on 13 August 2015

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

scientific article published in 2022

Normalizing alternate representations of large sequence variants across multiple bacterial genomes

scientific article published on 28 January 2015

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

scientific article

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement

scientific article

Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1

scientific article

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

scientific article published in 2023

Relating the metatranscriptome and metagenome of the human gut.

scientific article

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome

scientific article

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

scientific article published on 09 March 2020

Sporulation during growth in a gut isolate of Bacillus subtilis.

scientific article published on 15 September 2014

Structure, function and diversity of the healthy human microbiome

scientific article

The "most wanted" taxa from the human microbiome for whole genome sequencing

scientific article

The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression

scientific article

The success of acinetobacter species; genetic, metabolic and virulence attributes

scientific article

Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster

scientific article

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

scientific article

Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus

scientific article (publication date: 2012)

Whole-genome sequences of Bacillus subtilis and close relatives

scientific article

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