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Fast and exact gap-affine partial order alignment with POASTA

2025-01-02 | Other
Contributors: Lucas van Dijk; Abigail L. Manson; Ashlee Earl; Kiran Garimella; Thomas Abeel
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Crossref

Fast and exact gap-affine partial order alignment with POASTA

2024-05-27 | Preprint
Contributors: Lucas R. van Dijk; Abigail L. Manson; Ashlee M. Earl; Kiran V Garimella; Thomas Abeel
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Crossref

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

mSphere
2023-10-24 | Journal article
Contributors: Rauf Salamzade; Christi L. McElheny; Abigail L. Manson; Ashlee M. Earl; Nader Shaikh; Yohei Doi; Ana Cristina Gales
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Crossref

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

2023-05-23 | Preprint
Contributors: Alexis Jaramillo Cartagena; Kyra L. Taylor; Joshua T. Smith; Abigail L. Manson; Virginia M. Pierce; Ashlee M. Earl; Roby P. Bhattacharyya
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Crossref

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

2023-05-02 | Preprint
Contributors: Aysun Urhan; Bianca-Maria Cosma; Ashlee M. Earl; Abigail L. Manson; Thomas Abeel
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Crossref

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

Nature Communications
2022-05-09 | Journal article
Contributors: Erica J. Zheng; Ian W. Andrews; Alexandra T. Grote; Abigail L. Manson; Miguel A. Alcantar; Ashlee M. Earl; James J. Collins
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Crossref

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

Nature Communications
2021-08-26 | Journal article
Contributors: Ryan A. Bronson; Chhavi Gupta; Abigail L. Manson; Jan A. Nguyen; Asli Bahadirli-Talbott; Nicole M. Parrish; Ashlee M. Earl; Keira A. Cohen
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Crossref

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

eLife
2021-04-19 | Journal article
Contributors: Peijun Ma; Lorrie L He; Alejandro Pironti; Hannah H Laibinis; Christoph M Ernst; Abigail L Manson; Roby P Bhattacharyya; Ashlee M Earl; Jonathan Livny; Deborah T Hung
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Crossref

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

Science
2021-02-19 | Journal article
Contributors: Allison J. Lopatkin; Sarah C. Bening; Abigail L. Manson; Jonathan M. Stokes; Michael A. Kohanski; Ahmed H. Badran; Ashlee M. Earl; Nicole J. Cheney; Jason H. Yang; James J. Collins
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Crossref

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

Genome Medicine
2019-12 | Journal article
Contributors: Keira A. Cohen; Abigail L. Manson; Christopher A. Desjardins; Thomas Abeel; Ashlee M. Earl
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Crossref

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

Science Translational Medicine
2019-04-10 | Journal article
Contributors: Daria Van Tyne; Abigail L. Manson; Mark M. Huycke; John Karanicolas; Ashlee M. Earl; Michael S. Gilmore
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Crossref

Gut microbiota utilize immunoglobulin A for mucosal colonization

Science
2018-05-18 | Journal article
Contributors: G. P. Donaldson; M. S. Ladinsky; K. B. Yu; J. G. Sanders; B. B. Yoo; W.-C. Chou; M. E. Conner; A. M. Earl; R. Knight; P. J. Bjorkman et al.
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Crossref

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

2016 | Journal article
Contributors: Malinga LA; Abeel T; Desjardins CA; Dlamini TC; Cassell G; Chapman SB; Birren BW; Earl AM; van der Walt M
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali.

2016 | Journal article
Contributors: Maiga M; Cohen K; Baya B; Srikrishna G; Siddiqui S; Sanogo M; Somboro AM; Diarra B; Diallo MH; Mazumdar V et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2016-08 | Journal article
Contributors: Abed J; Emgård JE; Zamir G; Faroja M; Almogy G; Grenov A; Sol A; Naor R; Pikarsky E; Atlan KA et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2016-06 | Journal article
Contributors: Grant SS; Wellington S; Kawate T; Desjardins CA; Silvis MR; Wivagg C; Thompson M; Gordon K; Kazyanskaya E; Nietupski R et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2016-05 | Journal article
Contributors: Desjardins CA; Cohen KA; Munsamy V; Abeel T; Maharaj K; Walker BJ; Shea TP; Almeida DV; Manson AL; Salazar A et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2016-01 | Journal article
Contributors: Winglee K; Manson McGuire A; Maiga M; Abeel T; Shea T; Desjardins CA; Diarra B; Baya B; Sanogo M; Diallo S et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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.

2015 | Journal article
Contributors: Sizova MV; Chilaka A; Earl AM; Doerfert SN; Muller PA; Torralba M; McCorrison JM; Durkin AS; Nelson KE; Epstein SS
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Normalizing alternate representations of large sequence variants across multiple bacterial genomes.

2015 | Journal article
Contributors: Salazar A; Earl A; Desjardins C; Abeel T
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2015-11 | Journal article
Contributors: Cochrane K; Manson McGuire A; Priest ME; Abouelleil A; Cerqueira GC; Lo R; Earl AM; Allen-Vercoe E
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2015-09 | Journal article
Contributors: Cohen KA; Abeel T; Manson McGuire A; Desjardins CA; Munsamy V; Shea TP; Walker BJ; Bantubani N; Almeida DV; Alvarado L et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2015-08 | Journal article
Contributors: Sefik E; Geva-Zatorsky N; Oh S; Konnikova L; Zemmour D; McGuire AM; Burzyn D; Ortiz-Lopez A; Lobera M; Yang J et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2015-06 | Journal article
Contributors: Williams OM; Abeel T; Casali N; Cohen K; Pym AS; Mungall SB; Desjardins CA; Banerjee A; Drobniewski F; Earl AM et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2014 | Journal article
Contributors: Shen Z; Sheh A; Young SK; Abouelliel A; Ward DV; Earl AM; Fox JG
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2014 | Journal article
Contributors: Coyne MJ; Zitomersky NL; McGuire AM; Earl AM; Comstock LE
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Evolution of invasion in a diverse set of Fusobacterium species.

2014 | Journal article
Contributors: Manson McGuire A; Cochrane K; Griggs AD; Haas BJ; Abeel T; Zeng Q; Nice JB; MacDonald H; Birren BW; Berger BW et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2014 | Journal article
Contributors: Walker BJ; Abeel T; Shea T; Priest M; Abouelliel A; Sakthikumar S; Cuomo CA; Zeng Q; Wortman J; Young SK et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2014 | Journal article
Contributors: Valentino MD; McGuire AM; Rosch JW; Bispo PJ; Burnham C; Sanfilippo CM; Carter RA; Zegans ME; Beall B; Earl AM et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Sporulation during growth in a gut isolate of Bacillus subtilis.

2014-12 | Journal article
Contributors: Serra CR; Earl AM; Barbosa TM; Kolter R; Henriques AO
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2014-08 | Journal article
Contributors: Sizova MV; Muller PA; Stancyk D; Panikov NS; Mandalakis M; Hazen A; Hohmann T; Doerfert SN; Fowle W; Earl AM et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Relating the metatranscriptome and metagenome of the human gut.

2014-06 | Journal article
Contributors: Franzosa EA; Morgan XC; Segata N; Waldron L; Reyes J; Earl AM; Giannoukos G; Boylan MR; Ciulla D; Gevers D et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.

2013 | Journal article
Contributors: Lebreton F; van Schaik W; McGuire AM; Godfrey P; Griggs A; Mazumdar V; Corander J; Cheng L; Saif S; Young S et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2013 | Journal article
Contributors: Lebreton F; Valentino MD; Duncan LB; Zeng Q; Manson McGuire A; Earl AM; Gilmore MS
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome.

2013-08 | Journal article
Contributors: Bhatt AS; Freeman SS; Herrera AF; Pedamallu CS; Gevers D; Duke F; Jung J; Michaud M; Walker BJ; Young S et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2012 | Journal article
Contributors: Giannoukos G; Ciulla DM; Huang K; Haas BJ; Izard J; Levin JZ; Livny J; Earl AM; Gevers D; Ward DV et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Evaluation of 16S rDNA-based community profiling for human microbiome research.

2012 | Journal article
Contributors: Jumpstart Consortium Human Microbiome Project Data Generation Working Group
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2012 | Journal article
Contributors: Fodor AA; DeSantis TZ; Wylie KM; Badger JH; Ye Y; Hepburn T; Hu P; Sodergren E; Liolios K; Huot-Creasy H et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2012 | Journal article
Contributors: Peleg AY; de Breij A; Adams MD; Cerqueira GM; Mocali S; Galardini M; Nibbering PH; Earl AM; Ward DV; Paterson DL et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2012 | Journal article
Contributors: Peleg AY; Miyakis S; Ward DV; Earl AM; Rubio A; Cameron DR; Pillai S; Moellering RC Jr; Eliopoulos GM
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

A framework for human microbiome research.

2012-06 | Journal article
Contributors: Human Microbiome Project Consortium
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Structure, function and diversity of the healthy human microbiome.

2012-06 | Journal article
Contributors: Human Microbiome Project Consortium
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Whole-genome sequences of Bacillus subtilis and close relatives.

2012-05 | Journal article
Contributors: Earl AM; Eppinger M; Fricke WF; Rosovitz MJ; Rasko DA; Daugherty S; Losick R; Kolter R; Ravel J
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

2012-02 | Journal article
Contributors: Kostic AD; Gevers D; Pedamallu CS; Michaud M; Duke F; Earl AM; Ojesina AI; Jung J; Bass AJ; Tabernero J et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2011-12 | Journal article
Contributors: Earl AM; Desjardins CA; Fitzgerald MG; Arachchi HM; Zeng Q; Mehta T; Griggs A; Birren BW; Toney NC; Carr J et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2011-03 | Journal article
Contributors: Haas BJ; Gevers D; Earl AM; Feldgarden M; Ward DV; Giannoukos G; Ciulla D; Tabbaa D; Highlander SK; Sodergren E et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

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

2010 | Journal article
Contributors: Ciulla D; Giannoukos G; Earl A; Feldgarden M; Gevers D; Levin J; Livny J; Ward D; Gnirke A; Nusbaum C et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

A catalog of reference genomes from the human microbiome.

2010-05 | Journal article
Contributors: Human Microbiome Jumpstart Reference Strains Consortium; Nelson KE; Weinstock GM; Highlander SK; Worley KC; Creasy HH; Wortman JR; Rusch DB; Mitreva M; Sodergren E et al.
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Biofilm development with an emphasis on Bacillus subtilis.

2008 | Journal article
Contributors: Lemon KP; Earl AM; Vlamakis HC; Aguilar C; Kolter R
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central

Ecology and genomics of Bacillus subtilis.

2008-06 | Journal article
Contributors: Earl AM; Losick R; Kolter R
Source: Self-asserted source
Ashlee Earl via Europe PubMed Central
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Peer review (4 reviews for 3 publications/grants)

Review activity for Cell. (1)
Review activity for Nature communications (1)
Review activity for Nature microbiology. (2)