Ashlee M. Earl, Ph.D. - Publications

Affiliations: 
2003 Louisiana State University, Baton Rouge, LA, United States 
Area:
Microbiology Biology, General Biophysics

91 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung D. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife. 10. PMID 33871353 DOI: 10.7554/eLife.67310  0.01
2021 van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, et al. The global dissemination of hospital clones of Enterococcus faecium. Genome Medicine. 13: 52. PMID 33785076 DOI: 10.1186/s13073-021-00868-0  0.01
2021 Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science (New York, N.Y.). 371. PMID 33602825 DOI: 10.1126/science.aba0862  0.01
2021 Straub TJ, Chou WC, Manson AL, Schreiber HL, Walker BJ, Desjardins CA, Chapman SB, Kaspar KL, Kahsai OJ, Traylor E, Dodson KW, Hullar MAJ, Hultgren SJ, Khoo C, Earl AM. 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. 21: 53. PMID 33596852 DOI: 10.1186/s12866-021-02106-4  0.01
2020 Worby CJ, Earl AM, Turbett SE, Becker M, Rao SR, Oliver E, Taylor Walker A, Walters M, Kelly P, Leung DT, Knouse M, Hagmann SHF, Ryan ET, LaRocque RC. Acquisition and Long-term Carriage of Multidrug-Resistant Organisms in US International Travelers. Open Forum Infectious Diseases. 7: ofaa543. PMID 33409326 DOI: 10.1093/ofid/ofaa543  0.01
2020 Gilmore MS, Salamzade R, Selleck E, Bryan N, Mello SS, Manson AL, Earl AM. Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis. Mbio. 11. PMID 33234689 DOI: 10.1128/mBio.02962-20  0.01
2020 Anyansi C, Straub TJ, Manson AL, Earl AM, Abeel T. Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data. Frontiers in Microbiology. 11: 1925. PMID 33013732 DOI: 10.3389/Fmicb.2020.01925  0.01
2020 Abed J, Maalouf N, Manson AL, Earl AM, Parhi L, Emgård JEM, Klutstein M, Tayeb S, Almogy G, Atlan KA, Chaushu S, Israeli E, Mandelboim O, Garrett WS, Bachrach G. Colon Cancer-Associated May Originate From the Oral Cavity and Reach Colon Tumors via the Circulatory System. Frontiers in Cellular and Infection Microbiology. 10: 400. PMID 32850497 DOI: 10.3389/Fcimb.2020.00400  0.01
2020 Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT. Author Correction: Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nature Medicine. PMID 32587394 DOI: 10.1038/S41591-020-0974-5  0.01
2020 Cohen KA, Stott KE, Munsamy V, Manson AL, Earl AM, Pym AS. Evidence for expanding the role of streptomycin in the management of drug-resistant . Antimicrobial Agents and Chemotherapy. PMID 32540971 DOI: 10.1128/Aac.00860-20  0.01
2020 Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT. Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nature Medicine. PMID 32284589 DOI: 10.1038/S41591-020-0825-4  0.01
2020 Mellon G, Turbett SE, Worby C, Oliver E, Walker AT, Walters M, Kelly P, Leung DT, Knouse M, Hagmann S, Earl A, Ryan ET, LaRocque RC. Acquisition of Antibiotic-Resistant Bacteria by U.S. International Travelers. The New England Journal of Medicine. 382: 1372-1374. PMID 32242366 DOI: 10.1056/Nejmc1912464  0.01
2020 Donaldson GP, Chou WC, Manson AL, Rogov P, Abeel T, Bochicchio J, Ciulla D, Melnikov A, Ernst PB, Chu H, Giannoukos G, Earl AM, Mazmanian SK. Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nature Microbiology. PMID 32152589 DOI: 10.1038/S41564-020-0683-3  0.01
2020 Anyansi C, Keo A, Walker BJ, Straub TJ, Manson AL, Earl AM, Abeel T. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. Bmc Genomics. 21: 80. PMID 31992201 DOI: 10.1186/S12864-020-6486-3  0.01
2019 Bachmann NL, Salamzade R, Manson AL, Whittington R, Sintchenko V, Earl AM, Marais BJ. Key Transitions in the Evolution of Rapid and Slow Growing Identified by Comparative Genomics. Frontiers in Microbiology. 10: 3019. PMID 32038518 DOI: 10.3389/Fmicb.2019.03019  0.01
2019 Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, ... ... Earl AM, et al. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nature Medicine. PMID 31768064 DOI: 10.1038/S41591-019-0650-9  0.01
2019 Reis-Cunha JL, Bartholomeu DC, Manson AL, Earl AM, Cerqueira GC. ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database. Plos One. 14: e0223364. PMID 31577829 DOI: 10.1371/Journal.Pone.0223364  0.01
2019 Manson AL, Van Tyne D, Straub TJ, Clock S, Crupain M, Rangan U, Gilmore MS, Earl AM. Influence of agricultural antibiotic use on chicken meat-associated enterococci and their connection to the clinic. Applied and Environmental Microbiology. PMID 31471308 DOI: 10.1128/Aem.01559-19  0.01
2019 Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Medicine. 11: 45. PMID 31345251 DOI: 10.1186/S13073-019-0660-8  0.01
2019 Cohen KA, Manson AL, Abeel T, Desjardins CA, Chapman SB, Hoffner S, Birren BW, Earl AM. Extensive global movement of multidrug-resistant strains revealed by whole-genome analysis. Thorax. PMID 31048508 DOI: 10.1136/Thoraxjnl-2018-211616  0.01
2019 Van Tyne D, Manson AL, Huycke MM, Karanicolas J, Earl AM, Gilmore MS. Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. Science Translational Medicine. 11. PMID 30971455 DOI: 10.1126/Scitranslmed.Aat8418  0.01
2019 Ramaiah A, Nayak S, Rakshit S, Manson AL, Abeel T, Shanmugam S, Sahoo PN, John AJUK, Sundaramurthi JC, Narayanan S, D'Souza G, von Hoegen P, Ottenhoff THM, Swaminathan S, Earl AM, et al. Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Strains. Frontiers in Immunology. 10: 195. PMID 30814998 DOI: 10.3389/Fimmu.2019.00195  0.01
2018 Spencer MD, Winglee K, Passaretti C, Earl AM, Manson AL, Mulder HP, Sautter RL, Fodor AA. Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae. The Journal of Infection. PMID 30503842 DOI: 10.1016/J.Jinf.2018.11.003  0.01
2018 Georgescu CH, Manson AL, Griggs AD, Desjardins CA, Pironti A, Wapinski I, Abeel T, Haas BJ, Earl AM. SynerClust: a highly scalable, synteny-aware orthologue clustering tool. Microbial Genomics. PMID 30418868 DOI: 10.1099/mgen.0.000231  0.01
2018 Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK. Gut microbiota utilize immunoglobulin A for mucosal colonization. Science (New York, N.Y.). PMID 29724905 DOI: 10.1126/Science.Aaq0926  0.01
2018 Lebreton F, Valentino MD, Schaufler K, Earl AM, Cattoir V, Gilmore MS. Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium. The Journal of Antimicrobial Chemotherapy. PMID 29462403 DOI: 10.1093/Jac/Dky039  0.01
2018 Zhang W, Lun S, Wang SH, Jiang X, Yang F, Tang J, Manson AL, Earl AM, Gunosewoyo H, Bishai WR, Yu LF. Identification of Novel Coumestan Derivatives as Polyketide Synthase 13 Inhibitors Against Mycobacterium Tuberculosis. Journal of Medicinal Chemistry. PMID 29328655 DOI: 10.1021/Acs.Jmedchem.7B01319  0.01
2018 Bhattacharyya R, Pironti A, Walker BJ, Manson A, Pierce V, Ferraro MJ, Shenoy E, Hooper DC, Earl A. 1202. Multimodal Sequencing of a Clonal Case Cluster of Carbapenem-Resistant Citrobacter Reveals Unexpectedly Rapid Dynamics of KPC3-Containing Plasmids Open Forum Infectious Diseases. 5. DOI: 10.1093/Ofid/Ofy210.1035  0.01
2017 Manson AL, Abeel T, Galagan J, Chandrabose Sundaramurthi J, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Reply to Lee and Howden. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29040415 DOI: 10.1093/Cid/Cix751  0.01
2017 de Welzen L, Eldholm V, Maharaj K, Manson AL, Earl AM, Pym AS. Whole transcriptome and genomic analysis of extensively drug-resistant Mycobacterium tuberculosis clinical isolates identifies downregulation of ethA as a mechanism of ethionamide resistance. Antimicrobial Agents and Chemotherapy. PMID 28993337 DOI: 10.1128/Aac.01461-17  0.01
2017 Lebreton F, Manson AL, Saavedra JT, Straub TJ, Earl AM, Gilmore MS. Tracing the Enterococci from Paleozoic Origins to the Hospital. Cell. PMID 28502769 DOI: 10.1016/J.Cell.2017.04.027  0.01
2017 Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 28498943 DOI: 10.1093/Cid/Cix169  0.01
2017 Schreiber HL, Conover MS, Chou WC, Hibbing ME, Manson AL, Dodson KW, Hannan TJ, Roberts PL, Stapleton AE, Hooton TM, Livny J, Earl AM, Hultgren SJ. Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. Science Translational Medicine. 9. PMID 28330863 DOI: 10.1126/Scitranslmed.Aaf1283  0.01
2017 Duvall JR, Bedard L, Naylor-Olsen AM, Manson AL, Bittker JA, Sun W, Fitzgerald ME, He Z, Lee MD, Marie JC, Muncipinto G, Rush D, Xu D, Xu H, Zhang M, ... Earl AM, et al. Identification of highly specific diversity-oriented synthesis-derived inhibitors of Clostridium difficile. Acs Infectious Diseases. PMID 28215073 DOI: 10.1021/Acsinfecdis.6B00206  0.01
2017 Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, et al. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proceedings of the National Academy of Sciences of the United States of America. PMID 28096418 DOI: 10.1073/Pnas.1616248114  0.01
2017 Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, ... ... Earl AM, et al. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature Genetics. PMID 28092681 DOI: 10.1038/Ng.3767  0.01
2016 Wollenberg KR, Desjardins CA, Zalutskaya A, Slodovnikova V, Oler AJ, Quiñones M, Abeel T, Chapman SB, Tartakovsky M, Gabrielian A, Hoffner S, Skrahin A, Birren BW, Rosenthal A, Skrahina A, ... Earl AM, et al. Whole genome sequencing of Mycobacterium tuberculosis provides insight into the evolution and genetic composition of drug-resistant tuberculosis in Belarus. Journal of Clinical Microbiology. PMID 27903602 DOI: 10.1128/Jcm.02116-16  0.01
2016 Dehoux P, Marvaud JC, Abouelleil A, Earl AM, Lambert T, Dauga C. Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. Bmc Genomics. 17: 819. PMID 27769168 DOI: 10.1186/S12864-016-3152-X  0.01
2016 Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT. Genomic analysis of the evolution of fluoroquinolone resistance in Mycobacterium tuberculosis prior to tuberculosis diagnosis. Antimicrobial Agents and Chemotherapy. PMID 27572408 DOI: 10.1128/Aac.00664-16  0.01
2016 Maiga M, Cohen K, Baya B, Srikrishna G, Siddiqui S, Sanogo M, Somboro AM, Diarra B, Diallo MH, Mazumdar V, Yoder C, Orsega S, Belson M, Kassambara H, Goita D, ... ... Earl AM, et al. Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali. Journal of Breath Research. 10: 036012. PMID 27532494 DOI: 10.1088/1752-7155/10/3/036012  0.01
2016 Abed J, Emgård JE, Zamir G, Faroja M, Almogy G, Grenov A, Sol A, Naor R, Pikarsky E, Atlan KA, Mellul A, Chaushu S, Manson AL, Earl AM, Ou N, et al. Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc. Cell Host & Microbe. 20: 215-225. PMID 27512904 DOI: 10.1016/J.Chom.2016.07.006  0.01
2016 Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT. Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors. Cell Chemical Biology. PMID 27321573 DOI: 10.1016/J.Chembiol.2016.05.011  1
2016 Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O'Donnell MR, Mlisana KP, Wortman J, Birren BW, ... ... Earl AM, et al. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nature Genetics. PMID 27064254 DOI: 10.1038/Ng.3548  1
2016 Malinga LA, Abeel T, Desjardins CA, Dlamini TC, Cassell G, Chapman SB, Birren BW, Earl AM, van der Walt M. Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage. Genome Announcements. 4. PMID 26941159 DOI: 10.1128/Genomea.01771-15  0.01
2016 Velayati AA, Abeel T, Shea T, Konstantinovich Zhavnerko G, Birren B, Cassell GH, Earl AM, Hoffner S, Farnia P. Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization. International Journal of Mycobacteriology. 5: 66-73. PMID 26927992 DOI: 10.1016/J.Ijmyco.2015.12.001  1
2016 Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. Plos Neglected Tropical Diseases. 10: e0004332. PMID 26751217 DOI: 10.1371/Journal.Pntd.0004332  1
2016 Ramaiah A, Nayak S, Rakshit S, McGuire A, Shanmugam S, Chandrabose J, Narayanan S, EarL A, Swaminathan S, Vyakarnam A. Evolutionary patterns of T cell epitopes in mycobacterium tuberculosis strains isolated in India International Journal of Infectious Diseases. 45: 33. DOI: 10.1016/J.Ijid.2016.02.111  0.01
2015 Cochrane K, Manson McGuire A, Priest ME, Abouelleil A, Cerqueira GC, Lo R, Earl AM, Allen-Vercoe E. Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2. Anaerobe. PMID 26545740 DOI: 10.1016/J.Anaerobe.2015.10.013  1
2015 Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, ... ... Earl AM, et al. Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal. Plos Medicine. 12: e1001880. PMID 26418737 DOI: 10.1371/Journal.Pmed.1001880  1
2015 Sefik E, Geva-Zatorsky N, Oh S, Konnikova L, Zemmour D, McGuire AM, Burzyn D, Ortiz-Lopez A, Lobera M, Yang J, Ghosh S, Earl A, Snapper SB, Jupp R, Kasper D, et al. Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells. Science (New York, N.Y.). PMID 26272906 DOI: 10.1126/Science.Aaa9420  1
2015 Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Durkin AS, Nelson KE, Epstein SS. 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. Standards in Genomic Sciences. 10: 37. PMID 26221418 DOI: 10.1186/S40793-015-0027-8  0.01
2015 Williams OM, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, Desjardins CA, Banerjee A, Drobniewski F, Earl AM, Cooke GS. Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing. Emerging Infectious Diseases. 21: 1082-4. PMID 25988581 DOI: 10.3201/Eid2106.141903  1
2015 Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Scott Durkin A, Nelson KE, Epstein SS. 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 Standards in Genomic Sciences. 10: 1-12. DOI: 10.1186/s40793-015-0027-8  1
2015 Salazar A, Earl A, Desjardins C, Abeel T. Normalizing alternate representations of large sequence variants across multiple bacterial genomes Bmc Bioinformatics. 16: 1-2. DOI: 10.1186/1471-2105-16-S2-A8  0.01
2015 Cohen KA, Abeel T, McGuire AM, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman S, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, ... ... Earl AM, et al. Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa International Journal of Mycobacteriology. DOI: 10.1016/J.Ijmyco.2014.11.028  1
2014 Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. Plos One. 9: e112963. PMID 25409509 DOI: 10.1371/Journal.Pone.0112963  1
2014 Valentino MD, McGuire AM, Rosch JW, Bispo PJ, Burnham C, Sanfilippo CM, Carter RA, Zegans ME, Beall B, Earl AM, Tuomanen EI, Morris TW, Haas W, Gilmore MS. Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster. Nature Communications. 5: 5411. PMID 25388376 DOI: 10.1038/Ncomms6411  0.01
2014 Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM. Evolution of invasion in a diverse set of Fusobacterium species. Mbio. 5: e01864. PMID 25370491 DOI: 10.1128/Mbio.01864-14  1
2014 Serra CR, Earl AM, Barbosa TM, Kolter R, Henriques AO. Sporulation during growth in a gut isolate of Bacillus subtilis. Journal of Bacteriology. 196: 4184-96. PMID 25225273 DOI: 10.1128/Jb.01993-14  1
2014 Shen Z, Sheh A, Young SK, Abouelliel A, Ward DV, Earl AM, Fox JG. Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques. Genome Announcements. 2. PMID 25212613 DOI: 10.1128/Genomea.00857-14  0.01
2014 Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE. Evidence of extensive DNA transfer between bacteroidales species within the human gut. Mbio. 5: e01305-14. PMID 24939888 DOI: 10.1128/Mbio.01305-14  1
2014 Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C. Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences of the United States of America. 111: E2329-38. PMID 24843156 DOI: 10.1073/Pnas.1319284111  1
2014 Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS. Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. International Journal of Systematic and Evolutionary Microbiology. 64: 2642-9. PMID 24824639 DOI: 10.1099/Ijs.0.060988-0  1
2013 Lebreton F, Valentino MD, Duncan LB, Zeng Q, Manson McGuire A, Earl AM, Gilmore MS. High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides. Genome Announcements. 1. PMID 24371201 DOI: 10.1128/Genomea.01087-13  0.01
2013 Lebreton F, van Schaik W, McGuire AM, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJ, Earl AM, et al. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. Mbio. 4. PMID 23963180 DOI: 10.1128/Mbio.00534-13  1
2013 Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, Gevers D, Duke F, Jung J, Michaud M, Walker BJ, Young S, Earl AM, Kostic AD, Ojesina AI, Hasserjian R, Ballen KK, et al. Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. The New England Journal of Medicine. 369: 517-28. PMID 23924002 DOI: 10.1056/Nejmoa1211115  1
2012 Peleg AY, de Breij A, Adams MD, Cerqueira GM, Mocali S, Galardini M, Nibbering PH, Earl AM, Ward DV, Paterson DL, Seifert H, Dijkshoorn L. The success of acinetobacter species; genetic, metabolic and virulence attributes. Plos One. 7: e46984. PMID 23144699 DOI: 10.1371/Journal.Pone.0046984  1
2012 Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The "most wanted" taxa from the human microbiome for whole genome sequencing. Plos One. 7: e41294. PMID 22848458 DOI: 10.1371/Journal.Pone.0041294  1
2012 Ward DV, Gevers D, Giannoukos G, Earl AM, Methé BA, Sodergren E, Feldgarden M, Ciulla DM, Tabbaa D, Arze C, Appelbaum E, Aird L, Anderson S, Ayvaz T, Belter E, et al. Evaluation of 16s rDNA-based community profiling for human microbiome research Plos One. 7. PMID 22720093 DOI: 10.1371/Journal.Pone.0039315  1
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/Nature11209  1
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/Nature11234  1
2012 Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J. Whole-genome sequences of Bacillus subtilis and close relatives. Journal of Bacteriology. 194: 2378-9. PMID 22493193 DOI: 10.1128/Jb.05675-11  1
2012 Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biology. 13: R23. PMID 22455878 DOI: 10.1186/Gb-2012-13-3-R23  1
2012 Peleg AY, Miyakis S, Ward DV, Earl AM, Rubio A, Cameron DR, Pillai S, Moellering RC, Eliopoulos GM. Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus. Plos One. 7: e28316. PMID 22238576 DOI: 10.1371/Journal.Pone.0028316  1
2012 Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Research. 22: 292-8. PMID 22009990 DOI: 10.1101/Gr.126573.111  1
2011 Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC, Carr J, Posey J, Butler WR. High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)). Standards in Genomic Sciences. 5: 389-97. PMID 22675588 DOI: 10.4056/Sigs.2255041  1
2011 Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research. 21: 494-504. PMID 21212162 DOI: 10.1101/Gr.112730.110  1
2010 Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, ... ... Earl AM, et al. A catalog of reference genomes from the human microbiome. Science (New York, N.Y.). 328: 994-9. PMID 20489017 DOI: 10.1126/Science.1183605  1
2010 Ciulla D, Giannoukos G, Earl A, Feldgarden M, Gevers D, Levin J, Livny J, Ward D, Gnirke A, Nusbaum C, Birren B. Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes Genome Biology. 11: 9. DOI: 10.1186/Gb-2010-11-S1-P9  0.01
2008 Earl AM, Losick R, Kolter R. Ecology and genomics of Bacillus subtilis. Trends in Microbiology. 16: 269-75. PMID 18467096 DOI: 10.1016/J.Tim.2008.03.004  1
2008 Lemon KP, Earl AM, Vlamakis HC, Aguilar C, Kolter R. Biofilm development with an emphasis on Bacillus subtilis. Current Topics in Microbiology and Immunology. 322: 1-16. PMID 18453269 DOI: 10.1007/978-3-540-75418-3_1  1
2007 Rainey FA, Ferreira M, Nobre MF, Ray K, Bagaley D, Earl AM, Battista JR, Gómez-Silva B, McKay CP, da Costa MS. Deinococcus peraridilitoris sp. nov., isolated from a coastal desert. International Journal of Systematic and Evolutionary Microbiology. 57: 1408-12. PMID 17625166 DOI: 10.1099/Ijs.0.64956-0  1
2007 Earl AM, Losick R, Kolter R. Bacillus subtilis genome diversity Journal of Bacteriology. 189: 1163-1170. PMID 17114265 DOI: 10.1128/Jb.01343-06  1
2006 Harris DR, Tanaka M, Saveliev SV, Jolivet E, Earl AM, Cox MM, Battista JR. Correction: Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1 Plos Biology. 4. DOI: 10.1371/Journal.Pbio.0040385  0.24
2005 Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF, Bagaley D, Rash BA, Park MJ, Earl AM, Shank NC, Small AM, Henk MC, Battista JR, Kämpfer P, da Costa MS. 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. Applied and Environmental Microbiology. 71: 5225-35. PMID 16151108 DOI: 10.1128/Aem.71.9.5225-5235.2005  1
2004 Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics. 168: 21-33. PMID 15454524 DOI: 10.1534/Genetics.104.029249  1
2004 Harris DR, Tanaka M, Saveliev SV, Jolivet E, Earl AM, Cox MM, Battista JR. Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1. Plos Biology. 2: e304. PMID 15361932 DOI: 10.1371/Journal.Pbio.0020304  0.01
2004 Kim M, Wolff E, Huang T, Garibyan L, Earl AM, Battista JR, Miller JH. Developing a genetic system in Deinococcus radiodurans for analyzing mutations. Genetics. 166: 661-8. PMID 15020457 DOI: 10.1534/Genetics.166.2.661  1
2002 Earl AM, Mohundro MM, Mian IS, Battista JR. The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. Journal of Bacteriology. 184: 6216-24. PMID 12399492 DOI: 10.1128/Jb.184.22.6216-6224.2002  1
2002 Earl AM, Rankin SK, Kim KP, Lamendola ON, Battista JR. Genetic evidence that the uvsE gene product of Deinococcus radiodurans R1 is a UV damage endonuclease. Journal of Bacteriology. 184: 1003-9. PMID 11807060 DOI: 10.1128/Jb.184.4.1003-1009.2002  1
1999 Battista JR, Earl AM, Park MJ. Why is Deinococcus radiodurans so resistant to ionizing radiation? Trends in Microbiology. 7: 362-5. PMID 10470044 DOI: 10.1016/S0966-842X(99)01566-8  1
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