Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 57

1.

SynerClust: a highly scalable, synteny-aware orthologue clustering tool.

Georgescu CH, Manson AL, Griggs AD, Desjardins CA, Pironti A, Wapinski I, Abeel T, Haas BJ, Earl AM.

Microb Genom. 2018 Nov 12. doi: 10.1099/mgen.0.000231. [Epub ahead of print]

2.

Gut microbiota utilize immunoglobulin A for mucosal colonization.

Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK.

Science. 2018 May 18;360(6390):795-800. doi: 10.1126/science.aaq0926. Epub 2018 May 3.

PMID:
29724905
3.

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium.

Lebreton F, Valentino MD, Schaufler K, Earl AM, Cattoir V, Gilmore MS.

J Antimicrob Chemother. 2018 Jun 1;73(6):1479-1486. doi: 10.1093/jac/dky039.

PMID:
29462403
4.

Identification of Novel Coumestan Derivatives as Polyketide Synthase 13 Inhibitors against Mycobacterium tuberculosis.

Zhang W, Lun S, Wang SH, Jiang XW, Yang F, Tang J, Manson AL, Earl AM, Gunosewoyo H, Bishai WR, Yu LF.

J Med Chem. 2018 Feb 8;61(3):791-803. doi: 10.1021/acs.jmedchem.7b01319. Epub 2018 Jan 29.

PMID:
29328655
5.

Reply to Lee and Howden.

Manson AL, Abeel T, Galagan J, Sundaramurthi JC, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM.

Clin Infect Dis. 2018 Jan 6;66(1):160-161. doi: 10.1093/cid/cix751. No abstract available.

PMID:
29040415
6.

Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of ethA as a Mechanism of Ethionamide Resistance.

de Welzen L, Eldholm V, Maharaj K, Manson AL, Earl AM, Pym AS.

Antimicrob Agents Chemother. 2017 Nov 22;61(12). pii: e01461-17. doi: 10.1128/AAC.01461-17. Print 2017 Dec.

7.

Tracing the Enterococci from Paleozoic Origins to the Hospital.

Lebreton F, Manson AL, Saavedra JT, Straub TJ, Earl AM, Gilmore MS.

Cell. 2017 May 18;169(5):849-861.e13. doi: 10.1016/j.cell.2017.04.027. Epub 2017 May 11.

8.

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics.

Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM.

Clin Infect Dis. 2017 Jun 1;64(11):1494-1501. doi: 10.1093/cid/cix169.

9.

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

Schreiber HL 4th, Conover MS, Chou WC, Hibbing ME, Manson AL, Dodson KW, Hannan TJ, Roberts PL, Stapleton AE, Hooton TM, Livny J, Earl AM, Hultgren SJ.

Sci Transl Med. 2017 Mar 22;9(382). pii: eaaf1283. doi: 10.1126/scitranslmed.aaf1283.

10.

Identification of Highly Specific Diversity-Oriented Synthesis-Derived Inhibitors of Clostridium difficile.

Duvall JR, Bedard L, Naylor-Olsen AM, Manson AL, Bittker JA, Sun W, Fitzgerald ME, He Z, Lee MD 4th, Marie JC, Muncipinto G, Rush D, Xu D, Xu H, Zhang M, Earl AM, Palmer MA, Foley MA, Vacca JP, Scherer CA.

ACS Infect Dis. 2017 May 12;3(5):349-359. doi: 10.1021/acsinfecdis.6b00206. Epub 2017 Mar 7.

11.

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.

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, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1135-1140. doi: 10.1073/pnas.1616248114. Epub 2017 Jan 17.

12.

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

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE 3rd, Brand J; TBResist Global Genome Consortium, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM.

Nat Genet. 2017 Mar;49(3):395-402. doi: 10.1038/ng.3767. Epub 2017 Jan 16.

13.

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

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.

J Clin Microbiol. 2017 Feb;55(2):457-469. doi: 10.1128/JCM.02116-16. Epub 2016 Nov 30.

15.

Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis.

Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6600-6608. doi: 10.1128/AAC.00664-16. Print 2016 Nov.

16.

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

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, Murphy RL, Dao S, Polis M, Diallo S, Timmins GS, Dodd L, Earl AM, Bishai WR.

J Breath Res. 2016 Aug 17;10(3):036012. doi: 10.1088/1752-7155/10/3/036012.

17.

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

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, Brennan CA, Garrett WS, Bachrach G.

Cell Host Microbe. 2016 Aug 10;20(2):215-25. doi: 10.1016/j.chom.2016.07.006.

18.

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

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.

Cell Chem Biol. 2016 Jun 23;23(6):666-77. doi: 10.1016/j.chembiol.2016.05.011. Epub 2016 Jun 16.

19.

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

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, Grosset J, Earl AM, Pym AS.

Nat Genet. 2016 May;48(5):544-51. doi: 10.1038/ng.3548. Epub 2016 Apr 11.

20.

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

Malinga LA, Abeel T, Desjardins CA, Dlamini TC, Cassell G, Chapman SB, Birren BW, Earl AM, van der Walt M.

Genome Announc. 2016 Mar 3;4(2). pii: e01771-15. doi: 10.1128/genomeA.01771-15.

21.

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.

Velayati AA, Abeel T, Shea T, Konstantinovich Zhavnerko G, Birren B, Cassell GH, Earl AM, Hoffner S, Farnia P.

Int J Mycobacteriol. 2016 Mar;5(1):66-73. doi: 10.1016/j.ijmyco.2015.12.001. Epub 2015 Dec 28.

22.

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

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.

PLoS Negl Trop Dis. 2016 Jan 11;10(1):e0004332. doi: 10.1371/journal.pntd.0004332. eCollection 2016 Jan.

23.

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

Cochrane K, McGuire AM, Priest ME, Abouelleil A, Cerqueira GC, Lo R, Earl AM, Allen-Vercoe E.

Anaerobe. 2016 Apr;38:125-129. doi: 10.1016/j.anaerobe.2015.10.013. Epub 2015 Nov 3.

24.

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

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, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O'Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM.

PLoS Med. 2015 Sep 29;12(9):e1001880. doi: 10.1371/journal.pmed.1001880. eCollection 2015 Sep.

25.

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.

Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Durkin AS, Nelson KE, Epstein SS.

Stand Genomic Sci. 2015 Jul 18;10:37. doi: 10.1186/s40793-015-0027-8. eCollection 2015.

26.

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

Williams OM, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, Desjardins CA, Banerjee A, Drobniewski F, Earl AM, Cooke GS.

Emerg Infect Dis. 2015 Jun;21(6):1082-4. doi: 10.3201/eid2106.141903. No abstract available.

27.

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

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM.

PLoS One. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963. eCollection 2014.

28.

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

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.

Nat Commun. 2014 Nov 12;5:5411. doi: 10.1038/ncomms6411.

29.

Evolution of invasion in a diverse set of Fusobacterium species.

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.

MBio. 2014 Nov 4;5(6):e01864. doi: 10.1128/mBio.01864-14.

30.

Sporulation during growth in a gut isolate of Bacillus subtilis.

Serra CR, Earl AM, Barbosa TM, Kolter R, Henriques AO.

J Bacteriol. 2014 Dec;196(23):4184-96. doi: 10.1128/JB.01993-14. Epub 2014 Sep 15.

31.

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

Shen Z, Sheh A, Young SK, Abouelliel A, Ward DV, Earl AM, Fox JG.

Genome Announc. 2014 Sep 11;2(5). pii: e00857-14. doi: 10.1128/genomeA.00857-14.

32.

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

Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE.

MBio. 2014 Jun 17;5(3):e01305-14. doi: 10.1128/mBio.01305-14.

33.

Relating the metatranscriptome and metagenome of the human gut.

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.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19.

34.

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

Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS.

Int J Syst Evol Microbiol. 2014 Aug;64(Pt 8):2642-9. doi: 10.1099/ijs.0.060988-0. Epub 2014 May 13.

35.

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

Lebreton F, Valentino MD, Duncan LB, Zeng Q, Manson McGuire A, Earl AM, Gilmore MS.

Genome Announc. 2013 Dec 26;1(6). pii: e01087-13. doi: 10.1128/genomeA.01087-13.

36.

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

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, Gilmore MS.

MBio. 2013 Aug 20;4(4). pii: e00534-13. doi: 10.1128/mBio.00534-13.

37.

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

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, Chen YB, Hobbs G, Antin JH, Soiffer RJ, Baden LR, Garrett WS, Hornick JL, Marty FM, Meyerson M.

N Engl J Med. 2013 Aug 8;369(6):517-28. doi: 10.1056/NEJMoa1211115.

38.

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

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.

PLoS One. 2012;7(10):e46984. doi: 10.1371/journal.pone.0046984. Epub 2012 Oct 29.

39.

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

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.

PLoS One. 2012;7(7):e41294. doi: 10.1371/journal.pone.0041294. Epub 2012 Jul 26.

40.

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

Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC, Carr J, Posey J, Butler WR.

Stand Genomic Sci. 2011 Dec 31;5(3):389-97. doi: 10.4056/sigs.2255041. Epub 2011 Dec 30.

41.

Whole-genome sequences of Bacillus subtilis and close relatives.

Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J.

J Bacteriol. 2012 May;194(9):2378-9. doi: 10.1128/JB.05675-11.

42.

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

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.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

43.

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

Peleg AY, Miyakis S, Ward DV, Earl AM, Rubio A, Cameron DR, Pillai S, Moellering RC Jr, Eliopoulos GM.

PLoS One. 2012;7(1):e28316. doi: 10.1371/journal.pone.0028316. Epub 2012 Jan 6.

44.

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

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, Huttenhower C, Garrett WS, Meyerson M.

Genome Res. 2012 Feb;22(2):292-8. doi: 10.1101/gr.126573.111. Epub 2011 Oct 18.

45.

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

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ; Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW.

Genome Res. 2011 Mar;21(3):494-504. doi: 10.1101/gr.112730.110. Epub 2011 Jan 6.

46.

A catalog of reference genomes from the human microbiome.

Human Microbiome Jumpstart Reference Strains Consortium, 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, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.

Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.

47.

Ecology and genomics of Bacillus subtilis.

Earl AM, Losick R, Kolter R.

Trends Microbiol. 2008 Jun;16(6):269-75. doi: 10.1016/j.tim.2008.03.004. Epub 2008 May 28. Review.

48.

Biofilm development with an emphasis on Bacillus subtilis.

Lemon KP, Earl AM, Vlamakis HC, Aguilar C, Kolter R.

Curr Top Microbiol Immunol. 2008;322:1-16. Review.

49.

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

Rainey FA, Ferreira M, Nobre MF, Ray K, Bagaley D, Earl AM, Battista JR, Gómez-Silva B, McKay CP, da Costa MS.

Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1408-12.

PMID:
17625166
50.

Bacillus subtilis genome diversity.

Earl AM, Losick R, Kolter R.

J Bacteriol. 2007 Feb;189(3):1163-70. Epub 2006 Nov 17.

Supplemental Content

Support Center