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Items: 1 to 50 of 63

1.

Identification of hidden population structure in time-scaled phylogenies.

Volz EM, Wiuf C, Grad YH, Frost SDW, Dennis AM, Didelot X.

Syst Biol. 2020 Feb 12. pii: syaa009. doi: 10.1093/sysbio/syaa009. [Epub ahead of print]

PMID:
32049340
2.

Combining genomics and epidemiology to track mumps virus transmission in the United States.

Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PC.

PLoS Biol. 2020 Feb 11;18(2):e3000611. doi: 10.1371/journal.pbio.3000611. eCollection 2020 Feb.

3.

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.

Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP.

Nat Microbiol. 2020 Feb 10. doi: 10.1038/s41564-019-0656-6. [Epub ahead of print]

PMID:
32042129
4.

Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens.

Tedijanto C, Grad YH, Lipsitch M.

Elife. 2020 Feb 5;9. pii: e52307. doi: 10.7554/eLife.52307.

5.

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates.

Palace SG, Wang Y, Rubin DH, Welsh MA, Mortimer TD, Cole K, Eyre DW, Walker S, Grad YH.

Elife. 2020 Feb 3;9. pii: e51407. doi: 10.7554/eLife.51407.

6.

Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system.

Hadjineophytou C, Anonsen JH, Wang N, Ma KC, Viburiene R, Vik Å, Harrison OB, Maiden MCJ, Grad YH, Koomey M.

PLoS Genet. 2019 Dec 23;15(12):e1008532. doi: 10.1371/journal.pgen.1008532. eCollection 2019 Dec.

7.

Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus.

Coe KA, Lee W, Stone MC, Komazin-Meredith G, Meredith TC, Grad YH, Walker S.

PLoS Pathog. 2019 Nov 18;15(11):e1007862. doi: 10.1371/journal.ppat.1007862. eCollection 2019 Nov.

8.

Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics.

Hicks AL, Kissler SM, Lipsitch M, Grad YH.

PLoS Biol. 2019 Nov 12;17(11):e3000547. doi: 10.1371/journal.pbio.3000547. eCollection 2019 Nov.

9.

Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.

Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YH.

Mol Biol Evol. 2020 Feb 1;37(2):417-428. doi: 10.1093/molbev/msz225.

PMID:
31589312
10.

Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study.

Abuelezam NN, Reshef YA, Novak D, Grad YH, Seage Iii GR, Mayer K, Lipsitch M.

J Med Internet Res. 2019 Sep 12;21(9):e13766. doi: 10.2196/13766.

11.

Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era.

Williamson DA, Chow EPF, Gorrie CL, Seemann T, Ingle DJ, Higgins N, Easton M, Taiaroa G, Grad YH, Kwong JC, Fairley CK, Chen MY, Howden BP.

Nat Commun. 2019 Sep 5;10(1):3988. doi: 10.1038/s41467-019-12053-4.

12.

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.

Hicks AL, Wheeler N, Sánchez-Busó L, Rakeman JL, Harris SR, Grad YH.

PLoS Comput Biol. 2019 Sep 3;15(9):e1007349. doi: 10.1371/journal.pcbi.1007349. eCollection 2019 Sep.

13.

The impact of antimicrobials on gonococcal evolution.

Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M, Harris SR.

Nat Microbiol. 2019 Nov;4(11):1941-1950. doi: 10.1038/s41564-019-0501-y. Epub 2019 Jul 29.

14.

Impact of Species Diversity on the Design of RNA-Based Diagnostics for Antibiotic Resistance in Neisseria gonorrhoeae.

Wadsworth CB, Sater MRA, Bhattacharyya RP, Grad YH.

Antimicrob Agents Chemother. 2019 Jul 25;63(8). pii: e00549-19. doi: 10.1128/AAC.00549-19. Print 2019 Aug.

15.

Cumulative Probability of Receiving an Antibiotic Prescription over Time.

Olesen SW, MacFadden D, Grad YH.

N Engl J Med. 2019 May 9;380(19):1872-1873. doi: 10.1056/NEJMc1816699. No abstract available.

PMID:
31067381
16.

Outpatient Antibiotic Prescribing in Massachusetts, 2011-2015.

Klevens RM, Caten E, Olesen SW, DeMaria A, Troppy S, Grad YH.

Open Forum Infect Dis. 2019 Apr 8;6(5):ofz169. doi: 10.1093/ofid/ofz169. eCollection 2019 May.

17.

Response to comment on 'The distribution of antibiotic use and its association with antibiotic resistance'.

Olesen SW, Lipsitch M, Grad YH.

Elife. 2019 May 3;8. pii: e47124. doi: 10.7554/eLife.47124.

18.

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.

Järvenpää M, Sater MRA, Lagoudas GK, Blainey PC, Miller LG, McKinnell JA, Huang SS, Grad YH, Marttinen P.

PLoS Comput Biol. 2019 Apr 22;15(4):e1006534. doi: 10.1371/journal.pcbi.1006534. eCollection 2019 Apr.

19.

Deciphering the impact of bystander selection for antibiotic resistance in Neisseria gonorrhoeae.

Olesen SW, Grad YH.

J Infect Dis. 2019 Apr 8. pii: jiz156. doi: 10.1093/infdis/jiz156. [Epub ahead of print] No abstract available.

PMID:
30957162
20.

Photoinactivation of Neisseria gonorrhoeae: A Paradigm-Changing Approach for Combating Antibiotic-Resistant Gonococcal Infection.

Wang Y, Ferrer-Espada R, Baglo Y, Goh XS, Held KD, Grad YH, Gu Y, Gelfand JA, Dai T.

J Infect Dis. 2019 Jul 31;220(5):873-881. doi: 10.1093/infdis/jiz018.

PMID:
30629196
21.

The distribution of antibiotic use and its association with antibiotic resistance.

Olesen SW, Barnett ML, MacFadden DR, Brownstein JS, Hernández-Díaz S, Lipsitch M, Grad YH.

Elife. 2018 Dec 18;7. pii: e39435. doi: 10.7554/eLife.39435.

22.

Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora.

Tedijanto C, Olesen SW, Grad YH, Lipsitch M.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11988-E11995. doi: 10.1073/pnas.1810840115.

23.

Antimicrobial Resistance in Neisseria gonorrhoeae: Proceedings of the STAR Sexually Transmitted Infection-Clinical Trial Group Programmatic Meeting.

Cristillo AD, Bristow CC, Torrone E, Dillon JA, Kirkcaldy RD, Dong H, Grad YH, Nicholas RA, Rice PA, Lawrence K, Oldach D, Shafer WM, Zhou P, Wi TE, Morris SR, Klausner JD.

Sex Transm Dis. 2019 Mar;46(3):e18-e25. doi: 10.1097/OLQ.0000000000000929.

24.

Racial/Ethnic Disparities in Antimicrobial Drug Use, United States, 2014-2015.

Olesen SW, Grad YH.

Emerg Infect Dis. 2018 Nov;24(11):2126-2128. doi: 10.3201/eid2411.180762.

25.

Azithromycin Susceptibility Among Neisseria gonorrhoeae Isolates and Seasonal Macrolide Use.

Olesen SW, Torrone EA, Papp JR, Kirkcaldy RD, Lipsitch M, Grad YH.

J Infect Dis. 2019 Jan 29;219(4):619-623. doi: 10.1093/infdis/jiy551.

26.
27.

Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance.

Hicks ND, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune SM.

Nat Microbiol. 2018 Sep;3(9):1032-1042. doi: 10.1038/s41564-018-0218-3. Epub 2018 Aug 6.

28.

Trends in outpatient antibiotic use and prescribing practice among US older adults, 2011-15: observational study.

Olesen SW, Barnett ML, MacFadden DR, Lipsitch M, Grad YH.

BMJ. 2018 Jul 27;362:k3155. doi: 10.1136/bmj.k3155.

29.

Testing for gonorrhoea should routinely include the pharynx.

Whittles LK, Didelot X, Grad YH, White PJ.

Lancet Infect Dis. 2018 Jul;18(7):716-717. doi: 10.1016/S1473-3099(18)30341-4. No abstract available.

30.

Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae.

Mortimer TD, Grad YH.

Ann N Y Acad Sci. 2019 Jan;1435(1):93-109. doi: 10.1111/nyas.13871. Epub 2018 Jun 6. Review.

31.

Response to Skowronski and De Serres.

Cobey S, Grad YH.

Clin Infect Dis. 2018 Oct 15;67(9):1476. doi: 10.1093/cid/ciy352. No abstract available.

32.

Vaccine waning and mumps re-emergence in the United States.

Lewnard JA, Grad YH.

Sci Transl Med. 2018 Mar 21;10(433). pii: eaao5945. doi: 10.1126/scitranslmed.aao5945.

33.

Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013.

Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH.

Clin Infect Dis. 2018 Jul 18;67(3):327-333. doi: 10.1093/cid/ciy097.

34.

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP.

Genetics. 2018 Mar;208(3):1247-1260. doi: 10.1534/genetics.117.300662. Epub 2018 Jan 12.

35.

Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014.

Kanjilal S, Sater MRA, Thayer M, Lagoudas GK, Kim S, Blainey PC, Grad YH.

J Clin Microbiol. 2017 Dec 26;56(1). pii: e01160-17. doi: 10.1128/JCM.01160-17. Print 2018 Jan.

36.

Impact of Rapid Susceptibility Testing and Antibiotic Selection Strategy on the Emergence and Spread of Antibiotic Resistance in Gonorrhea.

Tuite AR, Gift TL, Chesson HW, Hsu K, Salomon JA, Grad YH.

J Infect Dis. 2017 Nov 27;216(9):1141-1149. doi: 10.1093/infdis/jix450.

37.

Genomic Characterization of Urethritis-Associated Neisseria meningitidis Shows that a Wide Range of N. meningitidis Strains Can Cause Urethritis.

Ma KC, Unemo M, Jeverica S, Kirkcaldy RD, Takahashi H, Ohnishi M, Grad YH.

J Clin Microbiol. 2017 Dec;55(12):3374-3383. doi: 10.1128/JCM.01018-17. Epub 2017 Sep 13.

38.

Deep sequencing of RSV from an adult challenge study and from naturally infected infants reveals heterogeneous diversification dynamics.

Lau JW, Kim YI, Murphy R, Newman R, Yang X, Zody M, DeVincenzo J, Grad YH.

Virology. 2017 Oct;510:289-296. doi: 10.1016/j.virol.2017.07.017. Epub 2017 Aug 3.

39.

Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis.

Piantadosi A, Mukerji SS, Chitneni P, Cho TA, Cosimi LA, Hung DT, Goldberg MB, Sabeti PC, Kuritzkes DR, Grad YH.

Open Forum Infect Dis. 2017 Jul 28;4(3):ofx138. doi: 10.1093/ofid/ofx138. eCollection 2017 Summer.

40.

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.

Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M.

Bull World Health Organ. 2017 Jul 1;95(7):517-525I. doi: 10.2471/BLT.16.182105. Epub 2016 Jul 18.

41.

Comparing nonpharmaceutical interventions for containing emerging epidemics.

Peak CM, Childs LM, Grad YH, Buckee CO.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):4023-4028. doi: 10.1073/pnas.1616438114. Epub 2017 Mar 28.

42.

WGS to predict antibiotic MICs for Neisseria gonorrhoeae.

Eyre DW, De Silva D, Cole K, Peters J, Cole MJ, Grad YH, Demczuk W, Martin I, Mulvey MR, Crook DW, Walker AS, Peto TEA, Paul J.

J Antimicrob Chemother. 2017 Jul 1;72(7):1937-1947. doi: 10.1093/jac/dkx067.

43.

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.

44.

Reply to Allan-Blitz and Klausner.

Grad YH, Lipsitch M.

J Infect Dis. 2017 Feb 1;215(3):491-492. doi: 10.1093/infdis/jiw552. No abstract available.

45.

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013.

Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M.

J Infect Dis. 2016 Nov 15;214(10):1579-1587. Epub 2016 Sep 16.

46.

Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study.

De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas DR, Foster K, Waldram A, Wilson DJ, Didelot X, Grad YH, Crook DW, Peto TE, Walker AS, Paul J, Eyre DW.

Lancet Infect Dis. 2016 Nov;16(11):1295-1303. doi: 10.1016/S1473-3099(16)30157-8. Epub 2016 Jul 12.

47.

Genomic analyses of Neisseria gonorrhoeae reveal an association of the gonococcal genetic island with antimicrobial resistance.

Harrison OB, Clemence M, Dillard JP, Tang CM, Trees D, Grad YH, Maiden MC.

J Infect. 2016 Dec;73(6):578-587. doi: 10.1016/j.jinf.2016.08.010. Epub 2016 Aug 26.

48.

Biodiversity and hypervirulence of Listeria monocytogenes.

Grad YH, Fortune SM.

Nat Genet. 2016 Mar;48(3):229-30. doi: 10.1038/ng.3515.

PMID:
26906682
49.

Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling.

Grad YH, Goldstein E, Lipsitch M, White PJ.

J Infect Dis. 2016 Mar 15;213(6):883-90. doi: 10.1093/infdis/jiv517. Epub 2015 Oct 30. Review.

50.

Origin and proliferation of multiple-drug resistance in bacterial pathogens.

Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M.

Microbiol Mol Biol Rev. 2015 Mar;79(1):101-16. doi: 10.1128/MMBR.00039-14. Review.

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