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piRNA-Guided CRISPR-like Immunity in Eukaryotes.

Ophinni Y, Palatini U, Hayashi Y, Parrish NF.

Trends Immunol. 2019 Nov;40(11):998-1010. doi: 10.1016/ Epub 2019 Oct 31. Review.


New β-Lactamase Inhibitors Nacubactam and Zidebactam Improve the In Vitro Activity of β-Lactam Antibiotics against Mycobacterium abscessus Complex Clinical Isolates.

Kaushik A, Ammerman NC, Parrish NM, Nuermberger EL.

Antimicrob Agents Chemother. 2019 Aug 23;63(9). pii: e00733-19. doi: 10.1128/AAC.00733-19. Print 2019 Sep.


In Vitro Activity of New Tetracycline Analogs Omadacycline and Eravacycline against Drug-Resistant Clinical Isolates of Mycobacterium abscessus.

Kaushik A, Ammerman NC, Martins O, Parrish NM, Nuermberger EL.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e00470-19. doi: 10.1128/AAC.00470-19. Print 2019 Jun.


A survey of antimicrobial resistance in Enterobacteriaceae isolated from the Chesapeake Bay and adjacent upper tributaries.

Riedel S, Boire N, Carson KA, Vadlamudi A, Khuvis J, Vadlamudi V, Atukorale V, Riedel VAA, Parrish NM.

Microbiologyopen. 2019 Sep;8(9):e00839. doi: 10.1002/mbo3.839. Epub 2019 Apr 4.


The Changing Face of Liver Transplantation in the United States: The Effect of HCV Antiviral Eras on Transplantation Trends and Outcomes.

Parrish NF, Feurer ID, Matsuoka LK, Rega SA, Perri R, Alexopoulos SP.

Transplant Direct. 2019 Feb 20;5(3):e427. doi: 10.1097/TXD.0000000000000866. eCollection 2019 Mar.


In Vitro Activity of the New β-Lactamase Inhibitors Relebactam and Vaborbactam in Combination with β-Lactams against Mycobacterium abscessus Complex Clinical Isolates.

Kaushik A, Ammerman NC, Lee J, Martins O, Kreiswirth BN, Lamichhane G, Parrish NM, Nuermberger EL.

Antimicrob Agents Chemother. 2019 Feb 26;63(3). pii: e02623-18. doi: 10.1128/AAC.02623-18. Print 2019 Mar.


An Update on Mycobacterial Taxonomy, 2016-2017.

Parrish N.

J Clin Microbiol. 2019 Apr 26;57(5). pii: e01408-18. doi: 10.1128/JCM.01408-18. Print 2019 May. Review.


Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity.

Joas S, Parrish EH, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Learn GH, Sauermann U, Neumann B, Rensing KM, Fuchs D, Billingsley JM, Bosinger SE, Silvestri G, Apetrei C, Huot N, Garcia-Tellez T, Müller-Trutwin M, Hotter D, Sauter D, Stahl-Hennig C, Hahn BH, Kirchhoff F.

Nat Commun. 2018 Apr 10;9(1):1371. doi: 10.1038/s41467-018-03762-3.


Automated broth-based systems versus the MYCOTB plate for antimicrobial susceptibility testing of the Mycobacterium tuberculosis complex: challenges in interpretation.

Martin IW, Dionne K, Deml SM, Wengenack NL, Parrish NM.

Diagn Microbiol Infect Dis. 2018 May;91(1):38-41. doi: 10.1016/j.diagmicrobio.2018.01.002. Epub 2018 Jan 6.


Activities of Dual Combinations of Antibiotics Against Multidrug-Resistant Nontuberculous Mycobacteria Recovered from Patients with Cystic Fibrosis.

Schwartz M, Fisher S, Story-Roller E, Lamichhane G, Parrish N.

Microb Drug Resist. 2018 Oct;24(8):1191-1197. doi: 10.1089/mdr.2017.0286. Epub 2018 Jan 25.


A Viral (Arc)hive for Metazoan Memory.

Parrish NF, Tomonaga K.

Cell. 2018 Jan 11;172(1-2):8-10. doi: 10.1016/j.cell.2017.12.029.


Extracorporeal Membrane Oxygenation Appropriateness: An Interdisciplinary Consensus-Based Approach.

Nurok M, Warsh J, Griner T, Kharabi M, Castongia J, Overbeck C, Krueger L, Coleman B, Ramzy D, Chung J, Chan A, Ley E, Kubendran S, Parrish N, Yu Z, Langberg M, Finder S, Rosen BT, Kaplan RS, Sax H, Arabia F.

Anesth Analg. 2019 Mar;128(3):e38-e41. doi: 10.1213/ANE.0000000000002723.


Using Reduced Inoculum Densities of Mycobacterium tuberculosis in MGIT Pyrazinamide Susceptibility Testing to Prevent False-Resistant Results and Improve Accuracy: A Multicenter Evaluation.

Morlock GP, Tyrrell FC, Baynham D, Escuyer VE, Green N, Kim Y, Longley-Olson PA, Parrish N, Pennington C, Tan D, Austin B, Posey JE.

Tuberc Res Treat. 2017;2017:3748163. doi: 10.1155/2017/3748163. Epub 2017 Nov 8.


The Consensus from the Mycobacterium avium ssp. paratuberculosis (MAP) Conference 2017.

Kuenstner JT, Naser S, Chamberlin W, Borody T, Graham DY, McNees A, Hermon-Taylor J, Hermon-Taylor A, Dow CT, Thayer W, Biesecker J, Collins MT, Sechi LA, Singh SV, Zhang P, Shafran I, Weg S, Telega G, Rothstein R, Oken H, Schimpff S, Bach H, Bull T, Grant I, Ellingson J, Dahmen H, Lipton J, Gupta S, Chaubey K, Singh M, Agarwal P, Kumar A, Misri J, Sohal J, Dhama K, Hemati Z, Davis W, Hier M, Aitken J, Pierce E, Parrish N, Goldberg N, Kali M, Bendre S, Agrawal G, Baldassano R, Linn P, Sweeney RW, Fecteau M, Hofstaedter C, Potula R, Timofeeva O, Geier S, John K, Zayanni N, Malaty HM, Kahlenborn C, Kravitz A, Bulfon A, Daskalopoulos G, Mitchell H, Neilan B, Timms V, Cossu D, Mameli G, Angermeier P, Jelic T, Goethe R, Juste RA, Kuenstner L.

Front Public Health. 2017 Sep 27;5:208. doi: 10.3389/fpubh.2017.00208. eCollection 2017.


Anaerobic adaptation of Mycobacterium avium subspecies paratuberculosis in vitro: similarities to M. tuberculosis and differential susceptibility to antibiotics.

Parrish N, Vadlamudi A, Goldberg N.

Gut Pathog. 2017 Jun 10;9:34. doi: 10.1186/s13099-017-0183-z. eCollection 2017.


Outbreaks of nontuberculous mycobacteria.

Sood G, Parrish N.

Curr Opin Infect Dis. 2017 Aug;30(4):404-409. doi: 10.1097/QCO.0000000000000386. Review.


Malaria over-diagnosis in Cameroon: diagnostic accuracy of Fluorescence and Staining Technologies (FAST) Malaria Stain and LED microscopy versus Giemsa and bright field microscopy validated by polymerase chain reaction.

Parsel SM, Gustafson SA, Friedlander E, Shnyra AA, Adegbulu AJ, Liu Y, Parrish NM, Jamal SA, Lofthus E, Ayuk L, Awasom C, Henry CJ, McArthur CP.

Infect Dis Poverty. 2017 Apr 4;6(1):32. doi: 10.1186/s40249-017-0251-0.


Combinations of avibactam and carbapenems exhibit enhanced potencies against drug-resistant Mycobacterium abscessus.

Kaushik A, Gupta C, Fisher S, Story-Roller E, Galanis C, Parrish N, Lamichhane G.

Future Microbiol. 2017 May;12:473-480. doi: 10.2217/fmb-2016-0234. Epub 2017 Feb 16.


An unusual antibiotic susceptibility pattern in a Mycobacterium Cosmeticum strain isolated from the chesapeake bay.

Atukorale V, Boire N, Dionne K, Riedel S, Parrish N.

Int J Mycobacteriol. 2017 Jan-Mar;6(1):38-42. doi: 10.4103/2212-5531.201897.


Validation of Autoclave Protocols for Successful Decontamination of Category A Medical Waste Generated from Care of Patients with Serious Communicable Diseases.

Garibaldi BT, Reimers M, Ernst N, Bova G, Nowakowski E, Bukowski J, Ellis BC, Smith C, Sauer L, Dionne K, Carroll KC, Maragakis LL, Parrish NM.

J Clin Microbiol. 2017 Feb;55(2):545-551. doi: 10.1128/JCM.02161-16. Epub 2016 Dec 7.


A rapid, standardized protein extraction method using adaptive focused acoustics for identification of mycobacteria by MALDI-ToF MS.

Adams LL, Dionne K, Fisher S, Parrish N.

Diagn Microbiol Infect Dis. 2016 Nov;86(3):284-288. doi: 10.1016/j.diagmicrobio.2016.06.001. Epub 2016 Jun 11.


An evolved oxazolidinone with selective potency against Mycobacterium tuberculosis and gram positive bacteria.

Kaushik A, Heuer AM, Bell DT, Culhane JC, Ebner DC, Parrish N, Ippoliti JT, Lamichhane G.

Bioorg Med Chem Lett. 2016 Aug 1;26(15):3572-6. doi: 10.1016/j.bmcl.2016.06.019. Epub 2016 Jun 9.


Endogenized viral sequences in mammals.

Parrish NF, Tomonaga K.

Curr Opin Microbiol. 2016 Jun;31:176-183. doi: 10.1016/j.mib.2016.03.002. Epub 2016 Apr 26. Review.


Potent Inhibition of Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome in Bats, by Cold-Pressed, Terpeneless, Valencia Orange Oil.

Boire N, Zhang S, Khuvis J, Lee R, Rivers J, Crandall P, Keel MK, Parrish N.

PLoS One. 2016 Feb 5;11(2):e0148473. doi: 10.1371/journal.pone.0148473. eCollection 2016.


Extensively drug-resistant tuberculosis in a young child after travel to India.

Salazar-Austin N, Ordonez AA, Hsu AJ, Benson JE, Mahesh M, Menachery E, Razeq JH, Salfinger M, Starke JR, Milstone AM, Parrish N, Nuermberger EL, Jain SK.

Lancet Infect Dis. 2015 Dec;15(12):1485-91. doi: 10.1016/S1473-3099(15)00356-4. Epub 2015 Nov 16. Review.


Recurrent Aeromonas Bacteremia Due to Contaminated Well Water.

Katz MJ, Parrish NM, Belani A, Shah M.

Open Forum Infect Dis. 2015 Oct 20;2(4):ofv142. doi: 10.1093/ofid/ofv142. eCollection 2015 Dec.


An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.


A novel protein extraction method for identification of mycobacteria using MALDI-ToF MS.

Adams LL, Salee P, Dionne K, Carroll K, Parrish N.

J Microbiol Methods. 2015 Dec;119:1-3. doi: 10.1016/j.mimet.2015.09.010. Epub 2015 Sep 25.


Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Sep 8;6:8389. doi: 10.1038/ncomms9389. No abstract available.


Transcription Profiling Demonstrates Epigenetic Control of Non-retroviral RNA Virus-Derived Elements in the Human Genome.

Sofuku K, Parrish NF, Honda T, Tomonaga K.

Cell Rep. 2015 Sep 8;12(10):1548-54. doi: 10.1016/j.celrep.2015.08.007. Epub 2015 Aug 28.


piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals.

Parrish NF, Fujino K, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa S, Nakano T, Siomi H, Honda T, Tomonaga K.

RNA. 2015 Oct;21(10):1691-703. doi: 10.1261/rna.052092.115. Epub 2015 Aug 17.


Carbapenems and Rifampin Exhibit Synergy against Mycobacterium tuberculosis and Mycobacterium abscessus.

Kaushik A, Makkar N, Pandey P, Parrish N, Singh U, Lamichhane G.

Antimicrob Agents Chemother. 2015 Oct;59(10):6561-7. doi: 10.1128/AAC.01158-15. Epub 2015 Aug 10.



Kelly KM, Wack AN, Bradway D, Simons BW, Bronson E, Osterhout G, Parrish NM, Montali RJ.

J Zoo Wildl Med. 2015 Jun;46(2):339-44. doi: 10.1638/2013-0246R2.1.


Mycobacterium tuberculosis resistance in pulmonary TB patients in Cameroon: a phenotypic susceptibility assay.

Jubulis J, Dionne K, Osterhout G, Ayuk L, Awasom C, Achu P, Noeske J, Warren R, McArthur C, Parrish N.

Int J Tuberc Lung Dis. 2015 Jul;19(7):823-7. doi: 10.5588/ijtld.14.0527.


Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256. Erratum in: Nat Commun. 2015;6:8389.


Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas.

Barbian HJ, Decker JM, Bibollet-Ruche F, Galimidi RP, West AP Jr, Learn GH, Parrish NF, Iyer SS, Li Y, Pace CS, Song R, Huang Y, Denny TN, Mouquet H, Martin L, Acharya P, Zhang B, Kwong PD, Mascola JR, Verrips CT, Strokappe NM, Rutten L, McCoy LE, Weiss RA, Brown CS, Jackson R, Silvestri G, Connors M, Burton DR, Shaw GM, Nussenzweig MC, Bjorkman PJ, Ho DD, Farzan M, Hahn BH.

mBio. 2015 Apr 21;6(2). pii: e00296-15. doi: 10.1128/mBio.00296-15.


Treatment of refractory Crohn's disease and pyoderma gangrenosum with a combination regimen of rifaximin, gentamicin and metronidazole.

Goldberg ND, Vadlamudi A, Parrish N.

Case Rep Gastroenterol. 2015 Jan 24;9(1):25-8. doi: 10.1159/000369965. eCollection 2015 Jan-Apr.


Borna disease virus possesses an NF-ĸB inhibitory sequence in the nucleoprotein gene.

Makino A, Fujino K, Parrish NF, Honda T, Tomonaga K.

Sci Rep. 2015 Mar 3;5:8696. doi: 10.1038/srep08696.


Simplified microarray system for simultaneously detecting rifampin, isoniazid, ethambutol, and streptomycin resistance markers in Mycobacterium tuberculosis.

Linger Y, Kukhtin A, Golova J, Perov A, Lambarqui A, Bryant L, Rudy GB, Dionne K, Fisher SL, Parrish N, Chandler DP.

J Clin Microbiol. 2014 Jun;52(6):2100-7. doi: 10.1128/JCM.00238-14. Epub 2014 Apr 9.


Mycotic aortic aneurysm due to intravesical BCG immunotherapy: Clinical manifestations and diagnostic challenges.

Holmes BJ, LaRue RW, Black JH 3rd, Dionne K, Parrish NM, Melia MT.

Int J Mycobacteriol. 2014 Mar;3(1):60-5. doi: 10.1016/j.ijmyco.2013.11.002. Epub 2013 Dec 7.


Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry.

Wojcechowskyj JA, Didigu CA, Lee JY, Parrish NF, Sinha R, Hahn BH, Bushman FD, Jensen ST, Seeholzer SH, Doms RW.

Cell Host Microbe. 2013 May 15;13(5):613-623. doi: 10.1016/j.chom.2013.04.011.


Phenotypic properties of transmitted founder HIV-1.

Parrish NF, Gao F, Li H, Giorgi EE, Barbian HJ, Parrish EH, Zajic L, Iyer SS, Decker JM, Kumar A, Hora B, Berg A, Cai F, Hopper J, Denny TN, Ding H, Ochsenbauer C, Kappes JC, Galimidi RP, West AP Jr, Bjorkman PJ, Wilen CB, Doms RW, O'Brien M, Bhardwaj N, Borrow P, Haynes BF, Muldoon M, Theiler JP, Korber B, Shaw GM, Hahn BH.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6626-33. doi: 10.1073/pnas.1304288110. Epub 2013 Mar 29.


Genome reassembly with high-throughput sequencing data.

Parrish N, Sudakov B, Eskin E.

BMC Genomics. 2013;14 Suppl 1:S8. doi: 10.1186/1471-2164-14-S1-S8. Epub 2013 Jan 21.


Transmitted/founder and chronic HIV-1 envelope proteins are distinguished by differential utilization of CCR5.

Parker ZF, Iyer SS, Wilen CB, Parrish NF, Chikere KC, Lee FH, Didigu CA, Berro R, Klasse PJ, Lee B, Moore JP, Shaw GM, Hahn BH, Doms RW.

J Virol. 2013 Mar;87(5):2401-11. doi: 10.1128/JVI.02964-12. Epub 2012 Dec 26.


Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones.

Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM.

Virology. 2013 Feb 5;436(1):33-48. doi: 10.1016/j.virol.2012.10.009. Epub 2012 Nov 1.


Evaluation of the Sensititre MycoTB plate for susceptibility testing of the Mycobacterium tuberculosis complex against first- and second-line agents.

Hall L, Jude KP, Clark SL, Dionne K, Merson R, Boyer A, Parrish NM, Wengenack NL.

J Clin Microbiol. 2012 Nov;50(11):3732-4. doi: 10.1128/JCM.02048-12. Epub 2012 Aug 15.


Probability of negative mycobacterium tuberculosis complex cultures based on time to detection of positive cultures: a multicenter evaluation of commercial-broth-based culture systems.

Tyrrell FC, Budnick GE, Elliott T, Gillim-Ross L, Hildred MV, Mahlmeister P, Parrish N, Pentella M, Vanneste J, Wang YF, Starks AM.

J Clin Microbiol. 2012 Oct;50(10):3275-82. doi: 10.1128/JCM.01225-12. Epub 2012 Jul 25.


Transmitted/founder and chronic subtype C HIV-1 use CD4 and CCR5 receptors with equal efficiency and are not inhibited by blocking the integrin α4β7.

Parrish NF, Wilen CB, Banks LB, Iyer SS, Pfaff JM, Salazar-Gonzalez JF, Salazar MG, Decker JM, Parrish EH, Berg A, Hopper J, Hora B, Kumar A, Mahlokozera T, Yuan S, Coleman C, Vermeulen M, Ding H, Ochsenbauer C, Tilton JC, Permar SR, Kappes JC, Betts MR, Busch MP, Gao F, Montefiori D, Haynes BF, Shaw GM, Hahn BH, Doms RW.

PLoS Pathog. 2012;8(5):e1002686. doi: 10.1371/journal.ppat.1002686. Epub 2012 May 31.


In vitro effects of citrus oils against Mycobacterium tuberculosis and non-tuberculous Mycobacteria of clinical importance.

Crandall PG, Ricke SC, O'Bryan CA, Parrish NM.

J Environ Sci Health B. 2012;47(7):736-41. doi: 10.1080/03601234.2012.669331.


Mucosal simian immunodeficiency virus transmission in African green monkeys: susceptibility to infection is proportional to target cell availability at mucosal sites.

Pandrea I, Parrish NF, Raehtz K, Gaufin T, Barbian HJ, Ma D, Kristoff J, Gautam R, Zhong F, Haret-Richter GS, Trichel A, Shaw GM, Hahn BH, Apetrei C.

J Virol. 2012 Apr;86(8):4158-68. doi: 10.1128/JVI.07141-11. Epub 2012 Feb 8.

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