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Items: 15

1.

Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics.

Chopyk J, Nasko DJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR.

Sci Total Environ. 2020 Mar 1;706:135395. doi: 10.1016/j.scitotenv.2019.135395. Epub 2019 Nov 25.

PMID:
31846873
2.

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications.

Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR.

Water Res. 2020 Feb 1;169:115250. doi: 10.1016/j.watres.2019.115250. Epub 2019 Oct 31.

PMID:
31726395
3.

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP.

mSystems. 2019 Oct 8;4(5). pii: e00392-19. doi: 10.1128/mSystems.00392-19.

4.

Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation.

Chopyk J, Kulkarni P, Nasko DJ, Bradshaw R, Kniel KE, Chiu P, Sharma M, Sapkota AR.

BMC Res Notes. 2019 Apr 11;12(1):223. doi: 10.1186/s13104-019-4251-y.

5.

CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes.

Nasko DJ, Ferrell BD, Moore RM, Bhavsar JD, Polson SW, Wommack KE.

mBio. 2019 Mar 5;10(2). pii: e02651-18. doi: 10.1128/mBio.02651-18.

6.

Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton.

Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE.

Front Microbiol. 2018 Dec 14;9:3053. doi: 10.3389/fmicb.2018.03053. eCollection 2018.

7.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ.

Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

8.

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.

Nasko DJ, Koren S, Phillippy AM, Treangen TJ.

Genome Biol. 2018 Oct 30;19(1):165. doi: 10.1186/s13059-018-1554-6.

9.

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations.

Chopyk J, Allard S, Nasko DJ, Bui A, Mongodin EF, Sapkota AR.

Front Microbiol. 2018 Apr 24;9:792. doi: 10.3389/fmicb.2018.00792. eCollection 2018.

10.

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.

Johnson TA, Looft T, Severin AJ, Bayles DO, Nasko DJ, Wommack KE, Howe A, Allen HK.

mBio. 2017 Aug 8;8(4). pii: e00709-17. doi: 10.1128/mBio.00709-17.

11.

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology.

Marine RL, Nasko DJ, Wray J, Polson SW, Wommack KE.

ISME J. 2017 Nov;11(11):2479-2491. doi: 10.1038/ismej.2017.102. Epub 2017 Jul 21.

12.

Counts and sequences, observations that continue to change our understanding of viruses in nature.

Wommack KE, Nasko DJ, Chopyk J, Sakowski EG.

J Microbiol. 2015 Mar;53(3):181-92. doi: 10.1007/s12275-015-5068-6. Epub 2015 Mar 3. Review.

PMID:
25732739
13.

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses.

Sakowski EG, Munsell EV, Hyatt M, Kress W, Williamson SJ, Nasko DJ, Polson SW, Wommack KE.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15786-91. doi: 10.1073/pnas.1401322111. Epub 2014 Oct 13.

14.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, Wommack KE.

Microbiome. 2014 Jan 30;2(1):3. doi: 10.1186/2049-2618-2-3.

15.

VIROME: a standard operating procedure for analysis of viral metagenome sequences.

Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ.

Stand Genomic Sci. 2012 Jul 30;6(3):427-39. doi: 10.4056/sigs.2945050. Epub 2012 Jul 27.

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