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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.
mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20.
mSystems. 2021.
PMID: 33727399
Free PMC article.
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R.
Sanders JG, et al.
Genome Biol. 2019 Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9.
Genome Biol. 2019.
PMID: 31672156
Free PMC article.
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Visualizing 'omic feature rankings and log-ratios using Qurro.
Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R.
Fedarko MW, et al.
NAR Genom Bioinform. 2020 Jun;2(2):lqaa023. doi: 10.1093/nargab/lqaa023. Epub 2020 Apr 28.
NAR Genom Bioinform. 2020.
PMID: 32391521
Free PMC article.
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Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India.
Huey SL, Jiang L, Fedarko MW, McDonald D, Martino C, Ali F, Russell DG, Udipi SA, Thorat A, Thakker V, Ghugre P, Potdar RD, Chopra H, Rajagopalan K, Haas JD, Finkelstein JL, Knight R, Mehta S.
Huey SL, et al. Among authors: fedarko mw.
mSphere. 2020 Sep 23;5(5):e00731-20. doi: 10.1128/mSphere.00731-20.
mSphere. 2020.
PMID: 32968008
Free PMC article.
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MetaCarvel: linking assembly graph motifs to biological variants.
Ghurye J, Treangen T, Fedarko M, Hervey WJ 4th, Pop M.
Ghurye J, et al.
Genome Biol. 2019 Aug 26;20(1):174. doi: 10.1186/s13059-019-1791-3.
Genome Biol. 2019.
PMID: 31451112
Free PMC article.
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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.
Meisel JS, et al.
Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.
Microbiome. 2018.
PMID: 30396371
Free PMC article.
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Analyzing rare mutations in metagenomes assembled using long and accurate reads.
Fedarko MW, Kolmogorov M, Pevzner PA.
Fedarko MW, et al.
Genome Res. 2022 Nov-Dec;32(11-12):2119-2133. doi: 10.1101/gr.276917.122. Epub 2022 Nov 23.
Genome Res. 2022.
PMID: 36418060
Free PMC article.
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