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Human-Gut Phages Harbor Sporulation Genes.
mBio. 2023 Jun 27;14(3):e0018223. doi: 10.1128/mbio.00182-23. Epub 2023 Apr 12.
mBio. 2023.
PMID: 37042671
Free PMC article.
DRAM for distilling microbial metabolism to automate the curation of microbiome function.
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, Liu P, Narrowe AB, Rodríguez-Ramos J, Bolduc B, Gazitúa MC, Daly RA, Smith GJ, Vik DR, Pope PB, Sullivan MB, Roux S, Wrighton KC.
Shaffer M, et al.
Nucleic Acids Res. 2020 Sep 18;48(16):8883-8900. doi: 10.1093/nar/gkaa621.
Nucleic Acids Res. 2020.
PMID: 32766782
Free PMC article.
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Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.
Rodríguez-Ramos JA, Borton MA, McGivern BB, Smith GJ, Solden LM, Shaffer M, Daly RA, Purvine SO, Nicora CD, Eder EK, Lipton M, Hoyt DW, Stegen JC, Wrighton KC.
Rodríguez-Ramos JA, et al.
mSystems. 2022 Aug 30;7(4):e0051622. doi: 10.1128/msystems.00516-22. Epub 2022 Jul 21.
mSystems. 2022.
PMID: 35861508
Free PMC article.
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Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.
Rodríguez-Ramos J, Oliverio A, Borton MA, Danczak R, Mueller BM, Schulz H, Ellenbogen J, Flynn RM, Daly RA, Schopflin L, Shaffer M, Goldman A, Lewandowski J, Stegen JC, Wrighton KC.
Rodríguez-Ramos J, et al.
bioRxiv [Preprint]. 2023 Apr 4:2023.04.04.535500. doi: 10.1101/2023.04.04.535500.
bioRxiv. 2023.
PMID: 37066413
Free PMC article.
Preprint.
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Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.
Leleiwi I, Rodriguez-Ramos J, Shaffer M, Sabag-Daigle A, Kokkinias K, Flynn RM, Daly RA, Kop LFM, Solden LM, Ahmer BMM, Borton MA, Wrighton KC.
Leleiwi I, et al.
Microbiome. 2023 May 20;11(1):114. doi: 10.1186/s40168-023-01529-7.
Microbiome. 2023.
PMID: 37210515
Free PMC article.
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Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.
Rodríguez-Ramos J, Nicora CD, Purvine SO, Borton MA, McGivern BB, Hoyt DW, Lipton MS, Wrighton KC.
Rodríguez-Ramos J, et al.
Microbiol Resour Announc. 2024 Apr 23:e0003324. doi: 10.1128/mra.00033-24. Online ahead of print.
Microbiol Resour Announc. 2024.
PMID: 38651910
Free article.
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Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.
Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB.
Trubl G, et al.
PeerJ. 2019 Jul 4;7:e7265. doi: 10.7717/peerj.7265. eCollection 2019.
PeerJ. 2019.
PMID: 31309007
Free PMC article.
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