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Ecology and molecular targets of hypermutation in the global microbiome.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23402-7
By:
- Roux, Simon;
- Paul, Blair G.;
- Bagby, Sarah C.;
- Nayfach, Stephen;
- Allen, Michelle A.;
- Attwood, Graeme;
- Cavicchioli, Ricardo;
- Chistoserdova, Ludmila;
- Gruninger, Robert J.;
- Hallam, Steven J.;
- Hernandez, Maria E.;
- Hess, Matthias;
- Liu, Wen-Tso;
- McAllister, Tim A.;
- O'Malley, Michelle A.;
- Peng, Xuefeng;
- Rich, Virginia I.;
- Saleska, Scott R.;
- Eloe-Fadrosh, Emiley A.
Publication type:
Article
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.
Published in:
Nature Biotechnology, 2022, v. 40, n. 4, p. 507, doi. 10.1038/s41587-021-01102-3
By:
- Shi, Zhou Jason;
- Dimitrov, Boris;
- Zhao, Chunyu;
- Nayfach, Stephen;
- Pollard, Katherine S.
Publication type:
Article
CheckV assesses the quality and completeness of metagenome-assembled viral genomes.
Published in:
Nature Biotechnology, 2021, v. 39, n. 5, p. 578, doi. 10.1038/s41587-020-00774-7
By:
- Nayfach, Stephen;
- Camargo, Antonio Pedro;
- Schulz, Frederik;
- Eloe-Fadrosh, Emiley;
- Roux, Simon;
- Kyrpides, Nikos C.
Publication type:
Article
Author Correction: A genomic catalog of Earth's microbiomes.
Published in:
2021
By:
- Nayfach, Stephen;
- Roux, Simon;
- Seshadri, Rekha;
- Udwary, Daniel;
- Varghese, Neha;
- Schulz, Frederik;
- Wu, Dongying;
- Paez-Espino, David;
- Chen, I-Min;
- Huntemann, Marcel;
- Palaniappan, Krishna;
- Ladau, Joshua;
- Mukherjee, Supratim;
- Reddy, T. B. K.;
- Nielsen, Torben;
- Kirton, Edward;
- Faria, José P.;
- Edirisinghe, Janaka N.;
- Henry, Christopher S.;
- Jungbluth, Sean P.
Publication type:
Correction Notice
Publisher Correction: A genomic catalog of Earth's microbiomes.
Published in:
2021
By:
- Nayfach, Stephen;
- Roux, Simon;
- Seshadri, Rekha;
- Udwary, Daniel;
- Varghese, Neha;
- Schulz, Frederik;
- Wu, Dongying;
- Paez-Espino, David;
- Chen, I-Min;
- Huntemann, Marcel;
- Palaniappan, Krishna;
- Ladau, Joshua;
- Mukherjee, Supratim;
- Reddy, T. B. K.;
- Nielsen, Torben;
- Kirton, Edward;
- Faria, José P.;
- Edirisinghe, Janaka N.;
- Henry, Christopher S.;
- Jungbluth, Sean P.
Publication type:
Correction Notice
A genomic catalog of Earth's microbiomes.
Published in:
Nature Biotechnology, 2021, v. 39, n. 4, p. 499, doi. 10.1038/s41587-020-0718-6
By:
- Nayfach, Stephen;
- Roux, Simon;
- Seshadri, Rekha;
- Udwary, Daniel;
- Varghese, Neha;
- Schulz, Frederik;
- Wu, Dongying;
- Paez-Espino, David;
- Chen, I-Min;
- Huntemann, Marcel;
- Palaniappan, Krishna;
- Ladau, Joshua;
- Mukherjee, Supratim;
- Reddy, T. B. K.;
- Nielsen, Torben;
- Kirton, Edward;
- Faria, José P.;
- Edirisinghe, Janaka N.;
- Henry, Christopher S.;
- Jungbluth, Sean P.
Publication type:
Article
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Published in:
Nature Biotechnology, 2021, v. 39, n. 1, p. 105, doi. 10.1038/s41587-020-0603-3
By:
- Almeida, Alexandre;
- Nayfach, Stephen;
- Boland, Miguel;
- Strozzi, Francesco;
- Beracochea, Martin;
- Shi, Zhou Jason;
- Pollard, Katherine S.;
- Sakharova, Ekaterina;
- Parks, Donovan H.;
- Hugenholtz, Philip;
- Segata, Nicola;
- Kyrpides, Nikos C.;
- Finn, Robert D.
Publication type:
Article
MIDAS2: Metagenomic Intra-species Diversity Analysis System.
Published in:
Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac713
By:
- Zhao, Chunyu;
- Dimitrov, Boris;
- Goldman, Miriam;
- Nayfach, Stephen;
- Pollard, Katherine S
Publication type:
Article
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
Published in:
PLoS Computational Biology, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pcbi.1004573
By:
- Nayfach, Stephen;
- Bradley, Patrick H.;
- Wyman, Stacia K.;
- Laurent, Timothy J.;
- Williams, Alex;
- Eisen, Jonathan A.;
- Pollard, Katherine S.;
- Sharpton, Thomas J.
Publication type:
Article
Maast: genotyping thousands of microbial strains efficiently.
Published in:
Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03030-8
By:
- Shi, Zhou Jason;
- Nayfach, Stephen;
- Pollard, Katherine S.
Publication type:
Article
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 51, doi. 10.1186/s13059-015-0611-7
By:
- Nayfach, Stephen;
- Pollard, Katherine S
Publication type:
Article
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.
Published in:
PLoS Biology, 2023, v. 21, n. 4, p. 1, doi. 10.1371/journal.pbio.3002083
By:
- Roux, Simon;
- Camargo, Antonio Pedro;
- Coutinho, Felipe H.;
- Dabdoub, Shareef M.;
- Dutilh, Bas E.;
- Nayfach, Stephen;
- Tritt, Andrew
Publication type:
Article
Identification of mobile genetic elements with geNomad.
Published in:
Nature Biotechnology, 2024, v. 42, n. 8, p. 1303, doi. 10.1038/s41587-023-01953-y
By:
- Camargo, Antonio Pedro;
- Roux, Simon;
- Schulz, Frederik;
- Babinski, Michal;
- Xu, Yan;
- Hu, Bin;
- Chain, Patrick S. G.;
- Nayfach, Stephen;
- Kyrpides, Nikos C.
Publication type:
Article
Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.
Published in:
Microbiome, 2018, v. 6, n. 1, p. N.PAG, doi. 10.1186/s40168-018-0539-8
By:
- Jarett, Jessica K.;
- Nayfach, Stephen;
- Podar, Mircea;
- Inskeep, William;
- Ivanova, Natalia N.;
- Munson-McGee, Jacob;
- Schulz, Frederik;
- Young, Mark;
- Jay, Zackary J.;
- Beam, Jacob P.;
- Kyrpides, Nikos C.;
- Malmstrom, Rex R.;
- Stepanauskas, Ramunas;
- Woyke, Tanja
Publication type:
Article
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.
Published in:
Nucleic Acids Research, 2024, v. 52, n. D1, p. D164, doi. 10.1093/nar/gkad964
By:
- Camargo, Antonio Pedro;
- Call, Lee;
- Roux, Simon;
- Nayfach, Stephen;
- Huntemann, Marcel;
- Palaniappan, Krishnaveni;
- Ratner, Anna;
- Chu, Ken;
- Mukherjeep, Supratim;
- Reddy, T B K;
- Chen, I-Min A;
- Ivanova, Natalia N;
- Eloe-Fadrosh, Emiley A;
- Woyke, Tanja;
- Baltrus, David A;
- Castañeda-Barba, Salvador;
- de la Cruz, Fernando;
- Funnell, Barbara E;
- Hall, James P J;
- Mukhopadhyay, Aindrila
Publication type:
Article
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.
Published in:
Nucleic Acids Research, 2023, v. 51, n. D1, p. D733, doi. 10.1093/nar/gkac1037
By:
- Camargo, Antonio Pedro;
- Nayfach, Stephen;
- Chen, I-Min A;
- Palaniappan, Krishnaveni;
- Ratner, Anna;
- Chu, Ken;
- Ritter, Stephan J;
- Reddy, T B K;
- Mukherjee, Supratim;
- Schulz, Frederik;
- Call, Lee;
- Neches, Russell Y;
- Woyke, Tanja;
- Ivanova, Natalia N;
- Eloe-Fadrosh, Emiley A;
- Kyrpides, Nikos C;
- Roux, Simon
Publication type:
Article
Inaccurate viral prediction leads to overestimated diversity of the archaeal virome in the human gut.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49902-w
By:
- Chibani, Cynthia M.;
- Shah, Shiraz A.;
- Schmitz, Ruth A.;
- Nayfach, Stephen
Publication type:
Article
A most wanted list of conserved microbial protein families with no known domains.
Published in:
PLoS ONE, 2018, v. 13, n. 10, p. 1, doi. 10.1371/journal.pone.0205749
By:
- Wyman, Stacia K.;
- Avila-Herrera, Aram;
- Nayfach, Stephen;
- Pollard, Katherine S.
Publication type:
Article
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Published in:
Bioinformatics, 2015, v. 31, n. 20, p. 3368, doi. 10.1093/bioinformatics/btv382
By:
- Nayfach, Stephen;
- Fischbach, Michael A.;
- Pollard, Katherine S.
Publication type:
Article
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.
Published in:
Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00889-8
By:
- Panwar, Pratibha;
- Allen, Michelle A.;
- Williams, Timothy J.;
- Hancock, Alyce M.;
- Brazendale, Sarah;
- Bevington, James;
- Roux, Simon;
- Páez-Espino, David;
- Nayfach, Stephen;
- Berg, Maureen;
- Schulz, Frederik;
- Chen, I-Min A.;
- Huntemann, Marcel;
- Shapiro, Nicole;
- Kyrpides, Nikos C.;
- Woyke, Tanja;
- Eloe-Fadrosh, Emiley A.;
- Cavicchioli, Ricardo
Publication type:
Article
Diversity, evolution, and classification of virophages uncovered through global metagenomics.
Published in:
Microbiome, 2019, v. 7, n. 1, p. 1, doi. 10.1186/s40168-019-0768-5
By:
- Paez-Espino, David;
- Zhou, Jinglie;
- Roux, Simon;
- Nayfach, Stephen;
- Pavlopoulos, Georgios A.;
- Schulz, Frederik;
- McMahon, Katherine D.;
- Walsh, David;
- Woyke, Tanja;
- Ivanova, Natalia N.;
- Eloe-Fadrosh, Emiley A.;
- Tringe, Susannah G.;
- Kyrpides, Nikos C.
Publication type:
Article
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
Published in:
PLoS Computational Biology, 2018, v. 14, n. 8, p. 1, doi. 10.1371/journal.pcbi.1006242
By:
- Bradley, Patrick H.;
- Nayfach, Stephen;
- Pollard, Katherine S.
Publication type:
Article

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