Stephen Nayfach

11.1k total citations · 9 hit papers
32 papers, 5.2k citations indexed

About

Stephen Nayfach is a scholar working on Molecular Biology, Ecology and Plant Science. According to data from OpenAlex, Stephen Nayfach has authored 32 papers receiving a total of 5.2k indexed citations (citations by other indexed papers that have themselves been cited), including 29 papers in Molecular Biology, 21 papers in Ecology and 8 papers in Plant Science. Recurrent topics in Stephen Nayfach's work include Genomics and Phylogenetic Studies (18 papers), Gut microbiota and health (16 papers) and Bacteriophages and microbial interactions (12 papers). Stephen Nayfach is often cited by papers focused on Genomics and Phylogenetic Studies (18 papers), Gut microbiota and health (16 papers) and Bacteriophages and microbial interactions (12 papers). Stephen Nayfach collaborates with scholars based in United States, Australia and Canada. Stephen Nayfach's co-authors include Katherine S. Pollard, Nikos C. Kyrpides, Simon Roux, Frederik Schulz, Antônio Pedro Camargo, Emiley A. Eloe‐Fadrosh, Zhou Jason Shi, R. Seshadri, Philip Hugenholtz and Michael A. Fischbach and has published in prestigious journals such as Nature, Cell and Nucleic Acids Research.

In The Last Decade

Stephen Nayfach

32 papers receiving 5.2k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

2020 905 citations Stephen Nayfach, Antônio Pedro Camargo et al. Nature Biotechnology profile →
A unified catalog of 204,938 reference genomes from the human gut microbiome

2020 736 citations Alexandre Almeida, Stephen Nayfach et al. Nature Biotechnology profile →
New insights from uncultivated genomes of the global human gut microbiome

2019 445 citations Stephen Nayfach, Zhou Jason Shi et al. Nature profile →
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

2021 313 citations Stephen Nayfach, David Páez-Espino et al. Nature Microbiology profile →
Identification of mobile genetic elements with geNomad

2023 301 citations Antônio Pedro Camargo, Simon Roux et al. Nature Biotechnology profile →
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

2020 221 citations Simon Roux, David Páez-Espino et al. profile →
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

2022 199 citations Antônio Pedro Camargo, Stephen Nayfach et al. profile →
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

2023 182 citations Simon Roux, Antônio Pedro Camargo et al. PLoS Biology profile →
Design of highly functional genome editors by modelling CRISPR–Cas sequences

2025 21 citations Jeffrey A. Ruffolo, Stephen Nayfach et al. Nature profile →

Peers

Countries citing papers authored by Stephen Nayfach

Since Specialization

Citations

This map shows the geographic impact of Stephen Nayfach's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Stephen Nayfach with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Stephen Nayfach more than expected).

Fields of papers citing papers by Stephen Nayfach

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Stephen Nayfach. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Stephen Nayfach. The network helps show where Stephen Nayfach may publish in the future.

Co-authorship network of co-authors of Stephen Nayfach

This figure shows the co-authorship network connecting the top 25 collaborators of Stephen Nayfach. A scholar is included among the top collaborators of Stephen Nayfach based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Stephen Nayfach. Stephen Nayfach is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Design of highly functional genome editors by modelling CRISPR–Cas sequences breakdown → 2025 ·Nature ·Jeffrey A. Ruffolo, Stephen Nayfach, Joseph P. Gallagher, (unknown), (unknown), (unknown), (unknown), Jennifer Yip, (unknown), Martin Pačesa, Alexander J. Meeske, Peter Cameron, Ali Madani	21
2	Identification of mobile genetic elements with geNomad breakdown → 2023 ·Nature Biotechnology ·Antônio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski, (unknown), Bin Hu, Patrick Chain, Stephen Nayfach, Nikos C. Kyrpides	301
3	iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria breakdown → 2023 ·PLoS Biology ·Simon Roux, Antônio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt	182
4	Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro 2023 ·STAR Protocols ·Zhou Jason Shi, Stephen Nayfach, Katherine S. Pollard	1
5	MIDAS2: Metagenomic Intra-species Diversity Analysis System 2022 ·Bioinformatics ·Chunyu Zhao, Boris Dimitrov, (unknown), Stephen Nayfach, Katherine S. Pollard	20
6	Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution 2021 ·The ISME Journal ·Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, (unknown), (unknown), Janey Lee, Danielle Goudeau, Emiley A. Eloe‐Fadrosh, Ramūnas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke	23
7	Ecology and molecular targets of hypermutation in the global microbiome 2021 ·Nature Communications ·Simon Roux, Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme T. Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven Hallam, Maria Hernandez, Matthias Hess, Wen‐Tso Liu, Tim A. McAllister, Michelle O’Malley, Xuefeng Peng, Virginia I. Rich, S. R. Saleska, Emiley A. Eloe‐Fadrosh	43
8	Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome breakdown → 2021 ·Nature Microbiology ·Stephen Nayfach, David Páez-Espino, (unknown), Soo Jen Low, Hila Sberro, Natalia Ivanova, Amy D. Proal, Michael A. Fischbach, Ami S. Bhatt, Philip Hugenholtz, Nikos C. Kyrpides	313
9	A unified catalog of 204,938 reference genomes from the human gut microbiome breakdown → 2020 ·Nature Biotechnology ·Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martín Beracochea, Zhou Jason Shi, Katherine S. Pollard, Ekaterina Sakharova, Donovan H. Parks, Philip Hugenholtz, Nicola Segata, Nikos C. Kyrpides, ROBERT FINN	736
10	CheckV assesses the quality and completeness of metagenome-assembled viral genomes breakdown → 2020 ·Nature Biotechnology ·Stephen Nayfach, Antônio Pedro Camargo, Frederik Schulz, Emiley A. Eloe‐Fadrosh, Simon Roux, Nikos C. Kyrpides	905
11	Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community 2020 ·Microbiome ·(unknown), Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, (unknown), (unknown), Simon Roux, David Páez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke, Emiley A. Eloe‐Fadrosh, Ricardo Cavicchioli	46
12	Global ecotypes in the ubiquitous marine clade SAR86 2019 ·The ISME Journal ·Adrienne Hoarfrost, Stephen Nayfach, Joshua Ladau, Shibu Yooseph, Carol Arnosti, Christopher L. Dupont, Katherine S. Pollard	40
13	Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria 2019 ·Nature Microbiology ·Elizabeth N. Bess, Jordan E. Bisanz, Fauna Yarza, Annamarie E. Bustion, (unknown), Xingnan Li, Seiya Kitamura, (unknown), Qi Yan Ang, Diana Alba, Peter Spanogiannopoulos, Stephen Nayfach, Suneil K. Koliwad, Dennis W. Wolan, Adrian A. Franke, Peter J. Turnbaugh	74
14	Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes 2019 ·Nature Microbiology ·Simon Roux, Mart Krupovìč, Rebecca A. Daly, Adair L. Borges, Stephen Nayfach, Frederik Schulz, Allison Sharrar, Paula B. Matheus Carnevali, Jan‐Fang Cheng, Natalia Ivanova, Joseph Bondy‐Denomy, Kelly Wrighton, Tanja Woyke, Axel Visel, Nikos C. Kyrpides, Emiley A. Eloe‐Fadrosh	162
15	Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis 2018 ·Microbiome ·Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William P. Inskeep, Natalia Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramūnas Stepanauskas, Tanja Woyke	35
16	Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases 2017 ·Cell ·(unknown), Fangyuan Chang, Thomas P. Wyche, Keriann M. Backus, Timothy M. Acker, Masanori Funabashi, Mao Taketani, Mohamed S. Donia, Stephen Nayfach, Katherine S. Pollard, Charles S. Craik, Benjamin F. Cravatt, Jon Clardy, Christopher A. Voigt, Michael A. Fischbach	169
17	Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota 2016 ·Cell Host & Microbe ·A. Sloan Devlin, Ãngela Marcobal, Dylan Dodd, Stephen Nayfach, Natalie S. Plummer, Tim Meyer, Katherine S. Pollard, Justin L. Sonnenburg, Michael A. Fischbach	223
18	Toward Accurate and Quantitative Comparative Metagenomics 2016 ·Cell ·Stephen Nayfach, Katherine S. Pollard	190
19	Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome 2015 ·Genome Biology ·Stephen Nayfach, Katherine S. Pollard	224
20	Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes 2015 ·PLoS Computational Biology ·Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy Laurent, (unknown), Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton	41

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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