Kyrpides, Nikos C.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 2,624

Insights into the phylogeny and coding potential of microbial dark matter

Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 2,394

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,367

New insights from uncultivated genomes of the global human gut microbiome

Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 737

A Catalog of Reference Genomes from the Human Microbiome

The Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K. E., Weinstock, G. M., Highlander, S. K., Worley, K. C., Creasy, H. H., Wortman, J. R., Rusch, D. B., Mitreva, M., Sodergren, E., et al. (2010) · Science

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 702

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology

Ruminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas Production

Cited by 624

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 580

Protein structure determination using metagenome sequence data

Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 520

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Camargo, A. P., Nayfach, S., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Ritter, S. J., Reddy, T. B. K., Mukherjee, S., Schulz, F., et al. (2023) · Nucleic Acids Research

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 446

Genome Project Standards in a New Era of Sequencing

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., et al. (2009) · Science

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 400

A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., et al. (2008) · Proceedings of the National Academy of Sciences

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 296

The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea

Wagner-Döbler, I., Ballhausen, B., Berger, M., Brinkhoff, T., Buchholz, I., Bunk, B., Cypionka, H., Daniel, R., Drepper, T., Gerdts, G., et al. (2010) · The ISME Journal

Microbial Community Ecology and PhysiologyProtist diversity and phylogeny

Cited by 271

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., & Bhatt, A. S. (2019) · Cell

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 237

Genomes OnLine database (GOLD) v.7: updates and new features

Mukherjee, S., Stamatis, D., Bertsch, J., Ovchinnikova, G., Katta, H. Y., Mojica, A., Chen, I.-M. A., Kyrpides, N. C., & Reddy, T. (2019) · Nucleic Acids Research

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 230

A Thermostable Cas9 with Increased Lifetime in Human Plasma

Harrington, L. B., Paez-Espino, D., Staahl, B. T., Chen, J. S., Ma, E., Kyrpides, N. C., & Doudna, J. A. (2017) · Nature Communications

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 205

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research

Genomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

Cited by 87

On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyperdiverse, enigmatic spacer repertoires

Silas, S., Makarova, K. S., Shmakov, S., Páez-Espino, D., Mohr, G., Liu, Y., Davison, M., Roux, S., Krishnamurthy, S. R., Fu, B. X. H., et al. (2017) · mBio

CRISPR and Genetic EngineeringBacterial Genetics and Biotechnology

Cited by 62

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., et al. (2014) · Standards in Genomic Sciences

Microbial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Cited by 62

Facile Recoding of Selenocysteine in Nature

Mukai, T., Englert, M., Tripp, H. J., Miller, C., Ivanova, N. N., Rubin, E. M., Kyrpides, N. C., & Söll, D. (2016) · Angewandte Chemie International Edition

RNA and protein synthesis mechanismsSelenium in Biological Systems

Cited by 61

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., Lundin, D., community, N.-C., Buluç, A., Kyrpides, N. C., et al. (2026) · GigaScience

Genomics and Phylogenetic StudiesScientific Computing and Data Management

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nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., Lundin, D., community, N.-C., Buluç, A., Kyrpides, N. C., et al. (2025) · GigaScience

Genomics and Phylogenetic StudiesScientific Computing and Data Management

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The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology

Chasapi, A., Michailidis, A., Schriml, L. M., Donati, C., Kyrpides, N. C., & Ouzounis, C. A. (2026) · Microbiology and Molecular Biology Reviews

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 0