Publications by authors named "Karthik Anantharaman"

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A new view of the tree of life.
Laura A Hug, Brett J Baker, Karthik Anantharaman, Christopher T Brown, Alexander J Probst, Cindy J Castelle, Cristina N Butterfield, Alex W Hernsdorf, Yuki Amano, Kotaro Ise

Nat Microbiol· April 2016

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Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.
James C Kosmopoulos, Karthik Anantharaman

Biochemistry· December 2025

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Ecosystem health shapes viral ecology in peatland soils.
James C Kosmopoulos, William Pallier, Ashish A Malik, Karthik Anantharaman

Nat Microbiol· December 2025

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Systematic genome-wide mapping of host determinants of bacteriophage infectivity.
Chutikarn Chitboonthavisuk, Cody Martin, Phil Huss, Jason M Peters, Karthik Anantharaman

Cell Syst· November 2025

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Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.
Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Laura A Hug

Virol J· November 2025

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Protein Set Transformer: a protein-based genome language model to power high-diversity viromics.
Cody Martin, Anthony Gitter, Karthik Anantharaman

Nat Commun· November 2025

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Mapping Structural Constraints and Adaptive Potential in a Capsule-Degrading Phage Tailspike Protein.
Sarah Evert, Phill Huss, Dinesh Kumar Kuppa Baskaran, Karthik Anantharaman, Srivatsan Raman

bioRxiv· October 2025

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A call for caution in the biological interpretation of viral auxiliary metabolic genes.
Cody Martin, Joanne B Emerson, Simon Roux, Karthik Anantharaman

Nat Microbiol· September 2025

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Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.
Tao Wang, Peiyu Zhang, Karthik Anantharaman, Huan Wang, Huan Zhang

Nat Commun· August 2025

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An updated view of metabolic handoffs in microbiomes.
Katherine M Klier, Karthik Anantharaman

Trends Microbiol· August 2025

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Author Correction: Elevated heterotrophic activity in Guaymas Basin hydrothermal plumes influences deep-sea carbon cycling.
Andrew Montgomery, Guang-Chao Zhuang, Zhichao Zhou, Marguerite V Langwig, María Del Carmen Millán-Motolinía, Karthik Anantharaman

Nat Commun· July 2025

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Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.
James C Kosmopoulos, Karthik Anantharaman

ArXiv· June 2025

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An expanded metabolic pathway for androgen production by commensal bacteria.
Taojun Wang, Saeed Ahmad, Angélica Cruz-Lebrón, Sarah E Ernst, Kelly Yovani Olivos Caicedo, Karthik Anantharaman

Nat Microbiol· May 2025

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Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.
Marguerite V Langwig, Faith Koester, Cody Martin, Zhichao Zhou, Samantha B Joye, Karthik Anantharaman

Nat Commun· May 2025

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Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites.
Yiyi Liu, Yu-Yu Cheng, Jaron Thompson, Zhichao Zhou, Eugenio I Vivas, Karthik Anantharaman

Cell Syst· May 2025

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Genetic keys to microbial gut colonization.
Karthik Anantharaman, Cody Martin

Cell Host Microbe· May 2025

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Elevated heterotrophic activity in Guaymas Basin hydrothermal plumes influences deep-sea carbon cycling.
Andrew Montgomery, Guang-Chao Zhuang, Zhichao Zhou, Marguerite V Langwig, María Del Carmen Millán-Motolinía, Karthik Anantharaman

Nat Commun· May 2025

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Engineering bacteriophages through deep mining of metagenomic motifs.
Phil Huss, Kristopher Kieft, Anthony Meger, Kyle Nishikawa, Karthik Anantharaman

Sci Adv· April 2025

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Pangenome Analysis of : A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.
Kelly Y Olivos-Caicedo, Francelys V Fernandez-Materan, Steven L Daniel, Karthik Anantharaman, Jason M Ridlon

Microorganisms· April 2025

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Publisher Correction: Massively parallel single-cell sequencing of diverse microbial populations.
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman

Nat Methods· February 2025

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Unravelling viral ecology and evolution over 20 years in a freshwater lake.
Zhichao Zhou, Patricia Q Tran, Cody Martin, Robin R Rohwer, Brett J Baker, Karthik Anantharaman

Nat Microbiol· January 2025

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Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.
Etan Dieppa-Colón, Cody Martin, James C Kosmopoulos, Karthik Anantharaman

Environ Microbiome· January 2025

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zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.
Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Karthik Anantharaman

Nucleic Acids Res· January 2025

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Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments.
Marguerite V Langwig, Sunny Lyn Sneed, Anna Rasmussen, Kiley W Seitz, Jessica A Lee, Karthik Anantharaman

ISME Commun· January 2025

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Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.
Yuki Amano, Rohan Sachdeva, Daniel Gittins, Karthik Anantharaman, Shufei Lei

Environ Microbiome· December 2024

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V- and V-Scores Uncover Viral Signatures and Origins of Protein Families.
Kun Zhou, James C Kosmopoulos, Etan Dieppa Colón, Peter John Badciong, Karthik Anantharaman

bioRxiv· October 2024

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