Publications by authors named "Ahmed A Zayed"

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Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.
Mohamed Mohssen, Ahmed A Zayed, Kristina A Kigerl, Jingjie Du, Garrett J Smith

bioRxiv· November 2025

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Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.
Zachary J Lewis, Angela Scott, Christopher Madden, Dean Vik, Ahmed A Zayed

Microbiome· October 2025

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Disruption of The Spinal Cord-Gut Axis Alters Gut Microbial Dynamics and Carbohydrate Cross-feeding.
Mohamed Mohssen, Ahmed A Zayed, Kristina A Kigerl, Jingjie Du, Garrett J Smith

bioRxiv· July 2025

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Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.
Zachary J Lewis, Angela Scott, Christopher Madden, Dean Vik, Ahmed A Zayed

Res Sq· August 2024

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Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.
Christine L Sun, Akbar Adjie Pratama, Maria Consuelo Gazitúa, Dylan Cronin, Bridget B McGivern, Ahmed A Zayed

Environ Microbiol· July 2024

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Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.
Joanna Warwick-Dugdale, Funing Tian, Michelle L Michelsen, Dylan R Cronin, Karen Moore, Ahmed A Zayed

Nat Commun· May 2024

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Environment-specific virocell metabolic reprogramming.
Cristina Howard-Varona, Morgan M Lindback, Jane D Fudyma, Azriel Krongauz, Natalie E Solonenko, Ahmed A Zayed

ISME J· January 2024

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Ocean-wide comparisons of mesopelagic planktonic community structures.
Janaina Rigonato, Marko Budinich, Alejandro A Murillo, Manoela C Brandão, Juan J Pierella Karlusich, Ahmed A Zayed

ISME Commun· August 2023

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The RNA virosphere: How big and diverse is it?
Guillermo Dominguez-Huerta, James M Wainaina, Ahmed A Zayed, Alexander I Culley, Jens H Kuhn

Environ Microbiol· January 2023

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Novel integrative elements and genomic plasticity in ocean ecosystems.
Thomas Hackl, Raphaël Laurenceau, Markus J Ankenbrand, Christina Bliem, Zev Cariani, Ahmed A Zayed

Cell· January 2023

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Biosynthetic potential of the global ocean microbiome.
Lucas Paoli, Hans-Joachim Ruscheweyh, Clarissa C Forneris, Florian Hubrich, Satria Kautsar, Ahmed A Zayed

Nature· July 2022

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Diversity and ecological footprint of Global Ocean RNA viruses.
Guillermo Dominguez-Huerta, Ahmed A Zayed, James M Wainaina, Jiarong Guo, Funing Tian

Science· June 2022

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Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome.
Ahmed A Zayed, James M Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo

Science· April 2022

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iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.
Benjamin Bolduc, Olivier Zablocki, Jiarong Guo, Ahmed A Zayed, Dean Vik

ISME Commun· December 2021

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efam: an expanded, metaproteome-supported HMM profile database of viral protein families.
Ahmed A Zayed, Dominik Lücking, Mohamed Mohssen, Dylan Cronin, Ben Bolduc

Bioinformatics· November 2021

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Environmental vulnerability of the global ocean epipelagic plankton community interactome.
Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Ahmed A Zayed

Sci Adv· August 2021

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Genome-resolved viral ecology in a marine oxygen minimum zone.
Dean Vik, Maria Consuelo Gazitúa, Christine L Sun, Ahmed A Zayed, Montserrat Aldunate

Environ Microbiol· June 2021

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Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.
Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A Zayed, Zhi-Ping Zhong, Jiarong Guo

PeerJ· June 2021

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Interaction dynamics and virus-host range for estuarine actinophages captured by epicPCR.
Eric G Sakowski, Keith Arora-Williams, Funing Tian, Ahmed A Zayed, Olivier Zablocki

Nat Microbiol· May 2021

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Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities.
Jingjie Du, Ahmed A Zayed, Kristina A Kigerl, Kylie Zane, Matthew B Sullivan

mSystems· May 2021

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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Jiarong Guo, Ben Bolduc, Ahmed A Zayed, Arvind Varsani, Guillermo Dominguez-Huerta

Microbiome· February 2021

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The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.
Ann C Gregory, Olivier Zablocki, Ahmed A Zayed, Allison Howell, Benjamin Bolduc

Cell Host Microbe· November 2020

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DRAM for distilling microbial metabolism to automate the curation of microbiome function.
Michael Shaffer, Mikayla A Borton, Bridget B McGivern, Ahmed A Zayed, Sabina Leanti La Rosa

Nucleic Acids Res· September 2020

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Phage-specific metabolic reprogramming of virocells.
Cristina Howard-Varona, Morgan M Lindback, G Eric Bastien, Natalie Solonenko, Ahmed A Zayed

ISME J· April 2020

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Global Trends in Marine Plankton Diversity across Kingdoms of Life.
Federico M Ibarbalz, Nicolas Henry, Manoela C Brandão, Séverine Martini, Greta Busseni, Ahmed A Zayed

Cell· November 2019

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