Author

Alexey Kazakov

Lawrence Berkeley National Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 5

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Research Focus:clustering· 2 Organism:E. coli· 2 Approach:genetic perturbation / CRISPR· 2 Organism:human· 2 Approach:machine learning (classical)· 2 Assay:metagenomics· 2 Assay:proteomics· 2

Frequent Co-Authors

Adam M. DeutschbaueriD· 5 shared Adam P. ArkiniD· 4 shared Denish PiyaiD· 4 shared Vivek K. MutalikiD· 4 shared Avery J. C. NoonaniD· 3 shared Hemaa SelvakumariD· 3 shared Isabella MurrayiD· 3 shared Madeline SvabiD· 3 shared

Activity by Year

2026-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersMicrobiology

Adam M. DeutschbauerORCID

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5 papers

Recent·Most cited

Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways

Isabella Murray, Roniya Thapa Magar, Denish Piya, Hemaa Selvakumar, Lucas Morinière, Sarshad Koderi Valappil, Madeline Svab, Jirapat Thongchol, Alexey Kazakov, Nathalie H. Elisabeth, Mohamad Alayouni, Prithvi Pal Singh, Artur Muszyński, Parastoo Azadi, Siân V. Owen, , Vivek K. Mutalik

This study identifies host factors critical for ssRNA and ssDNA phage infection in E. coli, revealing conserved dependencies and lineage-specific requirements.

bioRxiv · Sep 22, 2026 · PreprintMicrobiology

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7

Edwin Omar Rivera-Lopez, Lucas Morinière, Alexey Kazakov, Denish Piya, Melina Pena, Benjamin L. Weinberg, Jie Feng, Avery J. C. Noonan, David W. Lacher, Adam M. Deutschbauer, Adam P. Arkin, Vivek K. Mutalik, Edward G. Dudley

The study identifies surface glycan layers as primary or optional recognition substrates for phage infection in E. coli O157:H7, revealing their role in receptor access and infection outcomes.

bioRxiv · Sep 10, 2026 · PreprintMicrobiology

A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae

Hemaa Selvakumar, Avery J. C. Noonan, Ella R. Rotman, Mohamad Alayouni, Denish Piya, Flavien Maucourt, Sarshad Koderi Valappil, Madeline Svab, Britney Orihuela, Gina Cowser, Isabella Murray, Collis Bousliman, Alexey Kazakov, Adam M. Deutschbauer, Simon Roux, , Vivek K. Mutalik

This paper constructs a phage-bacteria interaction atlas for Klebsiella pneumoniae and develops a genome-guided machine learning model to predict phage-host interactions, outperforming traditional methods.

bioRxiv · Aug 17, 2026 · PreprintMicrobiology

Comprehensive interaction profiling and machine learning prediction of bacteriophage infectivity across clinically diverse Pseudomonas aeruginosa

Denish Piya, Avery J. C. Noonan, Hemaa Selvakumar, Mohamad Alayouni, Sarshad Koderi Valappil, Flavien Maucourt, Isabella Murray, Madeline Svab, Collis Bousliman, Matthew Heidenblut, Britney Orihuela, Alexey Kazakov, Hans K. Carlson, Yiyan Yao, Emerson Smith, , Vivek K. Mutalik

The paper develops a genome-based framework to predict bacteriophage infectivity against diverse Pseudomonas aeruginosa strains using machine learning and experimental data.

bioRxiv · May 20, 2026 · PreprintMicrobiology

Metagenome-guided substrate selection enriches Terriglobus, reveals co-occurring taxa, and enables isolation of a novel species

Dawn M. Chiniquy, Spencer Diamond, Hans K. Carlson, Alexey Kazakov, Devin Coleman‐Derr, Trent Northen, Jillian F. Banfield, Adam M. Deutschbauer

This study uses metagenome-guided substrate selection to enrich Terriglobus, identify co-occurring taxa, and isolate a novel species from soil.

bioRxiv · May 15, 2026 · PreprintMicrobiology