Author

A. Nekrutenko

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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Evolutionary Biology· 2 Microbiology· 2 Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 5 Approach:experimental assay· 3 Research Focus:benchmarking· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1 Organism:E. coli· 1

Frequent Co-Authors

S. L. Kosakovsky Pond· 3 shared A. G. Lucaci· 2 shared D. Callan· 2 shared D. P. Martin· 2 shared H. Mei· 2 shared S. Weaver· 2 shared A. De Klerk· 1 shared A. J. Greaney· 1 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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3 shared papersGenomics

S. L. Kosakovsky Pond

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Author profile →

6 papers

Recent·Most cited

PyEuk: a tool suite for catalogue-free multilocus typing

S. L. Kosakovsky Pond, D. Callan, A. Nekrutenko

PyEuk is a catalogue-free tool for multilocus typing of eukaryotic parasites, enabling accurate strain identification and transmission analysis without organism-specific tuning.

bioRxiv · Sep 16, 2026 · PreprintGenomics

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

S. L. Kosakovsky Pond, S. Weaver, D. Callan, J. D. Zehr, A. G. Lucaci, H. Verdonk, A. Selberg, G. Brown, M. Chikina, N. L. Clark, K. D. Makova, D. P. Martin, A. Nekrutenko

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

bioRxiv · Sep 10, 2026 · PreprintBioinformatics

Lineage tracing via associative chromosome/plasmid barcoding with siBar

A. Nekrutenko, H. Mei

The paper introduces siBar, a method for tracking plasmid and chromosomal lineages in bacteria, and evaluates its barcode complexity through an evolution experiment.

bioRxiv · Mar 17, 2022 · PreprintMicrobiology

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

D. P. Martin, S. Lytras, A. G. Lucaci, W. Maier, B. Gruning, S. D. Shank, S. Weaver, O. S. MacLean, R. J. Orton, P. Lemey, M. F. Boni, H. Tegally, G. W. Harkins, C. Scheepers, J. N. Bhiman, , S. L. Kosakovsky Pond

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

bioRxiv · Jan 14, 2022 · PreprintEvolutionary Biology

Reproducible and accessible analysis of transposon insertion data at scale

D. Lariviere, L. Wickham, K. C. Keiler, A. Nekrutenko

The paper develops workflows and tools for analyzing TIS data using a public Galaxy platform and interactive tutorials to improve reproducibility and accessibility.

bioRxiv · May 19, 2020 · PreprintMicrobiology

A high resolution view of adaptive events

H. Mei, B. Arbeithuber, M. Cremona, M. DeGeorgio, A. Nekrutenko

This study tracks mutations during coadaptation between E. coli and plasmid pBR322 using duplex sequencing, revealing clonal interference and chromosomal variant emergence as key adaptive events.

bioRxiv · Oct 10, 2018 · PreprintEvolutionary Biology