Author

Yury E Khudyakov

Centers for Disease Control and Prevention

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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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:whole-genome sequencing· 4 Research Focus:differential expression· 2 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1

Frequent Co-Authors

Pavel SkumsiD· 4 shared Alex ZelikovskyiD· 2 shared David S. CampoiD· 2 shared Pelin Icer BaykaliD· 2 shared Alina NemiraiD· 1 shared Fatemeh MohebbiiD· 1 shared J. Walker GussleriD· 1 shared James Lara· 1 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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4 shared papersBioinformatics

Pavel SkumsORCID

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4 papers

Recent·Most cited

SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework

Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer Baykal, Alina Nemira, Sumathi Ramachandran, Yury E Khudyakov

SOPHIE reconstructs viral transmission networks using a maximum likelihood framework integrating phylogenetic and random graph models, without requiring case-specific epidemiological data.

Cell Systems · Oct 1, 2022Peer-reviewedBioinformatics

Primary case inference in viral outbreaks through analysis of intra-host variant population

J. Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury E Khudyakov

This paper introduces PYCIVO, a framework to identify primary cases in viral outbreaks by analyzing intra-host viral variant populations, achieving 100% accuracy in some scenarios.

BMC Bioinformatics · Feb 8, 2022Peer-reviewedBioinformatics

Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections

Pelin Icer Baykal, James Lara, Yury E Khudyakov, Alex Zelikovsky, Pavel Skums

The paper compares intra-host HCV population characteristics between recent and persistent infections, finding significant differences and developing a machine learning classifier with 95.22% accuracy.

Virus Evolution · Dec 12, 2020Peer-reviewedBioinformatics

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants

Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury E Khudyakov, Pavel Skums

The paper presents a fast and scalable k-mer-based framework for efficiently extracting genetically similar sequences from large NGS datasets, targeting heterogeneous populations like viruses.

BMC Bioinformatics · Oct 1, 2018Peer-reviewedBioinformatics