Author

Pavel Avdeyev

George Washington UniversityORCID 0000-0002-7953-6259Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Max A. AlekseyeviD· 2 shared Nikita AlexeeviD· 2 shared Adam M. PhillippyiD· 1 shared Alaina ShumateiD· 1 shared Anton Eliseev· 1 shared Anton ZamyatiniD· 1 shared Arang RhieiD· 1 shared Atashi SharmaiD· 1 shared

Activity by Year

2016-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersGenomics

Max A. AlekseyevORCID

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4 papers

Recent·Most cited

A complete reference genome improves analysis of human genetic variation

Sergey S. Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E.G. Sauria, Mitchell Robert Vollger, , Michael C. Schatz

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

Science · Mar 31, 2022Peer-reviewedGenomics

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

Anton Zamyatin, Pavel Avdeyev, Jiangtao Liang, Atashi Sharma, Chujia Chen, Varvara Lukyanchikova, Nikita Alexeev, Zhijian Jake Tu, Max A. Alekseyev, Igor V. Sharakhov

This study produces chromosome-level genome assemblies for Anopheles coluzzii and Anopheles arabiensis using long-read sequencing and Hi-C scaffolding, improving reference-quality genomes and enabling identification of chromosomal inversion breakpoints.

GigaScience · Mar 1, 2021Peer-reviewedGenomics

Evaluation of haplotype callers for next-generation sequencing of viruses

Anton Eliseev, Keylie M. Gibson, Pavel Avdeyev, D. K. Novik, Matthew L. Bendall, Marcos Pérez‐Losada, Nikita Alexeev, Keith A. Crandall

This study evaluates twelve haplotype callers for NGS viral sequencing, finding they perform poorly under high genetic diversity, with PredictHaplo and PEHaplo showing better accuracy for HIV-like diversity levels.

Infection Genetics and Evolution · Mar 6, 2020Peer-reviewedBioinformatics

Reconstruction of ancestral genomes in presence of gene gain and loss.

Pavel Avdeyev, Shuai Jiang, Sergey Aganezov, Fei Hu, Max A. Alekseyev

This paper introduces MGRA2, an improved tool for reconstructing ancestral genomes that handles gene gain/loss and higher breakpoint reuse, outperforming existing methods.

Journal of Computational Biology · Mar 1, 2016Peer-reviewedBioinformatics