Pavel Avdeyev

Pavel Avdeyev

Trying to combine mathematics, computer science, and biology.

Check out Google Scholar profile for up-to-date list.

* – co-first authorship, ** – co-second authorship

J. P. Bernot*, P. Avdeyev*, A. Zamyatin, N. Dreyer, N. Alexeev, M. Pérez-Losada; K. A. Crandall. ‘‘Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes’’. GigaScience (2022), (accepted)

S. Aganezov, S. M. Yan, D. C. Soto, M. Kirsche, S. Zarate, P. Avdeyev, D. J. Taylor, et. al. ‘‘A complete reference genome improves analysis of human genetic variation’’. bioRxiv

S. Aganezov*, P. Avdeyev*, N. Alexeev, Y. Rong, and M. A. Alekseyev. ‘‘Orienting Ordered Scaffolds: Complexity and Algorithms’’, 2022. (submitted) arXiv

A. Zamyatin*, P. Avdeyev*, J. Liang, A. Sharma, C. Chen, V. Lukyanchikova, N. Alexeev, Z. Tu, M. A. Alekseyev, I. V. Sharakhov. ‘‘Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis’’. GigaScience 10:3 (2021). doi bioRxiv

Z. C. Dagdia, P. Avdeyev, M. S. Bayzid. ‘‘Biological computation and computational biology: survey, challenges, and discussion’’. Artificial Intelligence Review (2021), 1-67. doi

P. Avdeyev and M. A. Alekseyev. ‘‘Linearization of Ancestral Genomes with Duplicated Genes’’. Proceedings of the 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2020, Article 53. doi

A. Eliseev*, K. M. Gibson*, P. Avdeyev**, D. Novik**, M. L. Bendall, M. Pérez-Losada, N. Alexeev, and K. A. Crandall. ‘‘Evaluation of haplotype callers for next-generation sequencing of viruses’’. Infection, Genetics and Evolution, 2020. doi

P. Avdeyev*, N. Alexeev*, Y. Rong, and M. A. Alekseyev. ‘‘A Unified ILP Framework for Core Ancestral Genome Reconstruction Problems’’. Bioinformatics 36:10 (2020), 2993–3003. doi

P. Avdeyev, M. Atamanova, and M. A. Alekseyev. ‘‘A Uniform Theory of Adequate Subgraphs for the Genome Median, Halving, and Aliquoting Problems’’. Proceedings of the 6th International Conference on Algorithms for Computational Biology (AlCoB 2019), Lecture Notes in Computer Science 11488 (2019), 97–111. doi

P. Avdeyev, S. Jiang, and M. A. Alekseyev. ‘‘Linearization of Median Genomes under the Double-Cut-and-Join-Indel Model’’. Evolutionary Bioinformatics, 15 (2019), 1–12. doi

P. Avdeyev, S. Jiang, and M. A. Alekseyev. Implicit Transpositions in DCJ Scenarios, Front. Genet. 8 (2017), 212. doi

P. Avdeyev*, N. Alexeev*, Y. Rong, and M. A. Alekseyev. ‘‘A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems under DCJ’’. Proceedings of the 15th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2017), Lecture Notes in Computer Science 10562 (2017), 156–178. doi

N. Alexeev*, P. Avdeyev*, and M. A. Alekseyev. ‘‘Comparative Genomics Meets Topology: a Novel View on Genome Median and Halving Problems’’. Proceedings of the 14th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2016), BMC Bioinformatics 17:Suppl 14 (2016), 3. doi

P. Avdeyev, S. Jiang, S. Aganezov, F. Hu, and M. A. Alekseyev. ‘‘Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss’’. Journal of Computational Biology 23:3 (2016), 1–15. doi, bioRxiv.