Alla Mikheenko
Assistant Professor of Computational Biology
Research Interests
Professor Mikheenko's teaching and research interests span computational biology and neuroscience. Her research aims to improve our understanding of the molecular mechanisms of neurodegeneration using computational approaches, contributing to a deeper understanding of cell biology and splicing regulation. She develops computational methods that are useful for a broad range of researchers and applies these methods to diverse biomedical datasets, including bulk and single-cell sequencing data, with the aim of identifying pathological isoforms and disease-associated pathways, and to build predictive models that can guide future studies and target discovery.
Email
Prior to joining MBZUAI, Professor Mikheenko was a postdoctoral researcher at University College London, where she applied computational approaches to study neurodegenerative diseases using large-scale multi-omics data, aiming to identify novel biomarkers and therapeutic targets. She earned her Ph.D. in bioinformatics in 2021 at the Center for Algorithmic Biotechnology, Saint Petersburg State University. Her earlier work includes developing widely used tools for genomic, transcriptomic, and proteomics data analysis. As a member of the Telomere-to-Telomere Consortium, Professor Mikheenko contributed to the first complete human genome assembly.
- Postdoctoral Fellow, University College London, UK
- Ph.D. in Bioinformatics, Saint Petersburg State University, Russia
- Doctor of Medicine, Ulyanovsk State University, Russia
- Essential Open Source Software for Science program, Chan Zuckerberg Initiative, 2021
- Young Scientists Award, Saint Petersburg State University, 2019
- ECCB travel fellowship, European Conference of Computational Biology, 2015
- Prjibelski A.D., Mikheenko A., Joglekar A., et al: "Accurate isoform discovery with IsoQuant using long reads", Nature Biotechnology. 2023;41: 915ñ918 (co-first authorship).
- Mikheenko A., Saveliev V., Hirsch P., Gurevich A.: "WebQUAST: online evaluation of genome assemblies", Nucleic Acids Research, 2023;51(W1): W601ñW606.
- Mikheenko A., Prjibelski A.D., Joglekar A., Tilgner H.: "Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns", Genome Research, 2022.
- Bzikadze A.V., Mikheenko A., Pevzner P.A.: "Fast and accurate mapping of long reads to complete genome assemblies with VerityMap", Genome Research, 2022;32: 2107-2118 (co-first authorship).
- Rhie A., Nurk S., Cechova M., ..., Mikheenko A., et al.: "The complete sequence of a human Y chromosome", Nature. 2023; 1-11.
- Hardwick S.A., Hu W., Joglekar A., Ö, Mikheenko A., et al.: "Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue", Nature Biotechnology, 2022; 40: 1082ñ1092.
- Nurk S., Koren S., Rhie A., Rautiainen M., Bzikadze A.V., Mikheenko A., et al.: "The complete sequence of a human genome", Science, 2022;376 (6588): 44-53.
- Mikheenko A., Bzikadze A.V., Gurevich A., Miga K.H., Pevzner P.A.: "TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats", Bioinformatics, 2020;36: i75-i83.
- Mikheenko A., Prjibelski A., Saveliev V., Antipov D., Gurevich A.: "Versatile genome assembly evaluation with QUAST-LG", Bioinformatics, 2018;34: i142-i150.
- Mikheenko A., Kolmogorov M.: "Assembly Graph Browser: interactive visualization of assembly graphs", Bioinformatics, 2018;35: 3476-3478.
- Gurevich A., Mikheenko A., Shlemov A., et al.: "Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra", Nature Microbiology, 2018;3: 319-327.
- Mikheenko A., Saveliev V., Gurevich A.: "MetaQUAST: evaluation of metagenome assemblies", Bioinformatics, 2016;32: 1088-1090.