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Bio

I am a postdoctoral fellow with Steven L. Salzberg at Johns Hopkins University. My current work is focused on improving gene annotations using evolutionary evidence. I also completed a Ph.D. with Paul Medvedev at Pennsylvania State University, where I performed research on genome graphs and whole-genome alignment. Prior to that, I graduated with an M.Sc. from Alferov University (former Saint-Petersburg Academic University) in Saint-Peterburg, Russia. My master's thesis focused in synteny detection in bacterial genomes using de Bruijn grahps, a project supervised by Son Pham. In between my Ph.D. and M.Sc. studies, I worked as a Research Assistant in the group of Francis Chin at the University of Hong Kong.

Research Interests

  • Computational Biology/Bioinformatics: comparative genomics, sequence alignment, graph genomes, genome annotation

Selected Research Projects

  • Quality assessment of splice site annotation based on conservation across multiple species
    Ilia Minkin, Steven Salzberg
    bioRxiv, 2023
    [Paper]

  • Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
    Ilia Minkin, Paul Medvedev
    Nature Communications, 2020
    [Paper] [Code]

  • TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
    Ilia Minkin, Son Pham, Paul Medvedev
    Bioinformatics, 2017
    [Paper] [Code]

  • Sibelia: a scalable and comprehensive synteny block generation tool for closely related microbial genomes
    Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham
    WABI, 2013
    [Paper] [Code]