SCS Faculty Candidate

  • Remote Access - Zoom
  • Virtual Presentation - ET
  • Postdoctoral Scholar
  • Computer Science and Engineering Department
  • University of California San Diego

Algorithmic challenges in long-read genome assembly

Even though the first draft human genome was generated two decades ago, many important regions (such as centromeres) still represent the “terra incognita'' of genome sequencing. The recently emerged long-read DNA sequencing technologies promise to transform genome sequencing toward generating complete genomes and lead to a critical demand for fast and accurate genome assembly algorithms. They also raised novel algorithmic problems since all previously developed assembly approaches fail to unleash the full potential of long reads. These problems represent the key bottlenecks for the ongoing Big Data sequencing projects, such as the Vertebrate Genomes Project (aimed at sequencing genomes of all vertebrates) and the Human Pangenome Project (aimed at population-scale sequencing of complete human genomes). I will describe the new algorithmic challenges in genome assembly, discuss the recently developed algorithms for their solution, and show how these algorithms bring us closer to the goal of complete genome sequencing.

Anton Bankevich is a Postdoctoral Scholar at the Computer Science and Engineering Department at UCSD. After getting the B.S. degree in Mathematics from Saint Petersburg University, Russia in 2009, he started working on his Ph.D. in graph theory. However, after joining the Center for Algorithmic Biotechnology in Saint Petersburg in 2011, he switched to developing the SPAdes genome assembler (Bankevich et al., J. Comp. Biology, 2012) that, with over 11,000 citations to date, is now the most widely-used assembler in the world. Dr. Bankevich joined UCSD as a postdoctoral scholar after receiving his Ph.D. (2018) in Computer Science from Saint Petersburg University. His research interests cover genomics and metagenomics (with a focus on algorithms and data analysis for genome assembly) and include collaborations on the discovery of novel insecticide toxins (with Keith Turner), leaderboard metagenomics (with Rob Knight), and comparative genomics (with Stephen O’Brien).

Faculty Host:  Jian Ma

Computational Biology Department

Zoom Participation. See announcement.

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