Photo of Paul Medvedev

Paul Medvedev

Associate Professor
Department of Biochemistry and Molecular Biology, Genome Sciences Institute of the Huck


  • School of Electrical Engineering and Computer Science
  • Computer Science and Engineering
  • Huck Institutes of the Life Sciences

W205B Westgate Building


Personal or Departmental Website

Research Areas:

Computational Science; Data Science and Artificial Intelligence; Theoretical Computer Science




  • BS, Computer Science, University of CA, Los Angeles, 2002
  • M.Sc., Computer Science, University of Southern Denmark at Odense, 2004
  • Ph D, Computer Science, University of Toronto, 2010


Journal Articles

  • Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova and Nithin Varma*, 2020, "Bipartite Graphs of Small Readability", Theoretical Computer Science, 806, pp. 402-415
  • Robert Scott Harris and Paul Medvedev, 2019, "Improved Representation of Sequence Bloom Trees", Bioinformatics, 36, (3), pp. 721-727
  • Chen Sun* and Paul Medvedev, 2018, "Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics", Bioinformatics, pp. bty641
  • Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna*, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez-Perez, Paul Medvedev, Kateryna D Makova and Dick de Ridder, 2018, "Correcting palindromes in long reads after whole-genome amplification", BMC genomics, 19, (1), pp. 22 pages
  • Paul Medvedev, 2018, "Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly", Briefings in Bioinformatics, bby003, pp. 10 pages
  • Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D Makova and Paul Medvedev, 2018, "Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon", Nature Communications, 9, pp. 4601

Conference Proceedings

  • Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova and Nithin Varma*, 2018, "Bipartite Graphs of Small Readability", Springer, 10976, pp. 16 pages

Research Projects

  • February 2015 - January 2022, "CAREER: De Novo Assembly of Large Genomic Data," (Sponsor: National Science Foundation).
  • September 2014 - February 2020, "XPS: FULL: DSD: End-to-end Acceleration of Genomic Workflows on Emerging Heterogeneous Supercomputers," (Sponsor: National Science Foundation).
  • June 2014 - May 2018, "ABI Innovation: A Novel Framework for Detecting Genomic Structural Variation," (Sponsor: National Science Foundation).

Honors and Awards


Service to Penn State:

Service to External Organizations:




The School of Electrical Engineering and Computer Science was created in the spring of 2015 to allow greater access to courses offered by both departments for undergraduate and graduate students in exciting collaborative research fields.

We offer B.S. degrees in electrical engineering, computer science, computer engineering and data science and graduate degrees (master's degrees and Ph.D.'s) in electrical engineering and computer science and engineering. EECS focuses on the convergence of technologies and disciplines to meet today’s industrial demands.

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