Photo of Paul Medvedev

Paul Medvedev

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

Affiliation(s):

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

W316 Westgate Building

pzm11@psu.edu

814-863-1242

Personal or Departmental Website

Research Areas:

Interest Areas:

 
 

 

Education

  • 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

Publications

Journal Articles

  • Marta Tomaszkiewicz, Paul Medvedev and Kateryna D Makova, 2017, "Y and W Chromosome Assemblies: Approaches and Discoveries", Trends in Genetics, 33, (4), pp. 266-282
  • Chen Sun* and Paul Medvedev, 2016, "VarMatch: robust matching of small variant datasets using flexible scoring schemes", Bioinformatics, 33, (9), pp. 1301-1308
  • Ilia Minkin* and Paul Medvedev, 2016, "TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes", Bioinformatics, btw609
  • Rayan Chikhi*, Paul Medvedev, Martin Milanic and Sofya Raskhodnikova, 2016, "On the readability of overlap digraphs", Discrete Applied Mathematics, 205, pp. 35–44
  • M Agaba, E Ishengoma, Webb C Miller, Barbara C McGrath, C Hudson, O C Bedoya Reina, A Ratan, R Burhans, Rayan Chikhi* and Paul Medvedev, 2016, "Giraffe genome sequence reveals clues to its unique morphology and physiology", Nature Communication, 7, (11519)
  • Rayan Chikhi, Antoine Limasset* and Paul Medvedev, 2016, "Compacting de Bruijn graphs from sequencing data quickly and in lowmemory", Bioinformatics, 32, (12), pp. 201–208
  • Marta Tomaszkiewicz, Samarth Rangavittal*, Monika Cechova*, Rebeca C Sanchez, Howard W Fescemyer, Robert Scott Harris, D. Ye, P. C.M. O'Brien, Rayan Chikhi*, Oliver Ryder, M. A. Ferguson-Smith, Paul Medvedev and Kateryna D Makova, 2016, "A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y", Genome Research, 26, pp. 530-540
  • Rayan Chikhi*, Antoine Limasset*, Shaun Jackman, Jared T. Simpson and Paul Medvedev, 2015, "On the representation of de Bruijn graphs", Journal of Computational Biology, 22, (5), pp. 336-352
  • Rayan Chikhi* and Paul Medvedev, 2014, "Informed and automated k-mer size selection for genome assembly", Bioinformatics, 30, (1), pp. 31–37
  • Paul Medvedev, Monica Stanciu and Michael Brudno, 2009, "Computational methods for discovering structural variation with next-generation sequencing", Nature Methods, 6, (11), pp. S13-S20

Conference Proceedings

  • Chen Sun*, Robert Scott Harris, Rayan Chikhi and Paul Medvedev, 2017, "AllSome Sequence Bloom Trees", Springer, 10229, pp. 272-286
  • Alexandru I. Tomescu and Paul Medvedev, 2016, "Safe and Complete Contig Assembly Via Omnitigs", Springer, 9649, pp. 152–163
  • Rayan Chikhi*, Paul Medvedev, Martin Milanic and Sofya Raskhodnikova, 2015, "On the readability of overlap digraphs", Springer, 9133, pp. 124-137
  • Rayan Chikhi*, Antoine Limasset*, Shaun Jackman, Jared T. Simpson and Paul Medvedev, 2014, "On the Representation of de Bruijn Graphs", Springer, 8394, pp. 35–55

Research Projects

  • February 2015 - January 2020, "CAREER: De Novo Assembly of Large Genomic Data," (Sponsor: National Science Foundation).
  • September 2014 - August 2018, "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

Service to Penn State:

Service to External Organizations:

 


 

About

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 in 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.

School of Electrical Engineering and Computer Science

The Pennsylvania State University

207 Electrical Engineering West

University Park, PA 16802

814-863-6740

Department of Computer Science and Engineering

814-865-9505

Department of Electrical Engineering

814-865-7667