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).
  • January 2016 - June 2018, "Discovering the Genetic Profiles of Chronic Inflammation: An Ulcerative Colitis Model," (Sponsor: PA Tobacco Settlement Fund (TSF)).
  • June 2014 - May 2018, "ABI Innovation: A Novel Framework for Detecting Genomic Structural Variation," (Sponsor: National Science Foundation).

Honors and Awards

  • CAREER Award, National Science Foundation, February 2015 - January 2020
  • Quiggle Career Developmental Professorship, Penn State University, August 2012 - August 2015
  • Best Paper Award, Bioinformatics, July 2013
  • Named one of 2011’s “Tomorrow’s PIs”, Genome Technology Magazine, 2011
  • DAAD Research Fellowsihp, German Academic Exchange Service, October 2007 - July 2008
  • Regents Scholarship, University of California, 1998 - 2002

Service

Service to Penn State:

  • Committee Work, CSE Personnel Committee, August 2017 - May 2018
  • Committee Work, CSE awards committee, August 2017 - May 2018
  • Committee Work, CSE Web/Newsletter Committee, August 2017 - May 2018
  • Committee Work, Member, BMB Computer Resources Committee, August 2017 - May 2018
  • Committee Work, Member, CSE Honors and Awards Committee, August 2017 - May 2018
  • Committee Work, Member, BMB Computer Resources Committee, August 2016 - May 2017
  • Committee Work, CSE awards committee, August 2016 - May 2017
  • Committee Work, Member, Bioinformatics and Genomics Admissions Committee, December 2016 - May 2017
  • Committee Work, CSE Web/Newsletter Committee, August 2016 - May 2017
  • Committee Work, CSE Hiring Committee, November 2015 - May 2016
  • Committee Work, Member, BMB Hiring Committee, October 2015 - March 2016
  • Committee Work, Member, BMB Computer Resources Committee, August 2015 - May 2016
  • Committee Work, Member, BMB Computer Resources Committee, August 2014 - April 2015
  • Committee Work, Member, CSE Publications Committee, August 2014 - May 2016
  • Committee Work, Member, CSE Graduate Committee, August 2013 - July 2014
  • Committee Work, Administrator, Administer candidacy exam in Computational Molecular Biology for CSE, August 2013
  • Committee Work, Administrator, Co-administer candidacy exam in Theory for CSE, August 2012
  • Committee Work, Member, BioStar Faculty Advisory Committee, 2013
  • Committee Work, Member, Bioinformatics and Genomics Candidacy Exam Panel, 2014
  • Committee Work, Member, BioStar Governance Committee, 2014
  • Committee Work, Member, Bioinformatics and Genomics Candidacy Exam Panel, 2015
  • Committee Work, CSE Hiring Committee, 2013
  • Committee Work, Member, BMB Hiring Committee, 2014

Service to External Organizations:

  • Organizing Conferences and Service on Conference Committees, Member, Steering Committee, April 2017
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2017 - April 2017
  • Organizing Conferences and Service on Conference Committees, Chairperson, Publications Chair, January 2017 - May 2017
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2016 - July 2016
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2016 - September 2016
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2016 - April 2016
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2016 - April 2016
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, August 2016 - December 2016
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2015 - July 2015
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2015 - July 2015
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2015 - September 2015
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2014 - September 2014
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, September 2014 - April 2015
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, November 2013 - July 2014
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, January 2013 - September 2013
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, November 2012 - April 2013
  • Organizing Conferences and Service on Conference Committees, Chairperson, Program Committee, August 2011 - April 2012
  • Organizing Conferences and Service on Conference Committees, Member, Program Committee, November 2010 - March 2011
 


 

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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.

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