Photo of Paul Medvedev

Paul Medvedev

Assistant Professor

Affiliation(s):

  • School of Electrical Engineering and Computer Science
  • Computer Science and Engineering

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
  • Tobias Marschall and Paul Medvedev, 2016, "Computational Pan-Genomics: Status, Promises and Challenges", Briefings in Bioinformatics, bbw089, pp. 1-18
  • 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
  • Jan Schroeder, Santhosh Girirajan, Anthony T Papenfuss and Paul Medvedev, 2015, "Improving the Power of Structural Variation Detection by Augmenting the Reference", PLoS One, 10, (8), pp. e0136771
  • Arkarachai Fungtammasan, Guruprasad Ananda, Suzanne E. Hile, Marcia S. Su, Chen Sun*, Robert Scott Harris, Paul Medvedev, Kristin A Eckert and Kateryna D Makova, 2015, "Accurate typing of short tandem repeats from genome-wide sequencing data and its applications", Genome Research, 25, (5), pp. 736–749
  • 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
  • Luis Martínez, Martin Milanic, Leire Legarreta, Paul Medvedev, Iker Malaina and IldefonsoM. de la Fuente, 2014, "A combinatorial approach to the design of vaccines", Journal of Mathematical Biology, 70, (5), pp. 1327-1358
  • Rayan Chikhi* and Paul Medvedev, 2014, "Informed and automated k-mer size selection for genome assembly", Bioinformatics, 30, (1), pp. 31–37
  • David Golan and Paul Medvedev, 2013, "Using state machines to model the Ion Torrent sequencing process andto improve read error rates", Bioinformatics, 29, (13), pp. 344–351
  • Sangwoo Kim, Paul Medvedev, Tara Paton and Vineet Bafna, 2013, "Reprever: resolving low-copy duplicated sequences using template driven assembly", Nucleic Acids Research, 41, (12), pp. 14
  • Marcin Kaminski, Paul Medvedev and Martin Milanic, 2012, "Complexity of independent set reconfigurability problems", Theoretical Computer Science, 439, pp. 9–15
  • Marcin Kaminski, Paul Medvedev and Martin Milanic, 2011, "The plane-width of graphs", Journal of Graph Theory, 68, (3), pp. 229–245
  • Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler and Pavel A. Pevzner, 2011, "Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers", Journal of Computational Biology, 18, (11), pp. 1625–1634
  • Marcin Kaminski, Paul Medvedev and Martin Milanic, 2011, "Shortest paths between shortest paths", Theoretical Computer Science, 412, (39), pp. 5205–5210
  • Paul Medvedev, Eric Scott, Boyko Kakaradov and Pavel A. Pevzner, 2011, "Error correction of high-throughput sequencing datasets with non-uniform coverage", Bioinformatics, 27, (13), pp. 137–141
  • Paul Medvedev, Marc Fiume, Misko Dzamba, Tim Smith and Michael Brudno, 2010, "Detecting copy number variation with mated short reads", Genome Research, 20, (11), pp. 1613-1622
  • Anne Bergeron, Paul Medvedev and Jens Stoye, 2010, "Rearrangement Models and Single-Cut Operations", Journal of Computational Biology, 17, (9), pp. 1213–1225
  • Michael Brudno, Paul Medvedev, Jens Stoye and Francisco M. de la Vega, 2009, "A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)", Bioinformatics, 25, (21), pp. 2863–2864
  • 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
  • Paul Medvedev and Michael Brudno, 2009, "Maximum Likelihood Genome Assembly", Journal of Computational Biology, 16, (8), pp. 1101–1116
  • Joan Boyar and Paul Medvedev, 2008, "The relative worst order ratio applied to seat reservation", ACM Transactions on Algorithms, 4, (4)

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
  • Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler and Pavel A. Pevzner, 2011, "Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers", Springer, 6577, pp. 238–251
  • Marcin Kaminski, Paul Medvedev and Martin Milanic, 2010, "Shortest Paths between Shortest Paths and Independent Sets", Springer, 6460, pp. 56–67
  • Paul Medvedev and Jens Stoye, 2009, "Rearrangement Models and Single-Cut Operations", Springer, 5817, pp. 84–97
  • Marcin Kaminski, Martin Milanic and Paul Medvedev, 2009, "On the Plane-Width of Graphs", Electronic Notes in Discrete Mathematics, 34, pp. 633-637
  • Paul Medvedev and Michael Brudno, 2008, "Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads", Springer, 4955, pp. 50–64
  • Paul Medvedev, Konstantinos Georgiou, Gene Myers and Michael Brudno, 2007, "Computability of Models for Sequence Assembly", Springer, pp. 289–301
  • Joan Boyar and Paul Medvedev, 2004, "The Relative Worst Order Ratio Applied to Seat Reservation", Springer, 3111, pp. 90–101
  • Haiyun Luo, Paul Medvedev, Jerry Cheng and Songwu Lu, 2001, "A Self-Coordinating Approach to Distributed Fair Queueing in Ad HocWireless Networks", IEEE, pp. 1370–1379

Research Projects

  • September 2014 - August 2017, "III: Small: Reconstructing viral population without using a reference genome," (Sponsor: National Science Foundation).
  • September 2016 - August 2017, "III: Small: Reconstructing viral population without using a reference genome," (Sponsor: Board of Trustees of Indiana University).
  • January 2016 - June 2017, "Discovering the Genetic Profiles of Chronic Inflmmation: An Ulcerative Colitis Model," (Sponsor: Tobacco CURE project).
  •   -  , "Are human sexually dimorphic traits affected by variation in Y-chromosomal ampliconic gene copy number?," (Sponsor: The Center for Human Evolution and Diversity).

Honors and Awards

  • CAREER Award, National Science Foundation, February 2015 - January 2020
  • Best Poster Award, RECOMB 2016, July 2016
  • 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:

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

Service to External Organizations:

  • Member, Program Committee, January 2017 - April 2017
  • Chairperson, Publications Chair, January 2017 - May 2017
  • Member, Program Committee, January 2016 - July 2016
  • Member, Program Committee, January 2016 - September 2016
  • Member, Program Committee, January 2016 - April 2016
  • Member, Program Committee, January 2016 - April 2016
  • Member, Program Committee, August 2016 - December 2016
  • Member, Program Committee, January 2015 - July 2015
  • Member, Program Committee, January 2015 - July 2015
  • Member, Program Committee, January 2015 - September 2015
  • Member, Program Committee, September 2014 - April 2015
  • Member, Program Committee, November 2013 - July 2014
  • Member, Program Committee, January 2014 - September 2014
  • Member, Program Committee, January 2013 - September 2013
  • Member, Program Committee, November 2012 - April 2013
  • Chairperson, Program Committee, August 2011 - April 2012
  • Member, Program Committee, November 2010 - March 2011
  • Member, Steering Committee, April 2017
 


 

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 and computer engineering 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

209 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