Paul Medvedev

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Rayan ChikhiInstitut Pasteur & CNRSVerified email at ens-cachan.org
Kateryna MakovaProfessor of Biology, Penn State UniversityVerified email at psu.edu
Michael BrudnoProfessor of Computer Science, University of Toronto; Chief Data Scientist, UHNVerified email at cs.toronto.edu
Kristoffer SahlinAssistant Professor at Department of Mathematics, Stockholm UniversityVerified email at math.su.se
Martin MilaničUniversity of Primorska, Koper, SloveniaVerified email at upr.si
Robert S HarrisAssistant Research Professor, Pennsylvania State UniversityVerified email at bx.psu.edu
Amatur RahmanPostdoctoral Scholar, Department of Biology, The Pennsylvania State UniversityVerified email at psu.edu
Chen SunGoogleVerified email at cse.psu.edu
Alexandru I. TomescuDepartment of Computer Science, University of HelsinkiVerified email at helsinki.fi
Ilia MinkinJohns Hopkins UniversityVerified email at jh.edu
Pavel PevznerUniversity of California at San DiegoVerified email at ucsd.edu
Rahulsimham vegesnaGritstone BioVerified email at gritstone.com
Oliver A. RyderDirector of Conservation Genetics, San Diego Zoo Wildlife Alliance. Prof. of EBE U.C. San DiegoVerified email at sdzwa.org
Pierre PeterlongoInria - GenScale teamVerified email at inria.fr
David KoslickiComputer Science and Engineering, Biology, Huck Institutes of the Life Sciences, Penn StateVerified email at psu.edu
Antonio BlancaAssociate Professor, CSE Department, Penn StateVerified email at cse.psu.edu
Yoann DUFRESNEPhD, Institut Pasteur, ParisVerified email at pasteur.fr
Teo LemaneCEA/GenoscopeVerified email at genoscope.cns.fr
Jens StoyeBielefeld University, GermanyVerified email at uni-bielefeld.de
Barış EkimMassachusetts Institute of Technology (MIT)Verified email at mit.edu

Paul Medvedev

Penn State

Verified email at cse.psu.edu - Homepage

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Towards complete and error-free genome assemblies of all vertebrate species A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, ... Nature 592 (7856), 737-746, 2021	2270	2021
Informed and automated k-mer size selection for genome assembly R Chikhi, P Medvedev Bioinformatics 30 (1), 31-37, 2014	845	2014
Computational methods for discovering structural variation with next-generation sequencing P Medvedev, M Stanciu, M Brudno Nature methods 6, S13-S20, 2009	696	2009
Computational pan-genomics: status, promises and challenges Computational Pan-Genomics Consortium Briefings in Bioinformatics, bbw089, 2016	373	2016
The complete sequence of a human Y chromosome A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, ... Nature 621 (7978), 344-354, 2023	277	2023
Compacting de Bruijn graphs from sequencing data quickly and in low memory R Chikhi, A Limasset, P Medvedev Bioinformatics 32 (ISMB Proceedings), i201-i208, 2016	256	2016
Computability of models for sequence assembly P Medvedev, K Georgiou, G Myers, M Brudno International Workshop on Algorithms in Bioinformatics (WABI), 289-301, 2007	238	2007
Detecting copy number variation with mated short reads P Medvedev, M Fiume, M Dzamba, T Smith, M Brudno Genome research 20 (11), 1613-1622, 2010	226	2010
On the representation of de Bruijn graphs R Chikhi, A Limasset, S Jackman, JT Simpson, P Medvedev Journal of Computational Biology 22 (Journal version of RECOMB paper), 336-352, 2015	216	2015
Complexity of independent set reconfigurability problems M Kamiński, P Medvedev, M Milanič Theoretical computer science 439, 9-15, 2012	195	2012
Error correction of high-throughput sequencing datasets with non-uniform coverage P Medvedev, E Scott, B Kakaradov, P Pevzner Bioinformatics 27 (ISMB Proceedings), i137-i141, 2011	170	2011
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis K Sahlin, P Medvedev Nature communications 12 (1), 1-13, 2021	161	2021
Maximum likelihood genome assembly P Medvedev, M Brudno Journal of computational Biology 16 (Journal version of RECOMB paper), 1101-1116, 2009	156*	2009
A self-coordinating approach to distributed fair queueing in ad hoc wireless networks H Luo, P Medvedev, J Cheng, S Lu INFOCOM 2001. Twentieth Annual Joint Conference of the IEEE Computer and …, 2001	150	2001
Y and W chromosome assemblies: approaches and discoveries M Tomaszkiewicz, P Medvedev, KD Makova Trends in genetics 33 (4), 266-282, 2017	125	2017
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes I Minkin, S Pham, P Medvedev Bioinformatics 33 (24), 4024-4032, 2017	121	2017
Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers P Medvedev, S Pham, M Chaisson, G Tesler, P Pevzner Journal of Computational Biology 18 (Journal version of RECOMB paper), 1625-1634, 2011	121	2011
Data structures based on k-mers for querying large collections of sequencing data sets C Marchet, C Boucher, SJ Puglisi, P Medvedev, M Salson, R Chikhi Genome research 31 (1), 1-12, 2021	119	2021
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications KD Fungtammasan, Arkarachai and Ananda, Guruprasad and Hile, Suzanne E and ... Genome Research 25, 736--749, 2015	113	2015
A time-and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y M Tomaszkiewicz, S Rangavittal, M Cechova, RC Sanchez, ... Genome research 26 (4), 530-540, 2016	111	2016

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