Paul Medvedev
Computer Science and Engineering - Biochemistry and Molecular Biology, Pennsylvania State University
Interests
Education
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Ph.D. in Computer Science, 2010
University of Toronto
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M.Sc. in Computer Science, 2004
University of Southern Denmark at Odense
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B.S. in Computer Science, 2002
University of California, Los Angeles
Biography
Publications
A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, M Uliano-Silva, W Chow, A Fungtammasan, GL Gedman, LJ Cantin, F Thibaud-Nissen, L Haggerty, C Lee, BJ Ko, J Kim, I Bista, M Smith, B Haase, J Mountcastle, S Winkler, S Paez, J Howard, SC Vernes, TM Lama, F Grutzner, WC Warren, C Balakrishnan, D Burt, JM George, M Biegler, D Iorns, A Digby, D Eason, T Edwards, M Wilkinson, G Turner, A Meyer, AF Kautt, P Franchini, HW Detrich III, H Svardal, M Wagner, GJP Naylor, M Pippel, M Malinsky, M Mooney, M Simbirsky, BT Hannigan, T Pesout, M Houck, A Misuraca, SB Kingan, R Hall, Z Kronenberg, J Korlach, I Sović, C Dunn, Z Ning, A Hastie, J Lee, S Selvaraj, RE Green, NH Putnam, J Ghurye, E Garrison, Y Sims, J Collins, S Pelan, J Torrance, A Tracey, J Wood, D Guan, SE London, DF Clayton, CV Mello, SR Friedrich, PV Lovell, E Osipova, FO Al-Ajli, S Secomandi, H Kim, C Theofanopoulou, Y Zhou, RS Harris, KD Makova, P Medvedev, J Hoffman, P Masterson, K Clark, F Martin, K Howe, P Flicek, BP Walenz, W Kwak, H Clawson, M Diekhans, L Nassar, B Paten, RHS Kraus, H Lewin, AJ Crawford, MTP Gilbert, G Zhang, B Venkatesh, RW Murphy, KP Koepfli, B Shapiro, WE Johnson, F Di Palma, T Margues-Bonet, EC Teeling, T Warnow, JM Graves, OA Ryder, D Hausler, SJ O’Brien, K Howe, EW Myers, R Durbin, AM Phillippy, ED Jarvis.
Towards complete and error-free genome assemblies of all vertebrate species.
IN-PRESS Nature,
2021.
M Cechova, R Vegesna, M Tomaszkiewicz, RS Harris, D Chen, S Rangavittal, P Medvedev, KD Makova.
Dynamic evolution of great ape Y chromosomes.
P NATL ACAD SCI USA,
2020.
R Vegesna, M Tomaszkiewicz, OA Ryder, R Campos-Sánchez, P Medvedev, M DeGiorgio, KD Makova.
Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels.
GENOME BIOL EVOL,
2020.
R Vegesna, M Tomaszkiewicz, P Medvedev, KD Makova.
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes.
PLOS GENET,
2019.
S Rangavittal, N Stopa, M Tomaszkiewicz, K Sahlin, KD Makova, P Medvedev.
DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.
BMC GENOMICS,
2019.
K Sahlin, M Tomaszkiewicz, KD Makova, P Medvedev.
Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.
NAT COMMUN,
2018.
S Warris, E Schijlen, H van de Geest, R Vegesna, T Hesselink, B te Lintel Hekkert, G Sanchez Perez, P Medvedev, KD Makova, D de Ridder.
Correcting palindromes in long reads after whole-genome amplification.
BMC GENOMICS,
2018.
S Rangavittal, RS Harris, M Cechova, M Tomaszkiewicz, R Chikhi, KD Makova, P Medvedev.
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.
BIOINFORMATICS,
2018.
M Tomaszkiewicz, P Medvedev, KD Makova.
Y and W Chromosome Assemblies: Approaches and Discoveries.
TRENDS GENET,
2017.
M Tomaszkiewicz, S Rangavittal, M Cechova, R Campos-Sánchez, HW Fescemyer, RS Harris, D Ye, PCM O’Brien, R Chikhi, OA Ryder, MA Ferguson-Smith, P Medvedev, KD Makova.
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
GENOME RES,
2016.
A Fungtammasan, G Ananda, SE Hile, MS-W Su, C Sun, RS Harris, P Medvedev, KA Eckert, KD Makova.
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
GENOME RES,
2015.