Paul Medvedev
Computer Science and Engineering - Biochemistry and Molecular Biology, Pennsylvania State University
Interests
- Development of computer science techniques for analysis of biological data
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
Biography
Paul Medvedev is a Professor in the Department of Computer Science and Engineering and the Department of Biochemistry and Molecular Biology and the Director of the Center for Computational Biology and Bioinformatics at the Pennsylvania State University. His research is focused on developing computer science techniques for analysis of biological data and on answering fundamental biological questions using such methods.
Publications
KD Makova, BD Pickett, RS Harris, GA Hartley, M Cechova, K Pal, S Nurk, D Yoo, Q Li, P Hebbar, BC McGrath, F Antonacci, M Aubel, A Biddanda, M Borchers, E Bomberg, GG Bouffard, SY Brooks, L Carbone, L Carrel, A Carroll, PC Chang, CS Chin, DE Cook, SJC Craig, L de Gennaro, M Diekhans, A Dutra, GH Garcia, PGS Grady, RE Green, D Haddad, P Hallast, WT Harvey, G Hickey, DA Hillis, SJ Hoyt, H Jeong, K Kamali, SL Kosakovsky Pond, TM LaPolice, C Lee, AP Lewis, YE Loh, P Masterson, RC McCoy, P Medvedev, KH Miga, KM Munson, E Pak, B Paten, BJ Pinto, T Potapova, A Rhie, JL Rocha, F Ryabov, OA Ryder, S Sacco, K Shafin, VA Shepelev, V Slon, SJ Solar, JM Storer, PH Sudmant, Sweetalana, A Sweeten, MG Tassia, F Thibaud-Nissen, M Ventura, MA Wilson, AC Young, H Zeng, X Zhang, ZA Szpiech, CD Huber, JL Gerton, SV Yi, MC Schatz, IA Alexandrov, S Koren, RJ O’Neill, E Eichler, AM Phillippy.
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
NATURE,
2024.
M Tomaszkiewicz, K Sahlin, P Medvedev, KD Makova.
Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.
GENOME BIOL EVOL,
2023.
A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, S Koren, M Rautiainen, IA Alexandrov, J Allen, M Asri, AV Bzikadze, N-C Chen, C-S Chin, M Diekhans, P Flicek, G Formenti, A Fungtammasan, CG Giron, E Garrison, A Gershman, JL Gerton, PGS Grady, A Guarracino, L Haggerty, R Halabian, NF Hansen, R Harris, GA Hartley, WT Harvey, M Haukness, J Heinz, T Hourlier, RM Hubley, SE Hunt, S Hwang, M Jain, RK Kesharwani, AP Lewis, H Li, GA Logsdon, JK Lucas, W Makalowski, C Markovic, FJ Martin, AM McCartney, RC McCoy, J McDaniel, BM McNulty, P Medvedev, A Mikheenko, KM Munson, TD Murphy, HE Olsen, ND Olson, LF Paulin, D Porubsky, T Potapova, F Ryabov, SL Salzberg, MEG Sauria, FJ Sedlazeck, K Shafin, VA Shepelev, A Shumate, JM Storer, L Surapaneni, AM Taravella Oill, F Thibaud-Nissen, W Timp, M Tomaszkiewicz, MR Vollger, BP Walenz, AC Watwood, MH Weissensteiner, AM Wenger, MA Wilson, S Zarate, Y Zhu, JM Zook, EE Eichler, RJ O’Neill, MC Schatz, KH Miga, KD Makova, AM Phillippy.
The complete sequence of a human Y chromosome.
NATURE,
2023.
M Escalona, J VanCampen, NW Maurer, M Haukness, M Okhovat, RS Harris, A Watwood, GA Hartley, RJ O’Neill, P Medvedev, KD Makova, C Vollmers, L Carbone, RE Green.
Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch).
J HERED,
2022.
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.
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.