Anton Nekrutenko
Professor of Biochemistry and Molecular Biology, Pennsylvania State University
Interests
- Computational genomics
Education
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Ph.D. in Biology,
Texas Tech University
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M.S. in Biochemistry and Molecular Biology,
Kiev State University, Ukraine
Biography
Prof. Nekrutenko performed postdoctoral work at the University of Chicago where he found his interest in computational genomics. After moving to the Pennsylvania State University as an Assistant Professor, he and his collaborators developed the Galaxy platform for analysis of biological data. He is now a professor of biochemistry and molecular biology and founding member of galaxyproject.org.
Publications
N Stoler, B Arbeithuber, G Povysil, M Heinzl, R Salazar, KD Makova, I Tiemann-Boege, A Nekrutenko.
Family reunion via error correction: an efficient analysis of duplex sequencing data.
BMC BIOINFORMATICS,
2020.
A Zaidi, P Wilton, MS-W Su, IM Paul, B Arbeithuber, K Anthony, A Nekrutenko, R Nielsen, KD Makova.
Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees.
P NATL ACAD SCI USA,
2019.
SJC Craig, D Blankenberg, ACL Parodi, IM Paul, LL Birch, JS Savage, ME Marini, JL Stokes, A Nekrutenko, M Reimherr, F Chiaromonte, KD Makova.
Child Weight Gain Trajectories Linked To Oral Microbiota Composition.
SCI REP-UK,
2018.
N Stoler, B Arbeithuber, WM Guiblet, KD Makova, A Nekrutenko.
Streamlined analysis of duplex sequencing data with Du Novo.
GENOME BIOL,
2016.
B Rebolledo-Jaramillo, MS-W Su, N Stoler, JA McElhoe, B Dickins, D Blankenberg, TS Korneliussen, F Chiaromonte, R Nielsen, MM Holland, IM Paul, A Nekrutenko, KD Makova.
Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.
P NATL ACAD SCI USA,
2014.
B Dickins, B Rebolledo-Jaramillo, MS-W Su, IM Paul, D Blankenberg, N Stoler, KD Makova, A Nekrutenko.
Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach.
BIOTECHNIQUES,
2014.
E Afgan, D Baker, N Coraor, H Goto, IM Paul, KD Makova, A Nekrutenko, J Taylor.
Harnessing cloud computing with Galaxy Cloud.
NAT BIOTECHNOL,
2011.
H Goto, B Dickins, E Afgan, IM Paul, J Taylor, KD Makova, A Nekrutenko.
Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.
GENOME BIOL,
2011.
H Goto, OA Ryder, AR Fisher, B Schultz, SL Kosakovsky Pond, A Nekrutenko, KD Makova.
A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses.
GENOME BIOL EVOL,
2011.
SC Schuster, W Miller, A Ratan, LP Tomsho, B Giardine, LR Kasson, RS Harris, DC Petersen, F Zhao, J Qi, C Alkan, JM Kidd, Y Sun, DI Drautz, P Bouffard, DM Muzny, JG Reid, LV Nazareth, Q Wang, RC Burhans, C Riemer, NE Wittekindt, P Moorjani, EA Tindall, CG Danko, WS Teo, AM Buboltz, Z Zhang, Q Ma, A Oosthuysen, AW Steenkamp, H Oostuisen, P Venter, J Gajewski, Y Zhang, BF Pugh, KD Makova, A Nekrutenko, ER Mardis, N Patterson, TH Pringle, F Chiaromonte, JC Mullikin, EE Eichler, RC Hardison, RA Gibbs, TT Harkins, VM Hayes.
Complete Khoisan and Bantu genomes from southern Africa.
NATURE,
2010.
D Blankenberg, J Taylor, I Schenck, J He, Y Zhang, M Ghent, N Veeraraghavan, I Albert, W Miller, KD Makova, RC Hardison, A Nekrutenko.
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly.
GENOME RES,
2007.
W-Y Chung, R Albert, I Albert, A Nekrutenko, KD Makova.
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.
BMC BIOINFORMATICS,
2006.
A Nekrutenko, S Wadhawan, MP Goetting-Minesky, KD Makova.
Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay.
PLOS GENET,
2005.
International Chicken Genome Sequencing Consortium, LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, JB Dodgson, AT Chinwalla, PF Cliften, SW Clifton, KD Delehaunty, C Fronick, RS Fulton, TA Graves, C Kremitzki, D Layman, V Magrini, JD McPherson, TL Miner, P Minx, WE Nash, MN Nhan, JO Nelson, LG Oddy, CS Pohl, J Randall-Maher, SM Smith, JW Wallis, S-P Yang, MN Romanov, CM Rondelli, B Paton, J Smith, D Morrice, L Daniels, HG Tempest, L Robertson, JS Masabanda, DK Griffin, A Vignal, V Fillon, L Jacobbson, S Kerje, L Andersson, RPM Crooijmans, J Aerts, JJ van der Poel, H Ellegren, RB Caldwell, SJ Hubbard, DV Grafham, AM Kierzek, SR McLaren, IM Overton, H Arakawa, KJ Beattie, Y Bezzubov, PE Boardman, JK Bonfield, MDR Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WRA Brown, J Rogers, J-M Buerstedde, SA Wilson, L Stubbs, I Ovcharenko, L Gordon, S Lucas, MM Miller, H Inoko, T Shiina, J Kaufman, J Salomonsen, K Skjoedt, GK-S Wong, J Wang, B Liu, J Wang, J Yu, H Yang, M Nefedov, M Koriabine, PJ deJong, L Goodstadt, C Webber, NJ Dickens, I Letunic, M Suyama, D Torrents, C von Mering, EM Zdobnov, KD Makova, A Nekrutenko, L Elnitski, P Eswara, DC King, S Yang, S Tyekucheva, A Radakrishnan, RS Harris, F Chiaromonte, J Taylor, J He, M Rijnkels, S Griffiths-Jones, A Ureta-Vidal, MM Hoffman, J Severin, SMJ Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, EE Eichler, Z Bao, P Flicek, DD Shteynberg, MR Brent, JM Bye, EJ Huckle, S Chatterji, C Dewey, L Pachter, A Kouranov, Z Mourelatos, AG Hatzigeorgiou, AH Paterson, R Ivarie, M Brandstrom, E Axelsson, N Backstrom, S Berlin, MT Webster, O Pourquie, A Reymond, C Ucla, SE Antonarakis, M Long, JJ Emerson, E Betrán, I Dupanloup, H Kaessmann, AS Hinrichs, G Bejerano, TS Furey, RA Harte, B Raney, A Siepel, WJ Kent, D Haussler, E Eyras, R Castelo, JF Abril, S Castellano, F Camara, G Parra, R Guigo, G Bourque, G Tesler, PA Pevzner, AFA Smit, LA Fulton, ER Mardis, RK Wilson.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
NATURE,
2004.
W Miller, KD Makova, A Nekrutenko, RC Hardison.
COMPARATIVE GENOMICS.
ANNU REV GENOM HUM G,
2004.
Rat Genome Sequencing Project Consortium, RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, GO Okwuonu, S Hines, LR Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, AC Hawes, R Gill, CRA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, H-M Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ de Jong, K Osoegawa, B Zhu, MA Marra, JE Schein, I Bosdet, C Fjell, SM Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, JD McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, RA Gibbs, GM Weinstock, PH Havlak, R Chen, K James Durbin, A Egan, Y Ren, HX-Z Song, B Li, Y Liu, X Qin, S Cawley, GM Weinstock, KC Worley, AJ Cooney, RA Gibbs, LM D’Souza, K Martin, J Qian Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, EM Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, D Smith, H Huang, K Fechtel, H Wang, H Xing, K Weinstock, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, AFA Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, Y-A Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, KD Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SMJ Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, J Craig Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, MR Brent, M Arumugam, DD Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
NATURE,
2004.
A Nekrutenko, KD Makova, W-H Li.
The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study.
GENOME RES,
2002.
KD Makova, A Nekrutenko, RJ Baker.
Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus).
J MOL EVOL,
2000.
A Nekrutenko, KD Makova, RJ Baker.
Isolation of binary species-specific PCR-based markers and their value for diagnostic applications.
GENE,
2000.
A Nekrutenko, KD Makova, RK Chesser, RJ Baker.
Representational difference analysis to distinguish cryptic species.
MOL ECOL,
1999.