Publications by Anton Nekrutenko

2007

Chung, W. Y., S. Wadhawan, R. Szklarczyk, S. K. Pond, and A. Nekrutenko.  A first look at ARFome: dual-coding genes in mammalian genomes.  PLoS Comput. Biol. 3:e91#.

Blankenberg, D., J. Taylor, I. Schenck, J. He, Y. Zhang, M. Ghent, N. Veeraraghavan, I. Albert, W. Miller, K. Makova, R. C. Hardison, and A. Nekrutenko.  A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly.  Genome Res.17:960-964.

Szklarczyk, R., J. Heringa, S. K. Pond, and A. Nekrutenko.  Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function.  Proc. Natl. Acad. Sci. USA 104:12807-12812.

Miller, W., K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko, B. Giardine, R. S. Harris, S. Tyekucheva, M. Diekhans, T. H. Pringle, W. J. Murphy, A. Lesk, G. M. Weinstock, K. Lindblad-Toh, R. A. Gibbs, E. S. Lander, A. Siepel, D. Haussler, and W. J. Kent.  28-Way vertebrate alignment and conservation track in the UCSC Genome Browser.  Genome Res. 17:1797-1808.

Taylor, J., I. Schenck, D. Blankenberg, and A. Nekrutenko. Galaxy: Interactive analyses of genomic data by example.  In: Current Methods in Computational Biology.  (A. Baxevanis, ed.), vol. 2, Unit 10.5, Wiley & Sons, New York, NY.

2006

Nekrutenko, A. and J. He. Functionality of unspliced XBP1 is required to explain the evolution of overlapping reading frames. Trends Genet. 22:645-648.

Wilson, C. and A. Nekrutenko. mNSC1 shows no evidence of protein-coding capacity. Gene 29:83-85.

Chung, W.-Y., R. Albert, I. Albert, A. Nekrutenko, and K. Makova. Role of duplicate gene in the evolution and robustness of human gene co-expression network. BMC Bioinformatics 27:46-60.

2005

Nekrutenko, A., S. Wadhawan, P. Goetting-Minesky, and K. Makova. Oscillating evolution of a mammalian gene with overlapping reading frames: an XL-alpha-S/ALEX relay. PloS Genet. 1(2):e18.
 
Giardine, B., C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, W. Miller, J. Kent, and A. Nekrutenko. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15:1451-1455.

2004

Nekrutenko, A. Identification of novel exons from rat-mouse comparisons. J. Mol. Evol. 59:703-708.

Nekrutenko, A. Reconciling the numbers: ESTs versus protein-coding genes. Mol. Biol. Evol. 21:1278-1282.

Miller, W., K.D. Makova, A. Nekrutenko, and R.C. Hardison. Comparative Genomics. Annu. Rev. Genomics Hum. Genet. 5:15-56.

Gibbs, R.A., G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, P.E. Burch, G. Okwuonu, S. Hines, L. Lewis, C. DeRamo, O. Delgado, S. Dugan-Rocha, G. Miner, M. Morgan, A. Hawes, R. Gill, R.A. Holt, M.D. Adams, P.G. Amanatides, H. Baden-Tillson, M. Barnstead, S. Chin, C.A. Evans, S. Ferriera, C. Fosler, A. Glodek, Z. Gu, D. Jennings, C.L. Kraft, T. Nguyen, C.M. Pfannkoch, C. Sitter, G.G. Sutton, J.C. Venter, T. Woodage, D. Smith, H.M. Lee, E. Gustafson, P. Cahill, A. Kana, L. Doucette-Stamm, K. Weinstock, K. Fechtel, R.B. Weiss, D.M. Dunn, E.D. Green, R.W. Blakesley, G.G. Bouffard, P.J. De Jong, K. Osoegawa, B. Zhu, M. Marra, J. Schein, I. Bosdet, C. Fjell, S. Jones, M. Krzywinski, C. Mathewson, A. Siddiqui, N. Wye, J. McPherson, S. Zhao, C.M. Fraser, J. Shetty, S. Shatsman, K. Geer, Y. Chen, S. Abramzon, W.C. Nierman, P.H. Havlak, R. Chen, K.J. Durbin, A. Egan, Y. Ren, X.Z. Song, B. Li, Y. Liu, X. Qin, S. Cawley, K.C. Worley, A.J. Cooney, L.M. D'Souza, K. Martin, J.Q. Wu, M.L. Gonzalez-Garay, A.R. Jackson, K.J. Kalafus, M.P. McLeod, A. Milosavljevic, D. Virk, A. Volkov, D.A. Wheeler, Z. Zhang, J.A. Bailey, E.E. Eichler, E. Tuzun, E. Birney, E. Mongin, A. Ureta-Vidal, C. Woodwark, E. Zdobnov, P. Bork, M. Suyama, D. Torrents, M. Alexandersson, B.J. Trask, J.M. Young, H. Huang, H. Wang, H. Xing, S. Daniels, D. Gietzen, J. Schmidt, K. Stevens, U. Vitt, J. Wingrove, F. Camara, M. Mar Alba, J.F. Abril, R. Guigo, A. Smit, I. Dubchak, E.M. Rubin, O. Couronne, A. Poliakov, N. Hubner, D. Ganten, C. Goesele, O. Hummel, T. Kreitler, Y.A. Lee, J. Monti, H. Schulz, H. Zimdahl, H. Himmelbauer, H. Lehrach, H.J. Jacob, S. Bromberg, J. Gullings-Handley, M.I. Jensen-Seaman, A.E. Kwitek, J. Lazar, D. Pasko, P.J. Tonellato, S. Twigger, C.P. Ponting, J.M. Duarte, S. Rice, L. Goodstadt, S.A. Beatson, R.D. Emes, E.E. Winter, C. Webber, P. Brandt, G. Nyakatura, M. Adetobi, F. Chiaromonte, L. Elnitski, P. Eswara, R.C. Hardison, M. Hou, D. Kolbe, K. Makova, W. Miller, A. Nekrutenko, C. Riemer, S. Schwartz, J. Taylor, S. Yang, Y. Zhang, K. Lindpaintner, T.D. Andrews, M. Caccamo, M. Clamp, L. Clarke, V. Curwen, R. Durbin, E. Eyras, S.M. Searle, G.M. Cooper, S. Batzoglou, M. Brudno, A. Sidow, E.A. Stone, J.C. Venter, B.A. Payseur, G. Bourque, C. Lopez-Otin, X.S. Puente, K. Chakrabarti, S. Chatterji, C. Dewey, L. Pachter, N. Bray, V.B. Yap, A. Caspi, G. Tesler, P.A. Pevzner, D. Haussler, K.M. Roskin, R. Baertsch, H. Clawson, T.S. Furey, A.S. Hinrichs, D. Karolchik, W.J. Kent, K.R. Rosenbloom, H. Trumbower, M. Weirauch, D.N. Cooper, P.D. Stenson, B. Ma, M. Brent, M. Arumugam, D. Shteynberg, R.R. Copley, M.S. Taylor, H. Riethman, U. Mudunuri, J. Peterson, M. Guyer, A. Felsenfeld, S. Old, S. Mockrin, and F. Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.

Hillier, L.W., W. Miller, E. Birney, W. Warren, R.C. Hardison, C.P. Ponting, P. Bork, D.W. Burt, M.A. Groenen, M.E. Delany, J.B. Dodgson, A.T. Chinwalla, P.F. Cliften, S.W. Clifton, K.D. Delehaunty, C. Fronick, R.S. Fulton, T.A. Graves, C. Kremitzki, D. Layman, V. Magrini, J.D. McPherson, T.L. Miner, P. Minx, W.E. Nash, M.N. Nhan, J.O. Nelson, L.G. Oddy, C.S. Pohl, J. Randall-Maher, S.M. Smith, J.W. Wallis, S.P. Yang, M.N. Romanov, C.M. Rondelli, B. Paton, J. Smith, D. Morrice, L. Daniels, H.G. Tempest, L. Robertson, J.S. Masabanda, D.K. Griffin, A. Vignal, V. Fillon, L. Jacobbson, S. Kerje, L. Andersson, R.P. Crooijmans, J. Aerts, J.J. van der Poel, H. Ellegren, R.B. Caldwell, S.J. Hubbard, D.V. Grafham, A.M. Kierzek, S.R. McLaren, I.M. Overton, H. Arakawa, K.J. Beattie, Y. Bezzubov, P.E. Boardman, J.K. Bonfield, M.D. Croning, R.M. Davies, M.D. Francis, S.J. Humphray, C.E. Scott, R.G. Taylor, C. Tickle, W.R. Brown, J. Rogers, J.M. Buerstedde, S.A. Wilson, L. Stubbs, I. Ovcharenko, L. Gordon, S. Lucas, M.M. Miller, H. Inoko, T. Shiina, J. Kaufman, J. Salomonsen, K. Skjoedt, G.K. Wong, J. Wang, B. Liu, J. Yu, H. Yang, M. Nefedov, M. Koriabine, P.J. Dejong, L. Goodstadt, C. Webber, N.J. Dickens, I. Letunic, M. Suyama, D. Torrents, C. von Mering, E.M. Zdobnov, K. Makova, A. Nekrutenko, L. Elnitski, P. Eswara, D.C. King, S. Yang, S. Tyekucheva, A. Radakrishnan, R.S. Harris, F. Chiaromonte, J. Taylor, J. He, M. Rijnkels, S. Griffiths-Jones, A. Ureta-Vidal, M.M. Hoffman, J. Severin, S.M. Searle, A.S. Law, D. Speed, D. Waddington, Z. Cheng, E. Tuzun, E. Eichler, Z. Bao, P. Flicek, D.D. Shteynberg, M.R. Brent, J.M. Bye, E.J. Huckle, S. Chatterji, C. Dewey, L. Pachter, A. Kouranov, Z. Mourelatos, A.G. Hatzigeorgiou, A.H. Paterson, R. Ivarie, M. Brandstrom, E. Axelsson, N. Backstrom, S. Berlin, M.T. Webster, O. Pourquie, A. Reymond, C. Ucla, S.E. Antonarakis, M. Long, J.J. Emerson, E. Betran, I. Dupanloup, H. Kaessmann, A.S. Hinrichs, G. Bejerano, T.S. Furey, R.A. Harte, B. Raney, A. Siepel, W.J. Kent, D. Haussler, E. Eyras, R. Castelo, J.F. Abril, S. Castellano, F. Camara, G. Parra, R. Guigo, G. Bourque, G. Tesler, P.A. Pevzner, A. Smit, L.A. Fulton, E.R. Mardis, and R.K. Wilson. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.

2003

Nekrutenko, A., W.-Y. Chung, and W.-H. Li. ETOPE: Evolutionary test of predicted exons. Nucleic Acids Res. 31:3564-3567.

Thomas, M.A., B. Weston, M. Joseph, W. Wu, A. Nekrutenko, and P.J. Tonellato. Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes. Mol. Biol. Evol. 20:964-968.

Nekrutenko, A., W.-Y. Chung, and W.-H. Li. An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends Genet. 19:306-310.

Nekrutenko, A. and R.J. Baker. Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids. Gene 306:99-103.

Li, W.-H., Z. Gu, A.R.O. Cavalcanti, and A. Nekrutenko. Detection of gene duplications and block duplications in eukaryotic genomes. J. Struct. Funct. Genomics 3:27-34.

Li., W.-H., Z. Gu, A.R.O. Cavalcanti, and A. Nekrutenko. Detection of gene duplications and block duplications in eukaryotic genomes. In: Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions. (A. Meyer and Y. Van de Peer, eds.), pp. 27-34, Kluwer Academic Publishers, Netherlands.