publications from the Ray lab

6 September 2011Posted by Edward Braun

 

Previous publications from the Ray lab relevant to this project include:

publications from the green lab

12 October 2011Posted by Edward Braun

 

Previous publications from the Green lab relevant to this project include:

  • Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444:330-336
  • Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. 2008. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416-426
  • Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S. 2009. The Neandertal genome and ancient DNA authenticity. EMBO J. 28:2494-2502
  • Green, RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al..  2010.  A draft sequence of the Neandertal genome. Science. 328:710-722.
  • Burbano, HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z et al..  2010.  Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 328:723-725.
  • Reich, D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al..  2010.  Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 468:1053-1060.
  • Earl, DA, Bradnam K, St John J, Darling A, Lin D, Faas J, Yu HO, Vince B, Zerbino DR, Diekhans M et al..  2011.  Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research. in press.

publications from the braun lab

12 October 2011Posted by Edward Braun

 

Previous publications from the Braun lab relevant to this project include:

  • Chojnowski, J.L., J. Franklin, Y. Katsu, T. Iguchi, L.J. Guillette Jr, R.T. Kimball, and E.L. Braun. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. Journal of Molecular Evolution, 65: 259-266. [abstract]
  • Chojnowski, J.L. and E.L. Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48:454-462. [abstract]
  • Hackett, S.J., R.T. Kimball, S. Reddy, R.C.K. Bowie, E.L. Braun, M.J. Braun, J.L. Chojnowski, W.A. Cox, K.-L. Han, J. Harshman, C. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt and T. Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320: 1763-1768. [abstract]
  • Harshman, J., E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett, K-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, S.J. Steppan, C.C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences, 105:13462-13467. [abstract]
  • Katsu, Y., E.L. Braun, L.J. Guillette Jr., and T Iguchi. 2009. From reptilian phylogenomics to reptilian genomes: Analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenetic and Genome Research, 127:79-93. [abstract]
  • Han, K.-L., E.L. Braun, R.T. Kimball, S. Reddy, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt, and T. Yuri. 2011. Are transposable element insertions homoplasy free? An examination using the Avian Tree of Life . Systematic Biology, 60:375-386. [extract]
  • Braun, E.L., R.T. Kimball, K.-L. Han, N.R. Iuhasz, A.J. Bonilla, J.L. Chojnowski, J.V. Smith, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and T. Yuri. 2011. Homoplastic microinversions and the Avian Tree of Life. BMC Evolutionary Biology, 11:141. [abstract]
  • Lim, C.H., T. Hamazaki, E.L. Braun, J. Wade, and N. Terada. 2011. Evolutionary genomics implies a specific function of Ant4 in mammalian and anole lizard male germ cells. PLoS ONE, 6:e23122. [abstract]