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Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. Leebens-Mack J, et al. Among authors: harshman j. OMICS. 2006 Summer;10(2):231-7. doi: 10.1089/omi.2006.10.231. OMICS. 2006. PMID: 16901231 Free PMC article. Review.
A phylogenomic study of birds reveals their evolutionary history.
Hackett SJ, Kimball RT, Reddy S, Bowie RC, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han KL, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. Hackett SJ, et al. Among authors: harshman j. Science. 2008 Jun 27;320(5884):1763-8. doi: 10.1126/science.1157704. Science. 2008. PMID: 18583609
Homoplastic microinversions and the avian tree of life.
Braun EL, Kimball RT, Han KL, Iuhasz-Velez NR, Bonilla AJ, Chojnowski JL, Smith JV, Bowie RC, Braun MJ, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Witt CC, Yuri T. Braun EL, et al. Among authors: harshman j. BMC Evol Biol. 2011 May 25;11:141. doi: 10.1186/1471-2148-11-141. BMC Evol Biol. 2011. PMID: 21612607 Free PMC article.
Are transposable element insertions homoplasy free?: an examination using the avian tree of life.
Han KL, Braun EL, Kimball RT, Reddy S, Bowie RC, Braun MJ, Chojnowski JL, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. Han KL, et al. Among authors: harshman j. Syst Biol. 2011 May;60(3):375-86. doi: 10.1093/sysbio/syq100. Epub 2011 Feb 8. Syst Biol. 2011. PMID: 21303823 No abstract available.
A well-tested set of primers to amplify regions spread across the avian genome.
Kimball RT, Braun EL, Barker FK, Bowie RC, Braun MJ, Chojnowski JL, Hackett SJ, Han KL, Harshman J, Heimer-Torres V, Holznagel W, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Smith JV, Witt CC, Yuri T. Kimball RT, et al. Among authors: harshman j. Mol Phylogenet Evol. 2009 Mar;50(3):654-60. doi: 10.1016/j.ympev.2008.11.018. Epub 2008 Dec 6. Mol Phylogenet Evol. 2009. PMID: 19084073 No abstract available.
Phylogenomic evidence for multiple losses of flight in ratite birds.
Harshman J, Braun EL, Braun MJ, Huddleston CJ, Bowie RC, Chojnowski JL, Hackett SJ, Han KL, Kimball RT, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Steppan SJ, Witt CC, Yuri T. Harshman J, et al. Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13462-7. doi: 10.1073/pnas.0803242105. Epub 2008 Sep 2. Proc Natl Acad Sci U S A. 2008. PMID: 18765814 Free PMC article.