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Alignathon: a competitive assessment of whole-genome alignment methods.
Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Earl D, et al. Among authors: ma j. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1. Genome Res. 2014. PMID: 25273068 Free PMC article.
Reconstructing contiguous regions of an ancestral genome.
Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Ma J, et al. Genome Res. 2006 Dec;16(12):1557-65. doi: 10.1101/gr.5383506. Epub 2006 Sep 18. Genome Res. 2006. PMID: 16983148 Free PMC article.
The infinite sites model of genome evolution.
Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. Ma J, et al. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14254-61. doi: 10.1073/pnas.0805217105. Epub 2008 Sep 11. Proc Natl Acad Sci U S A. 2008. PMID: 18787111 Free PMC article.
Comparative and demographic analysis of orang-utan genomes.
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Locke DP, et al. Among authors: ma j, ma x. Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687. Nature. 2011. PMID: 21270892 Free PMC article.
Cactus graphs for genome comparisons.
Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Paten B, et al. Among authors: ma j. J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252. J Comput Biol. 2011. PMID: 21385048 Free PMC article.
Reference-assisted chromosome assembly.
Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA, Ma J. Kim J, et al. Among authors: ma j. Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1785-90. doi: 10.1073/pnas.1220349110. Epub 2013 Jan 10. Proc Natl Acad Sci U S A. 2013. PMID: 23307812 Free PMC article.
35,682 results
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