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Selected Recent Publications from Committee on Genetics, Genomics & Systems Biology Ph.D. candidates.

  • Steele, L, Sukhanova MJ, Gordon GM, Huang Y, Yu L, Du W. Retinoblastoma family protein promotes normal R8-photoreceptor differentiation in the absence of rhinoceros by inhibiting dE2F1 activity. Dev Biol. 2009 Sep 8. [Epub ahead of print].
  • Mefford, MA, Staley, JP. Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in  between these steps. RNA, 2009 Jul;15(7):1386-97. Epub 2009 May 20.
  • Lee JH, Gaetz J, Bugarija B, Fernandes CJ, Snyder GE, Bush EC, Lahn BT. Chromatin analysis of occluded genes. Hum Mol Genet. 2009 Jul 15;18(14):2567-74. Epub 2009 Apr 20.
  • Lee JH, Bugarija B, Millan EJ, Walton NM, Gaetz J, Fernandes CJ, Yu WH, Mekel-Bobrov N, Vallender TW, Snyder GE, Xiang AP, Lahn BT. Systemic identification of cis-silenced genes by trans complementation. Hum Mol Genet. 2009 Mar 1; 18(5):835-46. Epub 2008 Dec 2.
  • Douglas DS, Popko B. Mouse forward genetics in the study of the peripheral nervous system and human peripheral neuropathy. Neurochem Res. 2009 Jan:34(1):124-37. Epub 2008 May 15.
  • Vallender EJ, Mekel-Bobrov N, Lahn BT. Genetic basis of human brain evolution. Trends Neurosci. 2008 Dec; 31(12):637-44. Epub 2009 Oct. 8.
  • MacGregor DR, Deak KI, Ingram PA, Malamy JE, Root system architecture in Arabidopsis grown in culture is regulated by sucrose updates in the aerial tissues. The Plant Cell, Vol. 20:2643-2660, October 2008.
  • Jayathilaka K, Sheridan SD, Bold TD, Bochenska, K, Logan HL, Weichselbaum RR, Bishop, DK, Connell, PP. A chemical compound that stimulates the human homologous recombination protein RAD51. Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15848-53. Epub 2008 Oct 7.
  • Sheridan SD, Yu X, Roth R, Heuser JE, Sehorn MG, Sung P, Egelman EH, Bishop, DK. A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments. Nucleic Acids Res. 2008 Jul;36(12):4057-66. Epub 2008 Jun 4.
  • Nolan DK, Chen P, Das S, Ober C, Waggoner D. Fine mapping of a locus for nonsyndromic mental retardation on chromosome 19p13. Am J Med Genet A. 2008 Jun 1;146A(11):1414-22.
  • Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du W, Long M. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci U S A. 2008 May 27;105(21):7478-83. Epub 2008 May 27.
  • Prachumwat A, Li WH. Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Res. 2008 Feb; 18(2):221-32. Epub 2007 Dec 14.
  • Sangster TA, Salathia N, Undurraga S, Milo R, Schellenberg K, Lindquist S, Queitsch C. HSP90 affects the expression of genetic variation and developmental stability in quantitative traits. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2963-8. Epub 2008 Feb 19.
  • Sangster TA, Salathia N, Lee HN, Watanabe E, Schellenberg K, Morneau K, Wang H, Undurraga S, Queitsch C, Lindquist S. HSP90-buffered genetic variation is common in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2969-74. Epub 2008 Feb 19.
  • Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zaho R, Brunet F, Pent L, Long M, Want W. Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet. 2008. Jan;4(1). Epub 2007 Nov 2.
  • Fan C, Chen Y, Long M. Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila. Mol Biol Evol. 2008 Jul;25(7):1451-8. Epub 2008 April 11.</li>
  • Ouyang KJ, Woo LL, Ellis NA, Homologous recombination and maintenance of genome integrity: cancer and aging through the prism of human RecQ helicases. Mech Ageing Dev. 2008 Jul-Aug;129(7-8):425-40. Epub 2008 Mar 15.
  • Doherty KR, Demonbreun AR, Wallace GQ, Cave A, Posey AD, Heretis K, Pytel P, McNally EM. The endocytic recycling protein EHD2 interacts with myoferlin to regulate myoblast fusion. J Biol Chem. 2008. Jul 18;283(29):2052-60. Epub 2008 May 23.
  • McMahill MS, Sham CS, Bishop DK. (2007) Synthesis-dependent strand anneling in meiosis. PLoS Biol 2007 Nov 6;5(11):e299.
  • Lott SE, Kreitman, M. Palsson A, Alekseeva E, Ludwig MZ. Canalization of segmentation and its evolution in Drosophila. Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10926-31.
  • Hilliker AK, Mefford, MA, Staley JP. U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing. Genes Dev. 2007 Apr 1;21(7):821-34.
  • Dai H, Yoshimatsu T, Long, MY. Retrogene movement within- and between-chromosomes in Evolution of Drosophila genomes. Gene, 2006 Dec 30;385:96-102. Epub 2006 Sep 23.
  • Mekel-Bobrov N, Lahn BT. What makes us human: revisiting an age-old question in the genomic era. J Biomed Discov Collab. 2006 Nov 29;1:18.
  • Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, Lahn BT. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science. (2005) 309:1717-20.
  • Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science. (2005) 309:1720-2.
  • Dorus S, Anderson JR, Vallender EJ, Gilbert SL, Zhang L, Chemnick LG, Ryder OA, Li W, Lahn BT. Sonic Hedgehog, a key development gene, experienced intensified molecular evolution in primates. Hum Mol Genet. (2006) 15:2031-7.
  • Evans PD, Vallender EJ, Lahn BT. Molecular evolution of the brain size regulator genes CDK5RAP2 and CENPJ. Gene. (2006) 375:75-9.
  • Vallender EJ, Lahn BT. A primate-specific acceleration in the evolution of the caspase-dependent apoptosis pathway. Hum Mol Genet. (2006) 15:3034-40.
  • Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M, Wyckoff GJ, Malcom CM, Lahn BT. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell (2004)119:1027-40.
  • Thornton K, Long M. Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster. Mol Biol Evol. (2005) 22:273-84.
  • Hall, SE, Luo, S, Hall, AE, Preuss, D. Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics. (2005) 4:1913-27.
  • Peng Y, Kang Q, Luo Q, Jiang W, Si W, Liu BA, Luu HH, Park JK, Li X, Luo J, Montag AG, Haydon RC, He TC. Inhibitor of DNA binding/differentiation helix-loop-helix proteins mediate bone morphogenetic protein-induced osteoblast differentiation of mesenchymal stem cells. J Biol Chem. (2004) 279:32941-9.
  • Greenberg AJ, Moran JR, Fang S, Wu CI. Adaptive loss of an old duplicated gene during incipient speciation. Mol Biol Evol. (2006) 23:401-10.
  • Fitz Gerald JN, Lehti-Shiu MD, Ingram PA, Deak KI, Biesiada T, Malamy JE. Identification of quantitative trait loci that regulate Arabidopsis root system size and plasticity. Genetics. (2006) 172:485-98.
  • Deak KI, Malamy J. Osmotic regulation of root system architecture. Plant J. (2005) 43:17-28.
  • Holzen TM, Shah PP, Olivares HA, Bishop DK. Tid1/Rdh54 promotes dissociation of Dmc1 from nonrecombinogenic sites on meiotic chromatin. Genes Dev. (2006) 20:2593-604.
  • Sheridan S, Bishop DK. Red-Hed regulation: recombinase Rad51, though capable of playing the leading role, may be relegated to supporting Dmc1 in budding yeast meiosis. Genes Dev. (2006)13:1685-91.
  • Chizhikov VV, Lindgren AG, Currle DS, Rose MF, Monuki ES, Millen KJ. The roof plate regulates cerebellar cell-type specification and proliferation. Development. (2006)133:2793-804.
  • Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A. (2005) 102:18508-13.
  • Adams AM, Hudson RR. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics. (2004) 168:1699-712.
  • Mewborn SK, Lese Martin C, Ledbetter DH. The dynamic nature and evolutionary history of subtelomeric and pericentromeric regions. Cytogenet Genome Res. (2005) 108:22-5.
  • Thompson EE , Kuttab-Boulos H, Yang L., Roe B.A, Di Rienzo A. Sequence diversity and haplotype structure at the human CYP3A cluster. (2006) Pharmacogenomics J. 6: 105-114.

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