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Research: Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
- Eric J. Belfield,
- Xiangchao Gan,
- Aziz Mithani,
- Carly Brown,
- Caifu Jiang,
- Keara Franklin,
- Elizabeth Alvey,
- Anjar Wibowo,
- Marko Jung,
- Kit Bailey,
- Sharan Kalwani,
- Jiannis Ragoussis,
- Richard Mott,
- and Nicholas P. Harberd
Genome Res. July 2012 22: 1306-1315; Published in Advance April 12, 2012, doi:10.1101/gr.131474.111
...Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana Eric J. Belfield 1 , Xiangchao Gan 1 , 2 , Aziz Mithani 1 , 8 , Carly Brown 1 , Caifu Jiang 1...
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METHODS: Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes
- Justin O. Borevitz,
- David Liang,
- David Plouffe,
- Hur-Song Chang,
- Tong Zhu,
- Detlef Weigel,
- Charles C. Berry,
- Elizabeth Winzeler,
- and Joanne Chory
Genome Res. March 1, 2003 13: 513-523; Published in Advance February 12, 2003, doi:10.1101/gr.541303
...Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes Justin O. Borevitz 1 , David Liang 2 , David Plouffe 2 , Hur-Song Chang 3 , Tong Zhu 3 , Detlef Weigel 4 , Charles C. Berry 5 , Elizabeth...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
...-Olds, T., and Weisshaar, B. 2003 . Large-scale identification and analysis of -wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res. 13 : 1250 –1257. ↵ Smits, B.M.G., van Zutphen, B.F.M., Plasterk, R.H.A., and Cuppen, E. 2004 . Genetic variation in coding regions between...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
...al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613–619. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45–58. Fullwood MJ, Wei...
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Method: Prioritizing candidate disease genes by network-based boosting of genome-wide association data
- Insuk Lee,
- U. Martin Blom,
- Peggy I. Wang,
- Jung Eun Shim,
- and Edward M. Marcotte
Genome Res. July 2011 21: 1109-1121; Published in Advance May 2, 2011, doi:10.1101/gr.118992.110
...genes in a more efficient manner. A typical GWAS analysis involves comparing case and control individuals at selected single nucleotide polymorphisms (SNPs) or, more recently, copy number variants (CNVs). SNPs representing common haplotype blocks are measured wide (at approximately 500...
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Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
- Pingli Lu,
- Xinwei Han,
- Ji Qi,
- Jiange Yang,
- Asela J. Wijeratne,
- Tao Li,
- and Hong Ma
Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
...at nucleotide resolution. Comparing L er and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 443 genes have at least 10 nonsynonymous...
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Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
- Xu Zhang,
- Andrew J. Cal,
- and Justin O. Borevitz
Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
.... At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains &gt;38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage...
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LETTER: Ascertainment bias in studies of human genome-wide polymorphism
- Andrew G. Clark,
- Melissa J. Hubisz,
- Carlos D. Bustamante,
- Scott H. Williamson,
- and Rasmus Nielsen
Genome Res. November 2005 15: 1496-1502; doi:10.1101/gr.4107905
...Access option. ↵ 4 Corresponding author. E-mail ac347@cornell.edu ; fax (607) 255-6249. Accepted September 6, 2005. Received June 26, 2005. Cold Spring Harbor Laboratory Press References ↵ Akey, J.M., Zhang, K., Xiong, M., and Jin, L. 2003 . The effect of single nucleotide polymorphism identification...
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RESOURCE: Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster
- Roger A. Hoskins,
- Alexander C. Phan,
- Mohammed Naeemuddin,
- Felipa A. Mapa,
- David A. Ruddy,
- Jessica J. Ryan,
- Lynn M. Young,
- Trent Wells,
- Casey Kopczynski,
- and Michael C. Ellis
Genome Res. June 1, 2001 11: 1100-1113; Published in Advance May 14, 2001, doi:10.1101/gr.178001
...G. , Perkins N. , Winchester E. , Spencer J. , et al. ( 1998 ) Large-scale identification, mapping, and genotyping of single- nucleotide polymorphisms in the human . Science 280 : 1077 – 1082 . ↵ Werle E. , Schneider C. , Renner M. , Volker M. , Fiehn W. ( 1994 ) Convenient single-step, one tube...
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Methods: Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion
- Jon Reinders,
- Céline Delucinge Vivier,
- Grégory Theiler,
- Didier Chollet,
- Patrick Descombes,
- and Jerzy Paszkowski
Genome Res. March 2008 18: 469-476; Published in Advance January 24, 2008, doi:10.1101/gr.7073008
.... , Chang, H.-S. , Zhu, T. , Weigel, D. , Berry, C.C. , Winzeler, E. , Chory, J. ( 2003 ) Large-scale identification of single-feature polymorphisms in complex s . Genome Res. 13 : 513 – 523 . ↵ Chan, S.W. , Henderson, I.R. , Jacobsen, S.E. ( 2005 ) Gardening the : DNA methylation in Arabidopsis thaliana...

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