Search Results - "Cardle, Linda"

Tablet—next generation sequence assembly visualization by Milne, Iain, Bayer, Micha, Cardle, Linda, Shaw, Paul, Stephen, Gordon, Wright, Frank, Marshall, David

“…Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly…”
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Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis by Kalyna, Maria, Simpson, Craig G, Syed, Naeem H, Lewandowska, Dominika, Marquez, Yamile, Kusenda, Branislav, Marshall, Jacqueline, Fuller, John, Cardle, Linda, McNicol, Jim, Dinh, Huy Q, Barta, Andrea, Brown, John W S

“…Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a…”
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Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB‐LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations by Jupe, Florian, Witek, Kamil, Verweij, Walter, Śliwka, Jadwiga, Pritchard, Leighton, Etherington, Graham J., Maclean, Dan, Cock, Peter J., Leggett, Richard M., Bryan, Glenn J., Cardle, Linda, Hein, Ingo, Jones, Jonathan D.G.

“…Summary RenSeq is a NB‐LRR (nucleotide binding‐site leucine‐rich repeat) gene‐targeted, Resistance gene enrichment and sequencing method that enables discovery…”
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Flapjack—graphical genotype visualization by Milne, Iain, Shaw, Paul, Stephen, Gordon, Bayer, Micha, Cardle, Linda, Thomas, William T. B., Flavell, Andrew J., Marshall, David

“…New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide…”
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Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties by Rostoks, N, Ramsay, L, MacKenzie, K, Cardle, L, Bhat, P.R, Roose, M.L, Svensson, J.T, Stein, N, Varshney, R.K, Marshall, D.F

“…Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in…”
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Co-ordinated gene expression during phases of dormancy release in raspberry (Rubus idaeus L.) buds by Mazzitelli, Luca, Hancock, Robert D, Haupt, Sophie, Walker, Paul G, Pont, Simon D.A, McNicol, Jim, Cardle, Linda, Morris, Jenny, Viola, Roberto, Brennan, Rex, Hedley, Peter E, Taylor, Mark A

“…Bud break in raspberry (Rubus idaeus L.) is often poor and uneven, with many of the subapical buds remaining in a dormant state. In order to determine the…”
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Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants by Cardle, Linda, Ramsay, Luke, Milbourne, Dan, Macaulay, Malcolm, Marshall, David, Waugh, Robbie

“…The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in…”
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Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.) by Hedley, Peter E, Russell, Joanne R, Jorgensen, Linzi, Gordon, Sandra, Morris, Jenny A, Hackett, Christine A, Cardle, Linda, Brennan, Rex

“…The detrimental effects of mild winter temperatures on the consistency of cropping of blackcurrant (Ribes nigrum L.) in parts of Europe have led to increasing…”
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An eQTL analysis of partial resistance to Puccinia hordei in barley by Chen, Xinwei, Hackett, C.A, Niks, R.E, Hedley, P.E, Booth, C, Druka, A, Marcel, T.C, Vels, S.A, Bayer, M, Milne, I, Morris, J, Ramsay, L, Marshall, D, Cardle, L, Waugh, R

“…Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable…”
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tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species by Russell, Joanne R, Hedley, Peter E, Cardle, Linda, Dancey, Siobhan, Morris, Jenny, Booth, Allan, Odee, David, Mwaura, Lucy, Omondi, William, Angaine, Peter, Machua, Joseph, Muchugi, Alice, Milne, Iain, Kindt, Roeland, Jamnadass, Ramni, Dawson, Ian K

“…The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new…”
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Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum) by Russell, Joanne R, Bayer, Micha, Booth, Clare, Cardle, Linda, Hackett, Christine A, Hedley, Pete E, Jorgensen, Linzi, Morris, Jenny A, Brennan, Rex M

“…Background Deep-level second generation sequencing (2GS) technologies are now being applied to non-model species as a viable and favourable alternative to…”
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Use of genome sequence data in the design and testing of SSR markers for Phytophthora species by Schena, Leonardo, Cardle, Linda, Cooke, David E L

“…Microsatellites or single sequence repeats (SSRs) are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology,…”
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Highly parallel gene-to-BAC addressing using microarrays by Liu, Hui, McNicol, Jim, Bayer, Micha, Morris, Jenny A, Cardle, Linda, Marshall, David F, Schulte, Daniela, Stein, Nils, Shi, Bu-Jun, Taudien, Stefan, Waugh, Robbie, Hedley, Peter E

“…Second-generation sequencing now provides the potential for low-cost generation of whole-genome sequences. However, for large-genome organisms with high…”
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Single-feature polymorphism discovery in the barley transcriptome by Rostoks, Nils, Borevitz, Justin O, Hedley, Peter E, Russell, Joanne, Mudie, Sharon, Morris, Jenny, Cardle, Linda, Marshall, David F, Waugh, Robbie

“…A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two…”
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Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings by Milne, Iain, Bayer, Micha, Stephen, Gordon, Cardle, Linda, Marshall, David

“…This chapter is designed to be a practical guide to using Tablet for the visualization of next/second-generation (NGS) sequencing data. NGS data is being…”
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Using Tablet for visual exploration of second-generation sequencing data by Milne, Iain, Stephen, Gordon, Bayer, Micha, Cock, Peter J A, Pritchard, Leighton, Cardle, Linda, Shaw, Paul D, Marshall, David

“…The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include…”
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Comparative visualization of genetic and physical maps with Strudel by BAYER, Micha, MILNEL, Lain, STEPHEN, Gordon, SHAW, Paul, CARDLE, Linda, WRIGHT, Frank, MARSHALL, David

“…Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop…”
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Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing by Ho, Thien, Cardle, Linda, Xu, Xin, Bayer, Micha, Prince, K. Silvas Jebakumar, Mutava, Raymond N, Marshall, David F, Syed, Naeem

“…Sampling the sequence of a relatively small fraction of the genome in large numbers of individuals is an important objective for population genetics and…”
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Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome by Lyons, Maura, Cardle, Linda, Rostoks, Nils, Waugh, Robbie, Flavell, Andrew J

“…Four previously undescribed families of miniature inverted repeat transposable elements (MITEs) were isolated by searching barley genomic DNA using…”
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Changes in gene expression during meristem activation processes in Solanum tuberosum with a focus on the regulation of an auxin response factor gene by Faivre‐Rampant, Odile, Cardle, Linda, Marshall, David, Viola, Roberto, Taylor, Mark A.

“…A suppression subtractive hybridization approach (SSH) was used to generate a cDNA library enriched in clones representing genes that are up‐regulated in the…”
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