Search Results - "Peter Cock"

Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants by Cock, Peter J.A, Fields, Christopher J, Goto, Naohisa, Heuer, Michael L, Rice, Peter M

“…FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite…”
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Biopython: freely available Python tools for computational molecular biology and bioinformatics by Cock, Peter J. A., Antao, Tiago, Chang, Jeffrey T., Chapman, Brad A., Cox, Cymon J., Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, de Hoon, Michiel J. L.

“…The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of…”
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Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus by Kikuchi, Taisei, Cotton, James A, Dalzell, Jonathan J, Hasegawa, Koichi, Kanzaki, Natsumi, McVeigh, Paul, Takanashi, Takuma, Tsai, Isheng J, Assefa, Samuel A, Cock, Peter J A, Otto, Thomas Dan, Hunt, Martin, Reid, Adam J, Sanchez-Flores, Alejandro, Tsuchihara, Kazuko, Yokoi, Toshiro, Larsson, Mattias C, Miwa, Johji, Maule, Aaron G, Sahashi, Norio, Jones, John T, Berriman, Matthew

“…Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent…”
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Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets by Thorpe, Peter, Cock, Peter J A, Bos, Jorunn

“…Aphids are phloem-feeding insects that cause significant economic losses to agriculture worldwide. While feeding and probing these insects deliver molecules,…”
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Identification and localisation of the NB-LRR gene family within the potato genome by Jupe, Florian, Pritchard, Leighton, Etherington, Graham J, Mackenzie, Katrin, Cock, Peter J A, Wright, Frank, Sharma, Sanjeev Kumar, Bolser, Dan, Bryan, Glenn J, Jones, Jonathan D G, Hein, Ingo

“…The potato genome sequence derived from the Solanum tuberosum Group Phureja clone DM1-3 516 R44 provides unparalleled insight into the genome composition and…”
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Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython by Talevich, Eric, Invergo, Brandon M, Cock, Peter J A, Chapman, Brad A

“…Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and…”
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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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Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy by Espada, Margarida, Silva, Ana Cláudia, Eves van den Akker, Sebastian, Cock, Peter J. A., Mota, Manuel, Jones, John T.

“…The migratory endoparasitic nematode Bursaphelenchus xylophilus, which is the causal agent of pine wilt disease, has phytophagous and mycetophagous phases…”
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NCBI BLAST+ integrated into Galaxy by Cock, Peter J A, Chilton, John M, Grüning, Björn, Johnson, James E, Soranzo, Nicola

“…The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR…”
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Distinct circular single-stranded DNA viruses exist in different soil types by Reavy, Brian, Swanson, Maud M, Cock, Peter J A, Dawson, Lorna, Freitag, Thomas E, Singh, Brajesh K, Torrance, Lesley, Mushegian, Arcady R, Taliansky, Michael

“…The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types…”
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Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology by Cock, Peter J A, Grüning, Björn A, Paszkiewicz, Konrad, Pritchard, Leighton

“…The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present 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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metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual by Eves‐van den Akker, Sebastian, Lilley, Catherine J, Reid, Alex, Pickup, Jon, Anderson, Eric, Cock, Peter J.A, Blaxter, Mark, Urwin, Peter E, Jones, John T, Blok, Vivian C

“…Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of…”
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The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence by Eves-van den Akker, Sebastian, Laetsch, Dominik R, Thorpe, Peter, Lilley, Catherine J, Danchin, Etienne G J, Da Rocha, Martine, Rancurel, Corinne, Holroyd, Nancy E, Cotton, James A, Szitenberg, Amir, Grenier, Eric, Montarry, Josselin, Mimee, Benjamin, Duceppe, Marc-Olivier, Boyes, Ian, Marvin, Jessica M C, Jones, Laura M, Yusup, Hazijah B, Lafond-Lapalme, Joël, Esquibet, Magali, Sabeh, Michael, Rott, Michael, Overmars, Hein, Finkers-Tomczak, Anna, Smant, Geert, Koutsovoulos, Georgios, Blok, Vivian, Mantelin, Sophie, Cock, Peter J A, Phillips, Wendy, Henrissat, Bernard, Urwin, Peter E, Blaxter, Mark, Jones, John T

“…The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes…”
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THAPBI PICT-a fast, cautious, and accurate metabarcoding analysis pipeline by Cock, Peter J A, Cooke, David E L, Thorpe, Peter, Pritchard, Leighton

“…THAPBI PICT is an open source software pipeline for metabarcoding analysis of Illumina paired-end reads, including cases of multiplexing where more than one…”
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Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA by MCGAVIN, Wendy J, MITCHELL, Carolyn, COCK, Peter J. A, WRIGHT, Kathryn M, MACFARLANE, Stuart A

“…A new, segmented, negative-strand RNA virus with morphological and sequence similarities to other viruses in the genus Emaravirus was discovered in raspberry…”
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Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster by Vicente, Cláudia S. L., Nascimento, Francisco X., Barbosa, Pedro, Ke, Huei-Mien, Tsai, Isheng J., Hirao, Tomonori, Cock, Peter J. A., Kikuchi, Taisei, Hasegawa, Koichi, Mota, Manuel

“…Pine wilt disease (PWD) results from the interaction of three elements: the pathogenic nematode, Bursaphelenchus xylophilus; the insect-vector, Monochamus sp.;…”
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Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes by Thorpe, Peter, Escudero-Martinez, Carmen M, Cock, Peter J A, Eves-van den Akker, Sebastian, Bos, Jorunn I B

“…Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome…”
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Evolution of prokaryotic two-component systems: insights from comparative genomics by Whitworth, David E, Cock, Peter J. A

“…Two-component systems (TCSs) are diverse and abundant signal transduction pathways found predominantly in prokaryotes. This review focuses on insights into TCS…”
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Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins by Lu, Yuwen, McGavin, Wendy, Cock, Peter J A, Schnettler, Esther, Yan, Fei, Chen, Jianping, MacFarlane, Stuart

“…Members of the genus Emaravirus, including Raspberry leaf blotch virus (RLBV), are enveloped plant viruses with segmented genomes of negative-strand RNA,…”
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