Peter J A Cock

Peter J A Cock

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Peter J A Cock

Peter J A Cock

Publications by authors named "Peter J A Cock"

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Parallel Microbial Ecology of and Nematode Species in Scottish Soils.

Front Plant Sci 2019 28;10:1763. Epub 2020 Jan 28.

Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom.

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http://dx.doi.org/10.3389/fpls.2019.01763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997879PMC
January 2020

Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes.

Genome Biol Evol 2018 10 1;10(10):2716-2733. Epub 2018 Oct 1.

Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom.

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https://academic.oup.com/gbe/article/10/10/2716/5079402
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http://dx.doi.org/10.1093/gbe/evy183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186164PMC
October 2018

Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster.

Microb Ecol 2016 10 26;72(3):669-81. Epub 2016 Jul 26.

NemaLab/ICAAM-Institute of Mediterranean Agricultural and Environmental Sciences, Biology Department, University of Évora, Évora, Portugal.

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http://dx.doi.org/10.1007/s00248-016-0820-yDOI Listing
October 2016

NCBI BLAST+ integrated into Galaxy.

Gigascience 2015 25;4:39. Epub 2015 Aug 25.

CRS4, Loc. Piscina Manna, 09010 Pula, CA Italy.

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http://dx.doi.org/10.1186/s13742-015-0080-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557756PMC
July 2016

The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus.

BMC Genomics 2016 Apr 23;17:301. Epub 2016 Apr 23.

Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan.

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http://dx.doi.org/10.1186/s12864-016-2626-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841953PMC
April 2016

Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets.

BMC Genomics 2016 Mar 2;17:172. Epub 2016 Mar 2.

Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

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http://dx.doi.org/10.1186/s12864-016-2496-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776380PMC
March 2016

Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy.

Mol Plant Pathol 2016 Feb 16;17(2):286-95. Epub 2015 Jun 16.

Cell and Molecular Sciences Group/Information and Computer Sciences Group (PJAC), The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

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http://dx.doi.org/10.1111/mpp.12280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638532PMC
February 2016

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PLoS Comput Biol 2016 Feb 25;12(2):e1004691. Epub 2016 Feb 25.

Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767331PMC
February 2016

Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins.

J Gen Virol 2015 Nov 9;96(11):3432-3439. Epub 2015 Sep 9.

The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.

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http://dx.doi.org/10.1099/jgv.0.000277DOI Listing
November 2015

The Bioinformatics Open Source Conference (BOSC) 2013.

Bioinformatics 2015 Jan 14;31(2):299-300. Epub 2014 Jul 14.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS 972R525, Berkeley, CA 94720, USA, Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK, Bioinformatics Core, Harvard School of Public Health, Boston, MA 02115, USA, The Computational Biology Institute, George Washington University, Washington, DC 20052, USA, Bioinformatics Department, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland and National Evolutionary Synthesis Center (NESCent), Durham, NC 27705, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287938PMC
January 2015

Galaxy as a platform for identifying candidate pathogen effectors.

Methods Mol Biol 2014 ;1127:3-15

Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK,

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http://dx.doi.org/10.1007/978-1-62703-986-4_1DOI Listing
November 2014

The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.

Genome Biol Evol 2014 Aug 13;6(9):2181-94. Epub 2014 Aug 13.

Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom

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http://dx.doi.org/10.1093/gbe/evu171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202313PMC
August 2014

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

PeerJ 2013 17;1:e167. Epub 2013 Sep 17.

Information and Computational Sciences, James Hutton Institute , UK.

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http://dx.doi.org/10.7717/peerj.167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792188PMC
October 2013

Using Tablet for visual exploration of second-generation sequencing data.

Brief Bioinform 2013 Mar 24;14(2):193-202. Epub 2012 Mar 24.

Information & Computational Sciences, The James Hutton Institute JHI, Dundee DD2 5DA, Scotland, UK.

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http://dx.doi.org/10.1093/bib/bbs012DOI Listing
March 2013

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

BMC Bioinformatics 2012 Aug 21;13:209. Epub 2012 Aug 21.

Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602, USA.

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http://dx.doi.org/10.1186/1471-2105-13-209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468381PMC
August 2012

Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA.

J Gen Virol 2012 Feb 2;93(Pt 2):430-437. Epub 2011 Nov 2.

Cell and Molecular Sciences Group, The James Hutton Institute (JHI), Invergowrie, Dundee DD2 5DA, UK.

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http://dx.doi.org/10.1099/vir.0.037937-0DOI Listing
February 2012

Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora.

Mol Plant Microbe Interact 2012 Jan;25(1):6-17

Department of Crop Sciences, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1094/MPMI-08-11-0207DOI Listing
January 2012

Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps.

Mol Biol Evol 2010 Apr 14;27(4):753-6. Epub 2009 Dec 14.

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http://dx.doi.org/10.1093/molbev/msp302DOI Listing
April 2010

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Nucleic Acids Res 2010 Apr 16;38(6):1767-71. Epub 2009 Dec 16.

Plant Pathology, SCRI, Invergowrie, Dundee DD2 5DA, UK.

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http://dx.doi.org/10.1093/nar/gkp1137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217PMC
April 2010

Evolution of prokaryotic two-component systems: insights from comparative genomics.

Amino Acids 2009 Sep 25;37(3):459-66. Epub 2009 Feb 25.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK.

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http://dx.doi.org/10.1007/s00726-009-0259-2DOI Listing
September 2009

Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships.

Microbiology 2008 Feb;154(Pt 2):360-372

MOAC Doctoral Training Centre, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.

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http://dx.doi.org/10.1099/mic.0.2007/013672-0DOI Listing
February 2008

Evolution of prokaryotic two-component system signaling pathways: gene fusions and fissions.

Mol Biol Evol 2007 Nov 19;24(11):2355-7. Epub 2007 Aug 19.

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http://dx.doi.org/10.1093/molbev/msm170DOI Listing
November 2007

Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes.

J Mol Evol 2007 Apr 19;64(4):457-62. Epub 2007 Mar 19.

MOAC Doctoral Training Centre, University of Warwick, Coventry, UK.

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http://dx.doi.org/10.1007/s00239-006-0180-1DOI Listing
April 2007