Peter's Publications

The following list is manually curated, you can also try my semi-automatic list of Google Scholar profile (with citation counts of dubious accuracy), and there is also a listing on my James Hutton Institute page.

I am also registered as ORCID 0000-0001-9513-9993 (Europe PubMed Central search results), ResearcherID D-8730-2013, Scopus Author ID 35336601200 (schemes to uniquely identify individual researchers), and you can find my axXiv preprints here.

2016

Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster
C.S.L. Vicente et al. Microbial Ecology 2016 DOI: 10.1007/s00248-016-0820-y (altmetrics)

Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets Peter Thorpe, Peter J. A. Cock and Jorunn Bos. BMC Genomics 2016 DOI: 10.1186/s12864-016-2496-6 (altmetrics)

The 2015 Bioinformatics Open Source Conference (BOSC 2015). N.L. Harris, P.J.A. Cock, H. Lapp, B. Chapman, R. Davey, C. Fields, K. Hokamp, M. Munoz-Torres. PLOS Computational Biology 2016. DOI: 10.1371/journal.pcbi.1004691 (altmetrics)

2015

[Cover for Molecular Ecology] A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual. S. Eves-van den Akker, C.J. Lilley, A. Reid, J. Pickup, E. Anderson, P.J.A. Cock, et al. Molecular Ecology 2015 24(23):5842-5851. DOI: 10.1111/mec.13434 (altmetrics)

[Cover for Journal of General Virology] Newly identified RNAs of Raspberry leaf blotch virus encoding a related group of proteins
Y Lu, W McGavin, PJA Cock, E Schnettler, F Yan, J Chen, S MacFarlane. Journal of General Virology DOI: 10.1099/jgv.0.000277 (online) (altmetrics)

[Cover for MPP] Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy
M. Espada, A.C. Silva, S. Eves van den Akker, P.J.A. Cock, M. Mota and J.T. Jones
Molecular Plant Pathology 2015 DOI: 10.1111/mpp.12280 (altmetrics)

[Logo for bioRxiv] SAM/BAM format v1.5 extensions for de novo assemblies
Peter J. A. Cock, James K. Bonfield, Bastien Chevreux, Heng Li
bioRxiv DOI: 10.1101/020024 (PrePrint) (altmetrics)

[Cover of Applied and environmental microbiology v81] Distinct circular ssDNA Viruses Exist in Different Soil Types. B. Reavy, M.M. Swanson, P.J.A. Cock, L. Dawson, T.E. Freitag, B.K. Singh, L. Torrance, A.R. Mushegian, M. Taliansky. Applied and environmental microbiology 2015, 81(12): 3934-3945. DOI: 10.1128/AEM.03878-14 (altmetrics)

[Logo for GigaScience] NCBI BLAST+ integrated into Galaxy
Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo. GigaScience, 2015, 4:39
DOI: 10.1186/s13742-015-0080-7
(altmetrics) (preprint, altmetrics)

[Cover of Bioinformatics] The Bioinformatics Open Source Conference (BOSC) 2013. N.L. Harris, P.J.A. Cock, B.A. Chapman, J. Goecks, H. Hotz, H. Lapp. Bioinformatics 2015, 31:299-300, DOI: 10.1093/bioinformatics/btu413 (altmetrics; preprint)

2014

[BMC Bioinformatics] Community-driven development for computational biology at Sprints, Hackathons and Codefests
S. Möller et al. BMC Bioinformatics, 2014, DOI: 10.1186/1471-2105-15-S14-S7 (altmetrics)

[BMC Genomics] Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida
P. Thorpe et al. BMC Genomics, 2014, DOI: 10.1186/1471-2164-15-923 (altmetrics)

[Cropped figure from Genome Biol Evol] The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes
S. Eves van den Akker et al. Genome Biol Evol, 2014, 6(9): 2181-2194. DOI: 10.1093/gbe/evu171 (altmetrics)

[Cropped figure from Genome Biology] The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode
J.A. Cotton et al. Genome Biology, 2014, 15:R43 DOI: 10.1186/gb-2014-15-3-r43 (altmetrics)

[Logo of Journal of Biomedical Semantics] BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
T. Katayama, M.D. Wilkinson, et al. Journal of Biomedical Semantics, 2014, 5:5 DOI: 10.1186/2041-1480-5-5 (altmetrics)

[Logo for bioRxiv] FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation
J. Bolleman, C.J. Mungall, F. Strozzi, J. Barran, M. Dumontier, R.J.P. Bonnal, R. Buels, R. Hoendorf, T. Fujisawa, T. Katayama, P.J.A. Cock
bioRxiv DOI: 10.1101/002121 (PrePrint) (altmetrics)

[Cover of Plant-Pathogen Interactions: Methods and Protocols, Second Edition] Galaxy as a Platform for Identifying Candidate Pathogen Effectors. P.J.A. Cock and L. Pritchard.
Chapter 1 in Plant-Pathogen Interactions: Methods and Protocols, Second Edition (2014, P. Birch, J. Jones, and J.I. Bos, eds), ISBN 978-1-62703-985-7,
DOI: 10.1007/978-1-62703-986-4_1 (altmetrics)

[Cover of Nematology] Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase
T. Kikuchi, P.J.A. Cock, J. Helder, J.T. Jones
Nematology, 2014, 16(1), 99-107. DOI: 10.1163/15685411-00002748 (altmetrics)

2013

[PeerJ Preprints Logo] The Bioinformatics Open Source Conference (BOSC) 2013.
N.L. Harris, P.J.A. Cock, B.A. Chapman, J. Goecks, H. Hotz, H. Lapp.
PeerJ PrePrints 2013, 1:e83v1 (altmetrics)

[EMBnet.Journal cover 19] Sprints, Hackathons and Codefests as community gluons in computational biology.
S. Möller, E. Afgan, M. Banck, P. Cock, et al.
EMBnet.Journal 2013, 19(B), (NETTAB 2013), 40-42.

[PeerJ Logo] Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.
P.J.A. Cock, B.A. Grüning, K.H. Paszkiewicz and L. Pritchard. PeerJ, 2013, 1:e167. DOI: 10.7717/peerj.167 (altmetrics)

[The Plant Journal cover] Resistance gene enrichment sequencing (RenSeq) enables re-annotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. F. Jupe et al. The Plant Journal, 2013, 76(3), 530-544. (altmetrics)

[Logo of Journal of Biomedical Semantics] The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies T. Katayama et al.
Journal of Biomedical Semantics, 2013, 4:6. DOI: 10.1186/2041-1480-4-6 (altmetrics)

[Cover of SIADS] Computation of balanced equivalence relations and their lattice for a coupled cell network. H. Kamei and P.J.A. Cock. SIAM Journal on Applied Dynamical Systems (SIADS), 2013, 12(1), 352-382. Supplementary file; Preprint on arXiv (altmetrics)

[Cover of Parasitology April 2013] Activation of hatching in diapaused and quiescent Globodera pallida.
J.E. Palomares-Rius, J.T. Jones, P.J. Cock, P. Castillo, V. Blok.
Parasitology, 2013, 140(4), 445-454.

[Cover of Briefings in Bioinformatics] Using Tablet for visual exploration of second-generation sequencing data. I. Milne, G. Stephen, M. Bayer, P.J.A. Cock, L. Pritchard, L. Cardle, P.D. Shaw, and D. Marshall. Briefings in Bioinformatics, 2013, 14(2), 193-202. (altmetrics)

2012

[Cover of Molecular Plant Pathology Dec 2012] Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes. J.E. Palomares-Rius, P.E. Hedley, P.J. Cock, et al. Mol Plant Pathol., 2012, 13(9), 1120-1134.

[BMC Bioinformatics] Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. E. Talevich, B.M. Invergo, P.J.A. Cock and B.A. Chapman. BMC Bioinformatics, 2012, 13:209 (altmetrics)

[PLoS One] Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes. M.M. Swanson, B. Reavy, K.S. Kira, P.J.A. Cock, D.W. Hopkins, L. Torrance, E.V. Koonin, M. Taliansky. PLoS ONE, 2012, e40683. (altmetrics)

[BMC Genomics] Identification and localisation of the NB-LRR gene family within the potato genome F. Jupe, L. Pritchard, G.J. Etherington, K. MacKenzie, P.J.A. Cock, et al. BMC Genomics, 2012, 13:75. (altmetrics)

[Cover of Journal of General Virology Feb 2012] Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA. Wendy J. McGavin, Carolyn Mitchell, Peter J.A. Cock, et al. Journal of General Virology, 2012, 93(2), 430-437.

[Cover of Molecular Plant Pathology Feb 2012] Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors. R.R. McNally, I.K. Toth, P.J. Cock, et al. Molecular Plant Pathology, 2012, 13(2), 160-173.

[Cover of Molecular Plant-Microbe Interactions (MPMI) Jan 2012] Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. D. Wang, M. Qi, B. Calla, S.S. Korban, S.J. Clough, P.J.A. Cock, et al. Molecular Plant-Microbe Interactions, 2012, 25(1), 6-17.

2011

[Mock cover of PLOS Pathogens] Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus. T. Kikuchi, J.A. Cotton, J.J. Dalzell, K. Hasegawa, N. Kanzaki, et al.
PLoS Pathogens, 2011, 7(9), e1002219. (altmetrics)

[Cover of Plant Pathology] Partial sequence and RT-PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus.
W.J. McGavin, P.J.A. Cock and S.A. MacFarlane.
Plant Pathology, 2011, 60(3), 462-467.

2010, including some from PhD work

[Cover of Nucleic Acids Research] The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. P.J.A. Cock, C.J. Fields, N. Goto, M.L. Heuer and P.M. Rice. Nucleic Acids Research, 2010, 38(6), 1767-1771. (altmetrics)

[Cover of Molecular Biology and Evolution] Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps.
P.J.A. Cock and D.E. Whitworth
Molecular Biology and Evolution, 2010, 27(4), 753-756.

2009, including some from PhD work

[Cover of Molecular Plant Pathology] Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. J.T. Jones et al.
Molecular Plant Pathology, 2009, 10(6), 815-828.

[Cover of Bioinformatics] Biopython: freely available Python tools for computational molecular biology and bioinformatics P.J.A. Cock et al.
Bioinformatics, 2009, 25(11), 1422-1423. (altmetrics)

[Cover of Amino Acids] Evolution of prokaryotic two-component systems: insights from comparative genomics. D.E. Whitworth and P.J.A. Cock
Amino Acids, 2009, 37(3), 459-466.

2008, published during PhD

[Cover of Microbiology, Feb 2008] Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships.
D.E. Whitworth and P.J.A. Cock
Microbiology, 2008, 154(2), 360-372.

Myxobacterial Two-Component Systems
D.E. Whitworth and P.J.A. Cock
Chapter 10 in Myxobacteria: Multicellularity and Differentiation (2008, D.E. Whitworth, ed), ASM Press, ISBN: 978-1-55581-420-5

2007, published during PhD

[Cover of Molecular Biology and Evolution] Evolution of prokaryotic two-component system signalling pathways: gene fusions and fissions.
P.J.A. Cock and D.E. Whitworth
Molecular Biology and Evolution, 2007, 24(11), 2355-2357.

[Cover of Journal Of Molecular Evolution] Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes.
P.J.A. Cock and D.E. Whitworth
Journal Of Molecular Evolution, 2007, 64(4), 457-462.

Documentation

[Biopython logo, rotated] Biopython Tutorial and Cookbook
Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon and Peter Cock
See also: www.biopython.org

[The R-Project logo] Introducing the R Programming Language
A set of web-pages written for MOAC Module CH923
Martin Edwards, Samuel Robson and Peter Cock
See also: www.r-project.org