Peter's Publications

The following list is manually curated, you can also try Google's semi-automatic list of my publications (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 (a scheme to uniquely identify individual researchers), and you can find my axXiv preprints here.

2013

Visualizing genome assemblies
S. Andrews, M. Blaxter, P. Cock, et al.
Chapter 4 in Visualizing Biological Data: A Practical Guide (2013, S.I. O'Donoghue and J.B. Procter, eds), Cambridge University Press, ISBN 9781107018471.

[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

[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.

[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.

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.
Eric Talevich, Brandon M. Invergo, Peter J.A. Cock and Brad A. Chapman. BMC Bioinformatics, 2012, 13:209

[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.

[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.

[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.

[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.

[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.

[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