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). There is also a listing on my James Hutton Institute page.

Published after PhD, not based on work during PhD

[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, 2012, in press, online

[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.

[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, 2010, 60(3), 462-467.

[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 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.


Published after PhD, but based on work during PhD

[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.

[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.


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.

[Cover of Myxobacteria: Multicellularity and Differentiation]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

[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.


Acknowledgements

[Cover of PNAS 2006 volume 103 issue 41] Protein-protein interactions between two-component system transmitter and receiver domains of Myxococcus xanthus

D.E. Whitworth, A. Millard A, D.A. Hodgson and P.F. Hawkins
Proteomics, 2008, 8(9), 1839-1842.

[Cover of PNAS 2006 volume 103 issue 41] Evolution of sensory complexity recorded in a myxobacterial genome

B.S. Goldman et al.

Proc Natl Acad Sci USA, 2006, 103(41), 15200-15205.

[Cover of European Journal of Cognitive Psychology] Completely ruled out? Using response time data to investigate biconditional artificial grammar learning

J.J. Cock
European Journal of Cognitive Psychology, 2005, 17(6), 770-784.


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