John Pinney


I am a Royal Society University Research Fellow and a principal investigator in the Theoretical Systems Biology Group. My research focuses on computational systems biology, drawing together information from macromolecular sequences, protein structures, biological networks and other experimental data to study the evolution and function of biological systems.

I am interested in network analysis from a bioinformatic perspective, including the reconstruction and evolutionary modelling of metabolic, protein-protein interaction and gene regulatory networks. The application of these methods to study the various networks of interactions between host and pathogen has great potential for the discovery of new therapeutic targets in diseases such as HIV/AIDS, malaria and tuberculosis.

The analysis of large and complex data sets can produce results that are not easily summarised by conventional means. I am therefore also interested in the development of new information visualization strategies for various types of biological data.

Research in my group is funded by the Royal Society, the BBSRC, TMO Renewables and the Fundação para a Ciência e a Tecnologia, Portugal.

Publications

Derivative processes for modelling metabolic fluxes.

Zurauskienė J, Kirk P, Thorne T, Pinney J, Stumpf M.

Bioinformatics. 2014 Jul 1;30(13):1892-8. doi: 10.1093/bioinformatics/btu069. Epub 2014 Feb 26.

PMID:
24578401
[PubMed - in process]

Free PMC Article

Analysis of metabolic evolution in bacteria using whole-genome metabolic models.

Bryant WA, Faruqi AA, Pinney JW.

J Comput Biol. 2013 Oct;20(10):755-64. doi: 10.1089/cmb.2013.0079. Epub 2013 Aug 31.

PMID:
23992299
[PubMed - indexed for MEDLINE]

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.

Williams KJ, Bryant WA, Jenkins VA, Barton GR, Witney AA, Pinney JW, Robertson BD.

BMC Genomics. 2013 Jul 2;14:436. doi: 10.1186/1471-2164-14-436.

PMID:
23819599
[PubMed - indexed for MEDLINE]

Free PMC Article

Simple topological properties predict functional misannotations in a metabolic network.

Liberal R, Pinney JW.

Bioinformatics. 2013 Jul 1;29(13):i154-61. doi: 10.1093/bioinformatics/btt236.

PMID:
23812979
[PubMed - indexed for MEDLINE]

Free PMC Article

Modular biological function is most effectively captured by combining molecular interaction data types.

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.

PMID:
23658761
[PubMed - indexed for MEDLINE]

Free PMC Article

AMBIENT: Active Modules for Bipartite Networks–using high-throughput transcriptomic data to dissect metabolic response.

Bryant WA, Sternberg MJ, Pinney JW.

BMC Syst Biol. 2013 Mar 25;7:26. doi: 10.1186/1752-0509-7-26.

PMID:
23531303
[PubMed - indexed for MEDLINE]

Free PMC Article

Evolutionary characteristics of bacterial two-component systems.

Sheng X, Huvet M, Pinney JW, Stumpf MP.

Adv Exp Med Biol. 2012;751:121-37. doi: 10.1007/978-1-4614-3567-9_6.

PMID:
22821456
[PubMed - indexed for MEDLINE]

The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function.

Huvet M, Toni T, Sheng X, Thorne T, Jovanovic G, Engl C, Buck M, Pinney JW, Stumpf MP.

Mol Biol Evol. 2011 Mar;28(3):1141-55. doi: 10.1093/molbev/msq301. Epub 2010 Nov 8.

PMID:
21059793
[PubMed - indexed for MEDLINE]

Free PMC Article

Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems.

MacPherson JI, Dickerson JE, Pinney JW, Robertson DL.

PLoS Comput Biol. 2010 Jul 29;6(7):e1000863. doi: 10.1371/journal.pcbi.1000863.

PMID:
20686668
[PubMed - indexed for MEDLINE]

Free PMC Article

The biological context of HIV-1 host interactions reveals subtle insights into a system hijack.

Dickerson JE, Pinney JW, Robertson DL.

BMC Syst Biol. 2010 Jun 7;4:80. doi: 10.1186/1752-0509-4-80.

PMID:
20529270
[PubMed - indexed for MEDLINE]

Free PMC Article

Low-complexity regions within protein sequences have position-dependent roles.

Coletta A, Pinney JW, Solís DY, Marsh J, Pettifer SR, Attwood TK.

BMC Syst Biol. 2010 Apr 13;4:43. doi: 10.1186/1752-0509-4-43.

PMID:
20385029
[PubMed - indexed for MEDLINE]

Free PMC Article

From evidence to inference: probing the evolution of protein interaction networks.

Ratmann O, Wiuf C, Pinney JW.

HFSP J. 2009 Oct;3(5):290-306. doi: 10.2976/1.3167215. Epub 2009 Oct 19.

PMID:
20357887
[PubMed]

Free PMC Article

Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

Humphries JD, Byron A, Bass MD, Craig SE, Pinney JW, Knight D, Humphries MJ.

Sci Signal. 2009 Sep 8;2(87):ra51. doi: 10.1126/scisignal.2000396.

PMID:
19738201
[PubMed - indexed for MEDLINE]

Free PMC Article

Making the right connections: biological networks in the light of evolution.

Knight CG, Pinney JW.

Bioessays. 2009 Oct;31(10):1080-90. doi: 10.1002/bies.200900043.

PMID:
19722181
[PubMed - indexed for MEDLINE]

Free PMC Article

Evolving proteins at Darwin’s bicentenary.

Pinney JW, Stumpf MP.

Genome Biol. 2009;10(4):307. doi: 10.1186/gb-2009-10-4-307. Epub 2009 Apr 17.

PMID:
19435482
[PubMed - indexed for MEDLINE]

Free PMC Article

Back to basics–how the evolution of the extracellular matrix underpinned vertebrate evolution.

Huxley-Jones J, Pinney JW, Archer J, Robertson DL, Boot-Handford RP.

Int J Exp Pathol. 2009 Apr;90(2):95-100. doi: 10.1111/j.1365-2613.2008.00637.x. Review.

PMID:
19335547
[PubMed - indexed for MEDLINE]

Free PMC Article

JNets: exploring networks by integrating annotation.

Macpherson JI, Pinney JW, Robertson DL.

BMC Bioinformatics. 2009 Mar 26;10:95. doi: 10.1186/1471-2105-10-95.

PMID:
19323810
[PubMed - indexed for MEDLINE]

Free PMC Article

A unique dual activity amino acid hydroxylase in Toxoplasma gondii.

Gaskell EA, Smith JE, Pinney JW, Westhead DR, McConkey GA.

PLoS One. 2009;4(3):e4801. doi: 10.1371/journal.pone.0004801. Epub 2009 Mar 11.

PMID:
19277211
[PubMed - indexed for MEDLINE]

Free PMC Article

HIV-host interactions: a map of viral perturbation of the host system.

Pinney JW, Dickerson JE, Fu W, Sanders-Beer BE, Ptak RG, Robertson DL.

AIDS. 2009 Mar 13;23(5):549-54. doi: 10.1097/QAD.0b013e328325a495. No abstract available.

PMID:
19262354
[PubMed - indexed for MEDLINE]

Cataloguing the HIV type 1 human protein interaction network.

Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL, Rozanov MN, Katz KS, Maglott DR, Pruitt KD, Dieffenbach CW.

AIDS Res Hum Retroviruses. 2008 Dec;24(12):1497-502. doi: 10.1089/aid.2008.0113. Review.

PMID:
19025396
[PubMed - indexed for MEDLINE]

Free PMC Article

Identifying the important HIV-1 recombination breakpoints.

Archer J, Pinney JW, Fan J, Simon-Loriere E, Arts EJ, Negroni M, Robertson DL.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000178. doi: 10.1371/journal.pcbi.1000178.

PMID:
18787691
[PubMed - indexed for MEDLINE]

Free PMC Article

Methodology capture: discriminating between the “best” and the rest of community practice.

Eales JM, Pinney JW, Stevens RD, Robertson DL.

BMC Bioinformatics. 2008 Sep 1;9:359. doi: 10.1186/1471-2105-9-359.

PMID:
18761740
[PubMed - indexed for MEDLINE]

Free PMC Article

Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.

Adamo A, Pinney JW, Kunova A, Westhead DR, Meyer P.

PLoS One. 2008 Aug 6;3(8):e2889. doi: 10.1371/journal.pone.0002889.

PMID:
18682831
[PubMed - indexed for MEDLINE]

Free PMC Article

Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships.

Bland ND, Pinney JW, Thomas JE, Turner AJ, Isaac RE.

BMC Evol Biol. 2008 Jan 23;8:16. doi: 10.1186/1471-2148-8-16.

PMID:
18215274
[PubMed - indexed for MEDLINE]

Free PMC Article

Protein-protein interaction networks and biology–what’s the connection?

Hakes L, Pinney JW, Robertson DL, Lovell SC.

Nat Biotechnol. 2008 Jan;26(1):69-72. doi: 10.1038/nbt0108-69. No abstract available.

PMID:
18183023
[PubMed - indexed for MEDLINE]

Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.

Pinney JW, Amoutzias GD, Rattray M, Robertson DL.

Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20449-53. Epub 2007 Dec 12.

PMID:
18077348
[PubMed - indexed for MEDLINE]

Free PMC Article

Metabolic reconstruction and analysis for parasite genomes.

Pinney JW, Papp B, Hyland C, Wambua L, Westhead DR, McConkey GA.

Trends Parasitol. 2007 Nov;23(11):548-54. Epub 2007 Oct 22. Review.

PMID:
17950669
[PubMed - indexed for MEDLINE]

All duplicates are not equal: the difference between small-scale and genome duplication.

Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL.

Genome Biol. 2007;8(10):R209.

PMID:
17916239
[PubMed - indexed for MEDLINE]

Free PMC Article

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network.

Holden BJ, Pinney JW, Lovell SC, Amoutzias GD, Robertson DL.

BMC Bioinformatics. 2007 Aug 6;8:289.

PMID:
17683601
[PubMed - indexed for MEDLINE]

Free PMC Article

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

Hyland C, Pinney JW, McConkey GA, Westhead DR.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W725-8.

PMID:
16845107
[PubMed - indexed for MEDLINE]

Free PMC Article

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis.

Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9.

PMID:
16845059
[PubMed - indexed for MEDLINE]

Free PMC Article

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.

Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WG, Gilmartin PM, Westhead DR.

Plant J. 2006 Apr;46(2):336-48.

PMID:
16623895
[PubMed - indexed for MEDLINE]

Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus.

Taib M, Pinney JW, Westhead DR, McDowall KJ, Adams DJ.

Arch Microbiol. 2005 Oct;184(1):78-81. Epub 2005 Nov 3.

PMID:
16096835
[PubMed - indexed for MEDLINE]

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.

Pinney JW, Shirley MW, McConkey GA, Westhead DR.

Nucleic Acids Res. 2005 Mar 3;33(4):1399-409. Print 2005.

PMID:
15745999
[PubMed - indexed for MEDLINE]

Free PMC Article

Annotating the Plasmodium genome and the enigma of the shikimate pathway.

McConkey GA, Pinney JW, Westhead DR, Plueckhahn K, Fitzpatrick TB, Macheroux P, Kappes B.

Trends Parasitol. 2004 Feb;20(2):60-5. Review.

PMID:
14747018
[PubMed - indexed for MEDLINE]

Petri Net representations in systems biology.

Pinney JW, Westhead DR, McConkey GA.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1513-5. Review.

PMID:
14641101
[PubMed - indexed for MEDLINE]

Book Chapters

Host-Pathogen Systems Biology

Pinney JW
Handbook of Statistical Systems Biology (2011) Michael Stumpf, David J. Balding, Mark Girolami (eds)