Publications

(Contributions from lab members, past and present, in bold)

2012

  1. Reid, A.J., Vermont, S.J., Cotton, J.A., Harris, D., Hill-Cawthorne, G.A., Könen-Waisman, S., Latham, S., Mourier, T., Norton, R., Quail, M.A., Sanders, M., Shanmugam, D., Sohal, A., Wasmuth, J.D., Brunk, B., Grigg, M.E., Howard, J.C., Parkinson, J., Roos, D.S., Trees, A.J., Berriman, M., Pain, A. and Wastling, J.M. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens. In press.
  2. Song, H. and Parkinson, J. (2012) Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures. PLoS Computational Biol. In press.
  3. Cromar, G.L., Xiong, X., Chautard, E., Ricard-Blum, S. and Parkinson, J. (2012) Towards a systems level view of the ECM and related proteins: A framework for the systematic definition and analysis of biological systems. Proteins. In press. DOI: 10.1002/prot.24036

2011

  1. Babu, M., Díaz-Mejía, J.J., Vlasblom, J., Gagarinova, A., Phanse, S., Graham, C., Arnold, R., Yousif, F., Ding, H., Xiong, X., Nazarians-Armavil, A., Alamgir, M., Ali, M., Pogoutse, O., Pe′er, A., Parkinson, J., Golshani, A., Whitfield, C., Wodak, S.J., Moreno-Hagelsieb, G., Greenblatt, J.F. and Emil, A. (2011) Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways. PLoS Genetics. 7(11): e1002377.
  2. Kahr, W.H.A., Hinckley, J., Li, L., Schwertz, H., Christensen, H., Rowley, J.W., Pluthero, F.G., Urban, D., Fabbro, S., Nixon, B., Gadzinski, R., Storck, M., Wang, K., Ryu, G-Y., Jobe, S.M., Schutte, B.C., Moseley, J., Loughran, N.B., Parkinson, J., Weyrich, A.S., Di Paola, J. (2011) Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome. Nature Genetics. 43(8): 738-40.
  3. Xiong, X., Song, H., On, T., Lochovsky, L., Provart, N. and Parkinson, J. (2011) Phylopro: A web based tool for the generation and visualization of phylogenetic profiles across Eukarya. Bioinformatics. 27(6):877-8
  4. Turinsky, A.L., Turner, B., Borja, R.C., Gleeson, J.A., Heath, M., Pu, S., Switzer, T., Dong, D., Gong, Y., On, T., Xiong, X., Emili, A., Greenblatt, J., Parkinson, J., Zhang, Z., Wodak, S.J. (2011) DAnCER: Disease-Annotated Chromatin Epigenetics Resource. Nucleic Acids Res. 39:D889-94.
  5. Hung, S. and Parkinson, J. (2011) Post-genomics Resources and Tools for Studying Apicomplexan Metabolism. Trends in Parasitology. 27(3):131-40..

2010

  1. Pu, S., Turinsky, A.L., Vlasblom, J., On, T., Xiong, X., Emili, A., Zhang, Z., Greenblatt, J., Parkinson, J., and Wodak, S.J. (2010) Expanding the Landscape of Chromatin Modification (CM)-Related Functional Domains and Genes in Human. PloS ONE 5(11):e14122
  2. Yu, Z., Reichheld, S.E., Savchenko, A., Parkinson, J. and Davidson, A.R. (2010) A Comprehensive Analysis of Structural and Sequence Conservation in the TetR Family Transcriptional Regulators. J. Mol. Biol. 400: 847-864
  3. Hung, S., Wasmuth, J., Sanford, C. and Parkinson, J. (2010) DETECT - A Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum. Bioinformatics. 26: 1690-1698
  4. On, T., Xiong, X., Pu, S., Turinsky, A., Gong, Y., Emili, A., Zhang, Z., Greenblatt, J., Wodak, SJ. and Parkinson, J. (2010) The evolutionary landscape of the chromatin modification machinery. Proteins. 78:2075-2089
  5. Chong, Y., Gidda, S., Sanford, C., Parkinson, J., Mullen, R. and Goring, D. (2010) Characterisation of the Arabidopsis exocyst complex gene families by phylogenetic, expression profiling, and subcellular localisation studies. New Phytologist. 185: 401-19.

2009

  1. Peregrin-Alvarez, J.M., Xiong, X., Su, C. and Parkinson, J. (2009) The modular organization of protein interactions in Escherichia coli. PLoS Computational Biol. 5(10): e1000523.
  2. Persaud, A., Amsen, E.M.,Xiong, X., Wasmuth, J.,Saadon, Z., Fladd, C., Parkinson, J., and Rotin, D. (2009) Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Molecular Systems Biology. 5:333
  3. González, S., Fló, M., Margenat, M., Durán, R., González-Sapienza, G., Graña, M., Parkinson, J., Maizels, R., Salinas, G., Alvarez, B. and Fernandez, C. (2009) A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk. PLoS ONE. 4: e7009.
  4. Peregrin-Alvarez, J.M., Sanford, C and Parkinson, J. (2009) The conservation and evolutionary modularity of metabolism. Genome Biology. 10:R63
  5. Wasmuth, J., Daub, J., Peregrin-Alvarez, J.M.,Finney, C.A.M. and Parkinson, J. (2009) The origins of apicomplexan sequence innovation. Genome Research. 19:1202-1213.
  6. Parkinson, J. and Blaxter, M. (2009) Expressed sequence tags: an overview. Methods Mol Biol. 533:1-12.
  7. Peregrin-Alvarez, J.M. and Parkinson, J. (2009) Phylogenomic Analysis of EST Datasets. Methods Mol Biol. 533:257-276.

2008

  1. Aznarez, I., Barash, Y., Shai, O., He, D., Zielenski, J., Tsui, L-C., Parkinson, J., Frey, B.J., Rommens, J.M. and Blencowe, B.J. (2008) A systematic analysis of intronic sequences downstream of 5´ splice sites reveals a widespread role for U-rich motifs and TIA-1/TIAR proteins in alternative splicing regulation. Genome Research. 18: 1247-1258.
  2. He, D. and Parkinson, J. (2008) SubSeqer: A graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. Bioinformatics. 24: 1016-17.
  3. Su, C., Peregrin-Alvarez, J.M., Butland, G., Phanse, S., Fong, V., Emili, A. and Parkinson, J. (2008) Bacteriome.org – An integrated protein interaction database for E. coli. Nucleic Acids Research. 36: D632-36

2007

  1. Peregrin-Alvarez, J.M. and Parkinson, J. (2007) The Global Landscape of Sequence Diversity. Genome Biology. 8:R238
  2. Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J.E., Delcher, A.L., Guiliano, D.B., Miranda-Saavedra, D., Angiuoli, S.V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N.M., Wortman, J.R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S.L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G.J., Carlow, C.K.S., Crawford, M.J., Daub, J., Dimmic, M.W., Estes, C.F., Foster, J.M., Ganatra, M., Gregory, W.F., Johnson, N.M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B-W., Li, W., Lindblom, T.H., Lustigman, S., Ma, D., Maina, C., Martin, D., McCarter, J.P., McReynolds, L., Mitreva, M., Nutman, T.B., Parkinson, J., Peregrín-Alvarez, J.M., Poole, C., Ren, Q., Saunders, L., Sluder, A.E., Smith, K., Stanke, M., Unnasch, T.R., Ware, J., Wei, A.D., Weil, G., Williams, D.J., Zhang, Y., Williams, S.A., Fraser-Liggett, C., Slatko, B., Blaxter, M.L. and Scott, A.L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science. 317(5845):1756-60.
  3. He, D., Chung, M., Chan, E., Alleyne, T., Ha, K.C.H., Miao, M., Stahl, R.J., Keeley, F.W. and Parkinson, J. (2007) Comparative genomics of elastin: Sequence analysis of a highly repetitive protein. Matrix Biology. 26(7):524-540
  4. Gupta, R., Kus, B., Fladd, C., Wasmuth, J., Tonikian, R., Sidhu, S., Krogan, N., Parkinson, J. and Rotin, D. (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Molecular Systems Biology. 3:116

2006

  1. Sanford, C.*, Yip, M.L.K.*, White, C. and Parkinson, J. (2006) Cell++ - simulating biochemical pathways within a spatial context. Bioinformatics. 22(23):2918-25.
  2. Chung, M.I.S., Miao, M., Stahl, R.J., Chan, E., Parkinson, J. and Keeley, F.W. (2006) Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: clues to the evolutionary history of elastins. Matrix Biology. 25(8):492-504.
  3. Mitreva, M., Wendl, M.C., Martin, J., Wylie, T., Yin, Y., Larson, A., Parkinson, J., Waterston, R.H. and McCarter, J.P. (2006) Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biology 7, R75.
  4. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., Punna T., Peregrin-Alvarez J.M., Shales M., Zhang X., Davey M., Robinson M.D., Paccanaro A., Bray J.E., Sheung A., Beattie B., Richards D.P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M.M., Vlasblom J., Wu S., Orsi C., Collins S.R., Chandran S., Haw R., Rilstone J.J., Gandi K., Thompson N.J., Musso G., St Onge P., Ghanny S., Lam M.H., Butland G., Altaf-Ul A.M., Kanaya S., Shilatifard A., O'shea E., Weissman J.S., Ingles C.J., Hughes T.R., Parkinson J., Gerstein M., Wodak S.J., Emili A., Greenblatt J.F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440, 637-643.

2005

  1. Soares D.C., Gerloff D.L., Syme N.R., Coulson A.F., Parkinson J., Barlow P.N. (2005) Large-scale modelling as a route to multiple surface comparisons of the CCP module family. Protein Eng Des Sel. 18, 379-88.
  2. Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., Emili, A. (2005) Interaction Network Containing Conserved and Essential Protein Complexes in Escherichia coli. Nature. 433, 531-537.
  3. Peregrin-Alvarez, J., Yam, A., Sivakumar, G., Parkinson, J. (2005) PartiGeneDB - Collating partial genomes. Nucleic Acids Research. 33, D303-307
  4. Gordon, R., Parkinson, J., (2005) Potential Roles for Diatomists in Nanotechnology. J. NanoSci. Nanotech. 5, 35-40.

2004

  1. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R.H., McCarter, J.P., Blaxter, M.L., (2004) A transcriptomic analysis of the phylum Nematoda. Nature Genetics. 36, 1259-1267.
  2. Parkinson, J., Anthony, A., Wasmuth, J., Hedley, B.A. Blaxter, M. (2004) PartiGene - Constructing Partial Genomes. Bioinformatics 20, 1398-1404.
  3. Harcus, Y.M., Parkinson, J., Fernandez, C., Daub, J., Selkirk, M.E., Blaxter, M.L., Maizels, R.M. (2004) Signal sequence analysis of ESTs from the nematode Nippostrongylus brasiliensis and the evolution of parasite secreted proteins. Genome Biology. 5, R39.
  4. Parkinson, J., Whitton, C., Schmid, R., Thomson, M., Blaxter, M. (2004) NEMBASE - a resource for parasitic nematode ESTs. Nucleic Acids Research, 32, D427-D430.
  5. Parkinson, J., Blaxter, M. (2004) Expressed sequence tags: analysis and annotation. Methods Mol Biol. 270, 93-126.

2003

  1. Sturzenbaum, S.R., Parkinson, J., Blaxter, M., Morgan, A.J., Kille, P., Georgiev, O. (2003) The earthworm EST sequencing project. Pedobiologia. 47, 447-451.
  2. Parkinson, J., Mitreva, M., Hall, N., Blaxter, M., McCarter, J. (2003) 400,000 Nematode ESTs on the Net. TRENDS in Parasitol. 19, 283-286.
  3. Kenyon, F., Welsh, M., Parkinson, J., Whitton, C., Blaxter, M.L., Knox, D.P. (2003) Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis allergens, proteinases and free radical scavengers. Parasitology, 126, 451-460.
  4. Gregory, W., Parkinson, J. (2003) Caenorhabditis elegans - Entering the Post-Genomic Era. Comp. Funct. Genom. 4, 194-202.
  5. Parkinson, J. Blaxter, M.L. (2003) SimiTri - Visualising similarity relationships for groups of sequences. Bioinformatics. 19, 390-395.

2002

  1. Parkinson J., Guiliano D.B., Blaxter M. (2002) Making sense of EST sequences by CLOBBing them. BMC Bioinformatics. 3, 31.
  2. Loke P., Nair M.G., Parkinson J., Guiliano D., Blaxter M., Allen J.E. (2002) IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype. BMC Immunol. 3, 7.
  3. Parkinson, J., Blaxter, M. (2002) NEMBASE: Dealing with fragmented genomes. Comp. Biochem. Physiol. A. 132, S90-S91.
  4. Blaxter, M., Daub, J., Guiliano, D., Parkinson, J., Whitton, C., (2002) The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans. Roy. Soc. Trop. Med. Hyg. 96, 7-17.

Pre-2002

  1. Parkinson, J., Whitton, C., Guiliano, D., Daub, J., Blaxter, M. (2001) 200 000 nematode expressed sequence tags on the net. TRENDS in Parasitol. 17, 394-396.
  2. Loukas, A., Hintz, M., Linder, D., Mullin, N.P., Parkinson, J., Tetteh, K.K., Maizels, R.M. (2000) A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs. J. Biol. Chem. 275, 39600-39607.
  3. Liszewski, M.K., Leung, M., Cui, W., Subramanian, V.B., Parkinson, J., Barlow, P.N., Manchester, M., Atkinson, J.P (2000) Dissecting sites important for complement regulatory activity in membrane cofactor protein (MCP; CD46). J. Biol. Chem. 275, 37692-37701.
  4. Smith, S.A., Mullin, N.P., Parkinson, J., Shchelkunov, S.N., Totmenin, A.V., Loparev, V.N., Srisatjaluk, R., Reynolds, D.N., Keeling, K.L., Justus, D.E., Barlow, P.N., Kotwal, G.J. (2000) Conserved surface-exposed K/R-X-K/R motifs and net positive charge on poxvirus complement control proteins serve as putative heparin binding sites and contribute to inhibition of molecular interactions with human endothelial cells: a novel mechanism for evasion of host defense. J. Virol. 74, 5659-5666.
  5. Kirkitadze, M.D., Henderson, C., Price, N.C., Kelly, S.M., Mullin, N.P., Parkinson J., Dryden, D.T., Barlow, P.N. (1999) Central modules of the vaccinia virus complement control protein are not in extensive contact. Biochem J. 344, 167-175.
  6. Parkinson, J., Brechet, Y. & Gordon, R. (1999) Centric Diatom Morphogenesis : A Model Based on a DLA Algorithm Investigating the Potential Role of Microtubules. Biochim. Biophys. Acta. 1452, 89-102.
  7. Parkinson, J. & Gordon, R. (1999) Beyond micromaching : The potential of diatoms. TRENDS in Biotech. 17, 190-196.
  8. Parkinson, J., Brass, A., Canova, G. & Brechet, Y. (1997) Mechanical properties of simulated collagen fibrils. J. Biomech. 30, 549-554.
  9. Mack, D., Nishimura, K., Dennehey, B. K., Arbogast, T., Parkinson, J., Toh-E, A., Pringle, J. R., Bender, A. & Matsui, Y. (1996). Identification of the bud emergence gene BEM4 and its interactions with Rho-type GTPases in Saccharomyces cerevsiae. Mol. Cell. Biol. 16, 4387-4395.
  10. Parkinson, J., Kadler, K. E. & Brass, A. (1995). A model of type I collagen fibrillogenesis based on diffusion limited aggregation. J. Biol. Sys. 3, 1033-1039.
  11. Parkinson, J., Kadler, K. E. & Brass, A. (1995). Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation. J. Mol. Biol. 247, 823-831.
  12. Parkinson, J., Kadler, K. E. & Brass, A. (1994). Self-assembly of rod-like particles in two dimensions : a simple model of collagen fibrillogenesis. Phys. Rev. E 50, 2963-2966.