Difference between revisions of "User:Neil Saunders"

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Revision as of 00:40, 20 June 2008

Current Position

I work in the Kobe Lab at the University of Queensland. Our OWW pages are here.

Contact Info

Neil Saunders (an artistic interpretation)

You can find me at:

WordPress | Nature Network | Scintilla | Facebook | Nodalpoint | del.icio.us | LinkedIn

Flickr | last.fm | Technorati | SlideShare | CiteULike | MadSci

Education

  • 1997, D. Phil., University of Oxford
  • 1993, B. Sc., University of Edinburgh

Research interests

  1. Bioinformatics and computational biology
  2. Computational analysis of protein-protein interactions
  3. Microbial genomics
  4. Web 2.0 for scientists: data management, collaboration and communication

Publications

In Press

In PubMed

  1. Saunders NF, Brinkworth RI, Huber T, Kemp BE, and Kobe B. Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. BMC Bioinformatics. 2008 May 26;9:245. DOI:10.1186/1471-2105-9-245 | PubMed ID:18501020 | HubMed [NS22]
  2. Saunders NF and Kobe B. The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. DOI:10.1093/nar/gkn279 | PubMed ID:18477637 | HubMed [NS21]
  3. Frith MC, Saunders NF, Kobe B, and Bailey TL. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol. 2008 May 9;4(4):e1000071. DOI:10.1371/journal.pcbi.1000071 | PubMed ID:18437229 | HubMed [NS20]
  4. Lonic A, Barry EF, Quach C, Kobe B, Saunders N, and Guthridge MA. Fibroblast growth factor receptor 2 phosphorylation on serine 779 couples to 14-3-3 and regulates cell survival and proliferation. Mol Cell Biol. 2008 May;28(10):3372-85. DOI:10.1128/MCB.01837-07 | PubMed ID:18332103 | HubMed [NS19]
  5. Thakur AS, Robin G, Guncar G, Saunders NF, Newman J, Martin JL, and Kobe B. Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents. PLoS One. 2007 Oct 31;2(10):e1091. DOI:10.1371/journal.pone.0001091 | PubMed ID:17971854 | HubMed [NS18]
  6. Saunders NF, Ng C, Raftery M, Guilhaus M, Goodchild A, and Cavicchioli R. Proteomic and computational analysis of secreted proteins with type I signal peptides from the Antarctic archaeon Methanococcoides burtonii. J Proteome Res. 2006 Sep;5(9):2457-64. DOI:10.1021/pr060220x | PubMed ID:16944959 | HubMed [NS17]
  7. Goodchild A, Raftery M, Saunders NF, Guilhaus M, and Cavicchioli R. Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J Proteome Res. 2005 Mar-Apr;4(2):473-80. DOI:10.1021/pr049760p | PubMed ID:15822924 | HubMed [NS16]
  8. Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, and Cavicchioli R. Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res. 2005 Mar-Apr;4(2):464-72. DOI:10.1021/pr049797+ | PubMed ID:15822923 | HubMed [NS15]
  9. Goodchild A, Raftery M, Saunders NF, Guilhaus M, and Cavicchioli R. Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J Proteome Res. 2004 Nov-Dec;3(6):1164-76. DOI:10.1021/pr0498988 | PubMed ID:15595725 | HubMed [NS14]
  10. Roberts TH, Hejgaard J, Saunders NF, Cavicchioli R, and Curmi PM. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J Mol Evol. 2004 Oct;59(4):437-47. DOI:10.1007/s00239-004-2635-6 | PubMed ID:15638455 | HubMed [NS13]
  11. Goodchild A, Saunders NF, Ertan H, Raftery M, Guilhaus M, Curmi PM, and Cavicchioli R. A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Mol Microbiol. 2004 Jul;53(1):309-21. DOI:10.1111/j.1365-2958.2004.04130.x | PubMed ID:15225324 | HubMed [NS12]
  12. Saunders NF, Curmi PM, and Cavicchioli R. An online database for the detection of novel archaeal sequences in human ESTs. Bioinformatics. 2004 Oct 12;20(15):2361-2. DOI:10.1093/bioinformatics/bth249 | PubMed ID:15087319 | HubMed [NS11]
  13. Cavicchioli R, Curmi PM, Saunders N, and Thomas T. Pathogenic archaea: do they exist?. Bioessays. 2003 Nov;25(11):1119-28. DOI:10.1002/bies.10354 | PubMed ID:14579252 | HubMed [NS10]
  14. Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, and Cavicchioli R. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 2003 Jul;13(7):1580-8. DOI:10.1101/gr.1180903 | PubMed ID:12805271 | HubMed [NS09]
  15. Saunders NF, Hornberg JJ, Reijnders WN, Westerhoff HV, de Vries S, and van Spanning RJ. The NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase. J Bacteriol. 2000 Sep;182(18):5211-7. PubMed ID:10960107 | HubMed [NS08]
  16. Saunders NF, Ferguson SJ, and Baker SC. Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63. Microbiology. 2000 Feb;146 ( Pt 2):509-16. DOI:10.1099/00221287-146-2-509 | PubMed ID:10708389 | HubMed [NS07]
  17. Saunders NF, Houben EN, Koefoed S, de Weert S, Reijnders WN, Westerhoff HV, De Boer AP, and Van Spanning RJ. Transcription regulation of the nir gene cluster encoding nitrite reductase of Paracoccus denitrificans involves NNR and NirI, a novel type of membrane protein. Mol Microbiol. 1999 Oct;34(1):24-36. PubMed ID:10540283 | HubMed [NS06]
  18. Van Spanning RJ, Houben E, Reijnders WN, Spiro S, Westerhoff HV, and Saunders N. Nitric oxide is a signal for NNR-mediated transcription activation in Paracoccus denitrificans. J Bacteriol. 1999 Jul;181(13):4129-32. PubMed ID:10383987 | HubMed [NS05]
  19. Baker SC, Saunders NF, Willis AC, Ferguson SJ, Hajdu J, and Fülöp V. Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds. J Mol Biol. 1997 Jun 13;269(3):440-55. DOI:10.1006/jmbi.1997.1070 | PubMed ID:9199411 | HubMed [NS04]
  20. Hu W, Van Driessche G, Devreese B, Goodhew CF, McGinnity DF, Saunders N, Fulop V, Pettigrew GW, and Van Beeumen JJ. Structural characterization of Paracoccus denitrificans cytochrome c peroxidase and assignment of the low and high potential heme sites. Biochemistry. 1997 Jul 1;36(26):7958-66. DOI:10.1021/bi963131e | PubMed ID:9201942 | HubMed [NS03]
  21. Williams PA, Fülöp V, Garman EF, Saunders NF, Ferguson SJ, and Hajdu J. Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Nature. 1997 Sep 25;389(6649):406-12. DOI:10.1038/38775 | PubMed ID:9311786 | HubMed [NS02]
  22. Page MD, Saunders NF, and Ferguson SJ. Disruption of the Pseudomonas aeruginosa dipZ gene, encoding a putative protein-disulfide reductase, leads to partial pleiotropic deficiency in c-type cytochrome biogenesis. Microbiology. 1997 Oct;143 ( Pt 10):3111-22. DOI:10.1099/00221287-143-10-3111 | PubMed ID:9353916 | HubMed [NS01]
All Medline abstracts: PubMed | HubMed

No PubMed

  • Goodhew, C.F., Pettigrew, G.W., Devreese, B., Beeumen, J.V., van Spanning, R.J.M., Baker, S.C., Saunders, N.F.W., Ferguson, S.J. and Thompson, I.P. (1996). The cytochromes c -550 of Paracoccus denitrificans and Thiosphaera pantotropha: a need for re-evaluation of the history of Paracoccus cultures. FEMS Microbiol. Letts. 137: 95-101. Science Direct

Useful links