User:Neil Saunders

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Contents

Current Position

I work as a statistical bioinformatician for CSIRO Mathematical and Information Sciences. Before that, I worked in the Kobe Lab at the University of Queensland (OWW pages are here).

Contact Info

Neil Saunders, yesterday
Neil Saunders, yesterday
  • CSIRO Mathematical and Information Sciences - North Ryde
  • Building E6B
  • Macquarie University Campus
  • North Ryde NSW 1670
  • Australia

You can find me at:

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

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 N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, and Wu S. Microblogging the ISMB: a new approach to conference reporting. PLoS Comput Biol 2009 Jan; 5(1) e1000263. doi:10.1371/journal.pcbi.1000263 pmid:19180175. PubMed HubMed [NS24]
  2. Thomas T, Evans FF, Schleheck D, Mai-Prochnow A, Burke C, Penesyan A, Dalisay DS, Stelzer-Braid S, Saunders N, Johnson J, Ferriera S, Kjelleberg S, and Egan S. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One 2008 Sep 24; 3(9) e3252. doi:10.1371/journal.pone.0003252 pmid:18813346. PubMed HubMed [NS23]
  3. 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 pmid:18501020. PubMed HubMed [NS22]
  4. 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 pmid:18477637. PubMed HubMed [NS21]
  5. 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 pmid:18437229. PubMed HubMed [NS20]
  6. 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 pmid:18332103. PubMed HubMed [NS19]
  7. 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 pmid:17971854. PubMed HubMed [NS18]
  8. 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 pmid:16944959. PubMed HubMed [NS17]
  9. 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 pmid:15822924. PubMed HubMed [NS16]
  10. 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+ pmid:15822923. PubMed HubMed [NS15]
  11. 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 pmid:15595725. PubMed HubMed [NS14]
  12. 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 pmid:15638455. PubMed HubMed [NS13]
  13. 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 pmid:15225324. PubMed HubMed [NS12]
  14. 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 pmid:15087319. PubMed HubMed [NS11]
  15. 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 pmid:14579252. PubMed HubMed [NS10]
  16. 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 pmid:12805271. PubMed HubMed [NS09]
  17. 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. pmid:10960107. PubMed HubMed [NS08]
  18. 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. pmid:10708389. PubMed HubMed [NS07]
  19. 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. pmid:10540283. PubMed HubMed [NS06]
  20. 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. pmid:10383987. PubMed HubMed [NS05]
  21. 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 pmid:9199411. PubMed HubMed [NS04]
  22. 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 pmid:9201942. PubMed HubMed [NS03]
  23. 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 pmid:9311786. PubMed HubMed [NS02]
  24. 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. pmid:9353916. PubMed HubMed [NS01]
All Medline abstracts: PubMed HubMed

Not in 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

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