Publications

Journal articles

  1. Mitchell, S.M., Ross, J.P., Drew, H.R., Ho, T., Brown, G.S., Saunders, N.F.W., Duesing, K.R., Buckley, M.J., Dunne, R., Beetson, I., Rand, K.N., McEvoy, A., Thomas, M.L., Baker, R.T., Wattchow, D.A., Young, G.P., Lockett, T.J., Pedersen, S.K., LaPointe L.C. and Molloy, P.L. (2014). A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 14:54. [Open Access]
  2. Neylon, C., Aerts, J., Brown, C.T., Lemire, D., Millman, J., Murray-Rust, P., Perez, F., Saunders, N., Smith, A., Varoquaux, G. and Willighagen, W. (2012). Changing computational research. The challenges ahead. Source Code for Biology and Medicine 7:2. [Open Access | PubMed]
  3. Badge, J.L., Saunders, N.F.W. and Cann, A.J. (2012). Beyond marks: new tools to visualise student engagement via social networks. Research in Learning Technology 20: 16283. [Open Access]
  4. Maco, B., Ross I.L., Landsberg, M., Mouradov, D., Saunders, N.F.W., Hankamer, B. and Kobe, B. (2011). Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm. Molecular & Cellular Proteomics: in press – [online]
  5. Marfori, M., Mynott, A., Ellis, J.J., Mehdid, A.M., Saunders, N.F.W., Curmi, P.M., Forwood, J.K., Bodén, M. and Kobe, B. (2010). Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research: in press – corrected proof. [proof] | [PubMed]
  6. Saunders, N., Beltrão, P., Jensen, LJ, Jurczak, D., Krause, R., Kuhn, M. and Wu, S. (2009). Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Comput Biol 5(1): e1000263. [Open Access] | [PubMed]
  7. Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008). Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment. PLoS ONE 3:e3252. [Open Access]
  8. Saunders, N.F.W., Brinkworth, R.I., Huber, T., Kemp, B.E. and Kobe, B. (2008). Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. BMC Bioinformatics 9:245. [Open Access] | [PubMed]
  9. Saunders, N.F.W. and Kobe, B. (2008). The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. Nucleic Acids Res. 36:W286. [Open Access] | [PubMed]
  10. Lonic, A., Barry E.F., Quach, C., Kobe, B., Saunders, N. and Guthridge, M.A. (2008). FGFR2 phosphorylation on Serine 779 couples to 14-3-3 and regulates cell survival and proliferation. Mol. Cell. Biol. 28:3372. [PubMed].
  11. Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008). Discovering Sequence Motifs with Arbitrary Insertions and Deletions. PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed]
  12. Thakur, A.S., Robin, G., Guncar, G., Saunders, N.F.W., Newman, J., Martin, J.L. and Kobe, B. (2007). Improved Success of Protein Crystallization Sparse Matrix Screening with Heterogeneous Nucleating Agents. PLoS ONE 2:e1091. [Open Access] | [PubMed]
  13. Saunders, N.F.W., Ng, C., Raftery, M., Guilhaus, M., Goodchild, A. and Cavicchioli, R. (2006). Proteomic and Computational Analysis of Secreted Proteins with Type I Signal Peptides from the Antarctic Archaeon Methanococcoides burtonii. J. Prot. Res. 5: 2457 -2464. [PubMed]
  14. Goodchild, A., Raftery, M., Saunders, N.F.W., Guilhaus, M. and Cavicchioli, R. (2005). Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J. Prot. Res. 4: 473-480. [PubMed]
  15. Saunders, N.F.W, Goodchild, A., Raftery, M., Guilhaus, M., Curmi, P.M.G and Cavicchioli, R. (2005). Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J. Prot. Res. 4: 464-472. [PubMed]
  16. Goodchild, A., Raftery, M., Saunders, N.F.W., Guilhaus, M. and Cavicchioli, R. (2004). The biology of the cold-adapted Archaeon, Methanococcoides burtonii, determined by proteomics using liquid chromatography tandem mass spectrometry. J. Prot. Res. 3: 1164-1176. [Pubmed]
  17. Roberts, T.H., Hejgaard, J. Saunders, N.F.W., Cavicchioli, R. and Curmi, P.M.G. (2004). Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J. Mol. Evol. 59: 437-447. [PubMed]
  18. Goodchild, A., Saunders, N.F.W., Ertan, H., Raftery, M., Guilhaus, M., Curmi, P.M.G. and Cavicchioli, R. (2004). A Proteomic Determination of Cold Adaptation in the Antarctic Archaeon, Methanococcoides burtonii. Mol. Microbiol. 53: 309-321. [PubMed]
  19. Saunders, N.F.W., Curmi, P.M.G. and Cavicchioli, R. (2004). An online database for the detection of novel archaeal sequences in human ESTs. Bioinformatics 20: 2361-2362. [PubMed]
  20. Cavicchioli, R., Curmi, P.M.G., Saunders, N.F.W. and Thomas, T. (2003). Pathogenic archaea: do they exist? Bioessays 25: 1119-1128. [PubMed]
  21. Saunders, N.F.W., Thomas, T., Curmi, P.M.G., Mattick, J.S., Kuczek, E., Slade, R., Davis, J., Franzmann, P., 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. (2003). Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea, Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13: 1580-1588. [PubMed]
  22. Saunders, N.F.W., Hornberg, J.J., Reijnders, W.N.M., Westerhoff, H.V., de Vries,S. and van Spanning, R.J.M. (2000). The NosX and NirX Proteins of Paracoccus denitrificans are functional homologues: Their Role in Maturation of Nitrous Oxide Reductase. J. Bacteriol 182: 5211-5217. [PubMed]
  23. Saunders, N.F.W., Ferguson, S.J. and Baker, S.C. (2000). Transcriptional analysis of the nirS gene, coding for cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63. Microbiology 146: 509-516. [PubMed]
  24. Saunders, N., van Spanning, R.J.M., Houben, E., Koefoed, S., de Weert, S., Reijnders, W.N.M., Westerhoff, H.V. and de Boer, A.P.N. (1999). Transcription regulation of the nir gene cluster involves NNR and NirI, a novel type of membrane protein. Mol. Microbiol. 34: 24-36. [PubMed]
  25. Van Spanning, R.J.M., Houben, E., Reijnders, W.N.M., Spiro, S., Westerhoff, H.V. and Saunders, N. (1999). Nitric Oxide is a signal for NNR-mediated transcription activation in Paracoccus denitrificans. J. Bacteriol. 181: 4129-4132. [PubMed]
  26. Baker, S.C., Saunders, N.F.W., Willis, A.C., Ferguson, S.J., Hajdu, J. and Fülöp, V. (1997). Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds. J. Mol. Biol. 269: 440-455. [PubMed]
  27. Hu, W., Van Driessche, G., Devreese, B., Goodhew, C.F., McGinnity, D.F., Saunders, N., Fülöp, V., Pettigrew, G.W. and Van Beeumen, J.J. (1997). Structural characterization of Paracoccus denitrificans cytochrome c peroxidase and assignment of the low and high potential heme sites. Biochemistry 36: 7958-7966. [PubMed]
  28. Williams, P.A., Fülöp, V., Garman, E.F., Saunders, N.F.W., Ferguson, S.J. and Hajdu, J. (1997). Haem-ligand switching during catalysis in crystals of a nitrogen cycle enzyme. Nature 389: 406-412. [PubMed]
  29. Page, M.D., Saunders, N.F.W. and Ferguson, S.J. (1997). Disruption of the Pseudomonas aeruginosa dipZ gene, encoding a putative protein-disulfide reductase, leads to partial pleiotropic deficiency in c-type cytochrome biogenesis. Microbiology 143: 3111-3122. [PubMed]
  30. 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]

Books and book chapters

  1. Saunders, N.F.W., Brinkworth, R.I., Kemp, B.E. and Kobe, B. (2010). Substrates of Cyclic Nucleotide-Dependent Protein Kinases. In: Handbook of Cell Signalling (Bradshaw, R.A., Dennis, E., eds.). Academic Press San Diego, 182:1489-1495. [DOI]
  2. Cavicchioli, R., Saunders, N. and Thomas, T. (2001). Cold shock response in microorganisms. In: Extremophiles: Basic Concepts, (Gerday, C. and Glansdorff, N., eds.). UNESCO Encyclopedia of Life Support Systems. [EOLSS]

Conference talks

  1. Saunders, N. (2014). Learning from complete strangers: social networking for bioinformaticians. Bioinformatics Focus on Analytical Methods 2014, Melbourne, Australia, March 28 2014.
  2. Saunders, N. (2014). SQL, noSQL or no database at all? Are databases still a core skill? Bioinformatics Focus on Analytical Methods 2014, Melbourne, Australia, March 27 2014.
  3. Saunders, N. (2013). Version control in bioinformatics: our experience using Git. Bioinformatics Focus on Analytical Methods 2013, Melbourne, Australia, March 21-22 2013.
  4. Saunders, N.F.W., Huber, T. and Kobe, B. (2008). Using structural information to predict protein-protein interaction and enyzme specificity. ComBio 2008, Canberra, Australia, 21-25 September 2008.
  5. Saunders, N.F.W., Brinkworth, R.I., Huber, T. and Kobe, B. (2007). Predikin and PredikinDB: tools to predict protein kinase peptide specificity. Bioinformatics Australia 2007, Brisbane, Australia, 23-24 October 2007.
  6. Saunders, N.F.W. (2003). BioPerl in 2003: a users perspective. Bioinformatics Open Source Conference 2003, Brisbane, Australia, 27-28 June 2003.
  7. Saunders, N.F.W. (2003). Microbial genomes. 7th Australasian Gene Mapping Workshop, The University of New South Wales, 10-12 July 2002.

Conference posters

  1. Saunders, N.F.W. and Kobe, B. (2008). Kinome Browser: a graphical tool for the exploration of kinomes. 16th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2008, Toronto, Canada, 19-23 July 2008.
  2. Saunders, N.F.W., Brinkworth, R.I., Huber, T. and Kobe, B. (2007). Predikin and PredikinDB: computational tools for the prediction of protein kinase substrate specificity. ComBio 2007, Sydney, Australia, 22-26 September 2007.
  3. Saunders, N.F.W., Brinkworth, R.I., Huber, T. and Kobe, B. (2006). Prediction of protein kinase substrates using sequence-structure information. ComBio 2006, Brisbane, Australia, 24-28 September 2006.
  4. Saunders, N.F.W., Curmi, P.M.G., Thomas, T. and Cavicchioli, R. (2003). Pathogenic archaea: do they exist? Intelligent Systems in Molecular Biology, Brisbane, Australia, 29 June – 3 July 2003.
  5. Neilan, B.A. and Saunders, N.F.W. (2001). Junk DNA in microbial genomes: microcystin synthetase and other large clusters encoding secondary metabolites. 2nd Annual Symposium on functional genomics, gene expression and proteomics, University of Otago, New Zealand. 28-29 November 2001.
  6. Cavicchioli, R., Thomas T., Saunders, N., Curmi, P., Kuczek, E., Slade, R., Davis, J. and Mattick, J. (2000). Towards the genome of the psychrophilic archaeon Methanogenium frigidum. 8th International Conference on Small Genomes. 24-28 September 2000, Lake Arrowhead, CA.
  7. Baker, S.C., Saunders, N., Fülöp, V., Hajdu, J. and Ferguson, S.J. (1995). The structure of cd1 nitrite reductase and analysis of the nirS gene of the denitrifying bacterium Thiosphaera pantotropha. Beijerinck Centennial Conference on Microbial Physiology and Gene Regulation: Emerging Principles and Applications. 10-14 December 1995, The Hague, The Netherlands.

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