Dr Sarah Boyd - Researcher Profile

Biography

Sarah works in the School of Mathematical Sciences at Monash University as a Research Fellow.

 

Sarah’s research areas of interest are:

 

• Computational biology
• Bayesian statistics
• Functional genomics

Keywords

computational biology, Bayesian statistics, functional genomics

Qualifications

PHD

Institution: Monash University

Year awarded: 2005

BACH OF SCI(HONS)

Institution: Monash University

Year awarded: 2001

Publications

Journal Articles

Keith, J.M., Davey, C.M., Boyd, S.E., 2012, A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard, BMC Bioinformatics [P], vol 13, BioMed Central, London UK, pp. 1-11.

Boyd, S., Nair, B., Ng, S., Keith, J., Orian, J., 2012, Computational characterization of 3' slice variants in the GFAP isoform family, PLoS ONE [P], vol 7, issue 3, Public Library of Science, USA, pp. 1-13.

van Iersel, M.P., Villeger, A., Czauderna, T., Boyd, S.E., Bergmann, F.T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M.I., Mi, H., Moodie, S., Kitano, H., Le Novere, N., Schreiber, F., 2012, Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics [P], vol 28, issue 15, Oxford University Press, Oxford UK, pp. 2016-2021.

Song, J., Tan, H., Boyd, S.E., Shen, H., Mahmood, K., Webb, G., Akutsu, T., Whisstock, J., Pike, R., 2011, Bioinformatic approaches for predicting substrates of proteases, Journal of Bioinformatics and Computational Biology [P], vol 9, issue 1, Imperial College Press, UK, pp. 149-178.

Ng, N., Pierce, M.J., Webb, G., Ratnikov, B., Wijeyewickrema, L.C., Duncan, R., Robertson, A.L., Bottomley, S.P., Boyd, S.E., Pike, R.N., 2011, Discovery of amino acid motifs for thrombin cleavage and validation using a model substrate, Biochemistry [P], vol 50, issue 48, American Chemical Society, USA, pp. 10499-10507.

Boyd, S.E., Keith, J., Traven, A., Beilharz, T., 2011, Probing connectivity between transcriptional and post-transcriptional gene networks, Microbiology Australia [P], vol 32, issue 4, The Australian Society for Microbiology Inc, Australia, pp. 166-168.

He, C., Nora, G., Schneider, E., Kerr, I., Hansell, E., Hirata, K., Gonzalez, D., Sajid, M., Boyd, S.E., Hurz, P., Cobo, E., Le, C., Liu, W., Eckmann, L., Dorrestein, P., Houpt, E., Brinen, L., Craik, C., Roush, W., McKerrow, J., Reed, S., 2010, A novel entamoeba histolytica cysteine proteinase, EhCP4, is key for invasive amebiasis and a therapeutic target, Journal Of Biological Chemistry [P], vol 285, issue 24, American Society for Biochemistry and Molecular Biology Inc, USA, pp. 18516-18527.

Song, J., Tan, H., Shen, H., Mahmood, K., Boyd, S.E., Webb, G., Akutsu, T., Whisstock, J., 2010, Cascleave: towards more accurate prediction of caspase substrate cleavage sites, Bioinformatics [P], vol 26, issue 6, Oxford University Press, UK & USA, pp. 752-760.

Beckham, S.A., Boyd, S.E., Reynolds, S., Willis, C., Johnstone, M., Mika, A., Simerska, P., Wijeyewickrema, L.C., Smith, A.I., Kemp, D.J., Pike, R.N., Fischer, K., 2009, Characterization of a serine protease homologous to house dust mite group 3 allergens from the scabies mite sarcoptes scabiei, Journal Of Biological Chemistry [P], vol 284, issue 49, American Society for Biochemistry & Molecular Biology Inc, USA, pp. 34413-34422.

Boyd, S.E., Kerr, F.K., Albrecht, D.W., Garcia De La Banda, M.J., Ng, N., Pike, R.N., 2009, Cooperative effects in the substrate specificity of the complement protease C1s, Biological Chemistry [P], vol 390, issue 5/6, Walter De Gruyter & Co, Berlin Germany, pp. 503-507.

Igarashi, Y., Heureux, E., Doctor, K.S., Talwar, P., Gramatikova, S., Gramatikoff, K., Zhang, Y., Blinov, M., Ibragimova, S.S., Boyd, S.E., Ratnikov, B., Cieplak, P., Godzik, A., Smith, J.W., Osterman, A.L., Eroshkin, A.M., 2009, PMAP: Databases for analyzing proteolytic events and pathways, Nucleic Acids Research [P], vol 37, issue Database Issue, Oxford University Press, Oxford England UK, pp. D611-D618.

Ng, N.M., Pike, R.N., Boyd, S.E., 2009, Subsite cooperativity in protease specificity, Biological Chemistry, vol 390, issue 5-6, Walter de Gruyter GmbH & Co. KG, Germany, pp. 401-407.

Le Novere, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M.I., Wimalaratne, S.M., Bergman, F.T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S.E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T.C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D.B., Sander, C., Sauro, H., Snoep, J.L., Kohn, K., Kitano, H., 2009, The systems biology graphical notation, Nature Biotechnology [P], vol 27, issue 8, Nature Publishing Group, New York NY USA, pp. 735-741.

Scott, F.L., Fuchs, G.J., Boyd, S.E., Denault, J., Hawkins, C.J., Dequiedt, F., Salvesen, G., 2008, Caspase-8 cleaves Histone Deacetylase 7 and abolishes its transcription repressor function, The Journal of Biological Chemistry, vol 283, issue 28, The American Society for Biochemistry and Molecular Biology Inc, Bethesda MD USA, pp. 19499-19510.

Kerr, F.K., Thomas, A.R., Wijeyewickrema, L.C., Whisstock, J., Boyd, S.E., Kaiserman, D., Matthews, A.Y., Bird, P.I., Thielens, N.M., Rossi, V., Pike, R.N., 2008, Elucidation of the substrate specificity of the MASP-2 protease of the lectin complement pathway and identification of the enzyme as a major physiological target of the serpin, C1-inhibitor, Molecular Immunology, vol 45, Pergamon-Elsevier Science Ltd, Oxford England UK, pp. 670-677.

Furmonoviciene, R., Ghaemmaghami, A., Boyd, S.E., Jones, N., Bailey, K., Willis, A.C., Sewell, H., Mitchell, D., Shakib, F., 2007, The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: Experimental analysis of in silico substrate identification and implications in allergic responses, Clinical and Experimental Allergy, vol 37, issue 2, Blackwell Publishing Ltd, UK, pp. 231-242.

Kerr, F.K., O'Brien, G., Quinsey, N.S., Whisstock, J., Boyd, S.E., Garcia De La Banda, M.J., Kaiserman, D., Matthews, A.Y., Bird, P.I., Pike, R.N., 2005, Elucidation of the substrate specificity of the C1s protease of the classical complement pathway, Journal of Biological Chemistry, vol 280, issue 47, American Society for Biochemistry and Molecular Biology, Inc., Bethesda USA, pp. 39510-39514.

Golubkov, V.S., Boyd, S.E., Savinov, A.Y., Chekanov, A.V., Osterman, A.L., Remacle, A., Rozanov, D.V., Doxsey, S.J., Strongin, A.Y., 2005, Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability, The Journal of Biological Chemistry, vol 280, issue 26, American Society for Biochemistry and Molecular Biology, Inc., USA, pp. 25079-25086.

Boyd, S.E., Pike, R.N., Rudy, G.B., Whisstock, J., Garcia De La Banda, M.J., 2005, PoPS: A computational tool for modeling and predicting protease specificity, Journal of Bioinformatics and Computational Biology, vol 3, issue 3, Imperial College Press, London UK, pp. 551-585.

Conference Proceedings

Boyd, S.E., Garcia De La Banda, M.J., Kerr, F.K., O'Brien, G., 2007, Cooperative effects in the substrate specificity of the complement protease CIS, 5th General Meeting of the International Proteolysis Society Book of Abstracts, 20 October 2007 to 24 October 2007, Novartis Pharma A, Basel Switzerland, p. 361.

Scott, F.L., Boyd, S.E., Salvesen, G., 2007, Histone deacetylase 7 is a caspase-8 substrate, 5th General Meeting of the International Proteolysis Society Book of Abstracts, 20 October 2007 to 24 October 2007, Novartis Pharma A, Basel Switzerland, p. 283.

Ng, N., Boyd, S.E., Bird, P.I., Thompson, P., Matthews, A.Y., Kaiserman, D., Pike, R.N., 2007, The effects of thrombomodulin on the substrate specificity of thrombin, 5th General Meeting of the International Proteolysis Society Book of Abstracts, 20 October 2007 to 24 October 2007, Novartis Pharma A, Basel Switzerland, p. 375.

Boyd, S.E., Garcia De La Banda, M.J., Pike, R.N., Whisstock, J., Rudy, G.B., 2004, PoPS: a computational tool for modeling and predicting protease specificity, Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference, 16 August 2004 to 19 August 2004, IEEE Computer Society Press, Los Alamitos USA, pp. 372-381.

Irving, J., Boyd, S., Pike, R.N., Whisstock, J.C., 1999, The phylogeny of the serpin superfamily, Proceedings, 24th Annual Lorne Conference on Protein Structure and Function, Lorne Vic 7-11 February 1999, Lorne Protein Workshop, Inc., Melbourne Vic Australia, p. C40.

Other

Boyd, S.E., 2005, Computational Modelling and Prediction of Protease Specificity.