19992019

Research output per year

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Research Output

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Article
2019
2018

Adaptation to reef habitats through selection on the coral animal and its associated microbiome

van Oppen, M. J. H., Bongaerts, P., Frade, P., Peplow, LM., Boyd, S. E., Nim, H. T. & Bay, L. K., 1 Jul 2018, In : Molecular Ecology. 27, 14, p. 2956-2971 16 p.

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

Bayesian change-point modeling with segmented ARMA model

Sadia, F., Boyd, S. & Keith, J. M., 1 Dec 2018, In : PLoS ONE. 13, 12, 23 p., e0208927.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017
Open Access
File
3 Citations (Scopus)

Muscle Stem Cells Undergo Extensive Clonal Drift during Tissue Growth via Meox1-Mediated Induction of G2 Cell-Cycle Arrest

Nguyen, P. D., Gurevich, D. B., Sonntag, C., Hersey, L., Alaei, S., Nim, H. T., Siegel, A., Hall, T. E., Rossello, F. J., Boyd, S. E., Polo, J. M. & Currie, P. D., 6 Jul 2017, In : Cell Stem Cell. 21, 1, p. 107-119.e6 19 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
23 Citations (Scopus)
2016

View from the heart: Cardiac fibroblasts in development, scarring and regeneration

Furtado, M. B., Nim, H. T., Boyd, S. E. & Rosenthal, N. A., 1 Feb 2016, In : Development (Cambridge). 143, 3, p. 387-397 11 p.

Research output: Contribution to journalArticleResearchpeer-review

49 Citations (Scopus)
2015

CARFMAP: a curated pathway map of cardiac fibroblasts

Nim, H. T., Furtado, M. B., Costa, M. W., Kitano, H., Rosenthal, N. A. & Boyd, S. E., 2015, In : PLoS ONE. 10, 12, 16 p., e0143274.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
7 Citations (Scopus)
5 Citations (Scopus)

VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery

Nim, H. T., Furtado, M. B., Da Costa, M., Rosenthal, N. A., Kitano, H. & Boyd, S. E., 2015, In : BMC Bioinformatics. 16, 1 (Art. No: 141), p. 1 - 7 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
3 Citations (Scopus)
2014

Analysis of the minimal specificity of caspase-2 and identification of Ac-VDTTD-AFC as a caspase-2-selective peptide substrate

Kitevska, T., Roberts, S., Pantaki-Eimany, D., Boyd, S. E., Scott, F. & Hawkins, C., 2014, In : Bioscience Reports. 34, 2, p. 127 - 137 11 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Microarray profiling to analyse adult cardiac fibroblast identity

Furtado, M. B., Nim, H. T., Gould, J. A., Costa, M. W., Rosenthal, N. A. & Boyd, S. E., 2014, In : Genomics Data. 2, p. 345 - 350 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
12 Citations (Scopus)
2012

A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard

Keith, J. M., Davey, C. M. & Boyd, S. E., 2012, In : BMC Bioinformatics. 13, p. 1 - 11 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
2 Citations (Scopus)

Computational characterization of 3' splice variants in the GFAP isoform family

Boyd, S., Nair, B., Ng, S. W., Keith, J. & Orian, J., 2012, In : PLoS ONE. 7, 3, 13 p., e33565.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
7 Citations (Scopus)

Software support for SBGN maps: SBGN-ML and LibSBGN

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, In : Bioinformatics. 28, 15, p. 2016 - 2021 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
45 Citations (Scopus)
2011

Bioinformatic approaches for predicting substrates of proteases

Song, J., Tan, H., Boyd, S. E., Shen, H., Mahmood, K., Webb, G., Akutsu, T., Whisstock, J. & Pike, R., 2011, In : Journal of Bioinformatics and Computational Biology. 9, 1, p. 149 - 178 30 p.

Research output: Contribution to journalArticleResearchpeer-review

24 Citations (Scopus)

Discovery of amino acid motifs for thrombin cleavage and validation using a model substrate

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, In : Biochemistry. 50, 48, p. 10499 - 10507 9 p.

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)

Probing connectivity between transcriptional and post-transcriptional gene networks

Boyd, S., Keith, J. M., Traven, A. & Beilharz, T. H., 1 Nov 2011, In : Microbiology Australia. 32, 4, p. 166-168 3 p.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
2010

A novel entamoeba histolytica cysteine proteinase, EhCP4, is key for invasive amebiasis and a therapeutic target

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. & 1 others, Reed, S., 2010, In : Journal of Biological Chemistry. 285, 24, p. 18516 - 18527 12 p.

Research output: Contribution to journalArticleResearchpeer-review

44 Citations (Scopus)

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

Song, J., Tan, H., Shen, H., Mahmood, K., Boyd, S. E., Webb, G., Akutsu, T. & Whisstock, J., 2010, In : Bioinformatics. 26, 6, p. 752 - 760 9 p.

Research output: Contribution to journalArticleResearchpeer-review

114 Citations (Scopus)
2009

Characterization of a serine protease homologous to house dust mite group 3 allergens from the scabies mite sarcoptes scabiei

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, In : Journal of Biological Chemistry. 284, 49, p. 34413 - 34422 10 p.

Research output: Contribution to journalArticleResearchpeer-review

31 Citations (Scopus)

Cooperative effects in the substrate specificity of the complement protease C1s

Boyd, S. E., Kerr, F. K., Albrecht, D. W., Garcia De La Banda, M. J., Ng, N. & Pike, R. N., 2009, In : Biological Chemistry. 390, 5/6, p. 503 - 507 5 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Erratum: The systems biology graphical notation

Le Novere, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F. U., 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. & 19 others, 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, In : Nature Biotechnology. 27, 9, p. 864 - 864 1 p.

Research output: Contribution to journalArticleOther

2 Citations (Scopus)

PMAP: Databases for analyzing proteolytic events and pathways

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, In : Nucleic Acids Research. 37, Database Issue, p. D611 - D618 8 p.

Research output: Contribution to journalArticleResearchpeer-review

40 Citations (Scopus)

Subsite cooperativity in protease specificity

Ng, N. M., Pike, R. N. & Boyd, S. E., 2009, In : Biological Chemistry. 390, 5-6, p. 401 - 407 7 p.

Research output: Contribution to journalArticleResearchpeer-review

39 Citations (Scopus)

The systems biology graphical notation

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. & 19 others, 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, In : Nature Biotechnology. 27, 8, p. 735 - 741 7 p.

Research output: Contribution to journalArticleResearchpeer-review

513 Citations (Scopus)
2008

Caspase-8 cleaves Histone Deacetylase 7 and abolishes its transcription repressor function

Scott, F. L., Fuchs, G. J., Boyd, S. E., Denault, J-B., Hawkins, C. J., Dequiedt, F. & Salvesen, G. S., 2008, In : Journal of Biological Chemistry. 283, 28, p. 19499 - 19510 12 p.

Research output: Contribution to journalArticleResearchpeer-review

35 Citations (Scopus)

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

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, In : Molecular Immunology. 45, p. 670 - 677 7 p.

Research output: Contribution to journalArticleResearchpeer-review

51 Citations (Scopus)
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

Furmonoviciene, R., Ghaemmaghami, A., Boyd, S. E., Jones, N., Bailey, K., Willis, A. C., Sewell, H., Mitchell, D. & Shakib, F., 2007, In : Clinical & Experimental Allergy. 37, 2, p. 231 - 242 12 p.

Research output: Contribution to journalArticleResearchpeer-review

63 Citations (Scopus)
2005

Elucidation of the substrate specificity of the C1s protease of the classical complement pathway

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, In : Journal of Biological Chemistry. 280, 47, p. 39510 - 39514 5 p.

Research output: Contribution to journalArticleResearchpeer-review

30 Citations (Scopus)

Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability

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, In : Journal of Biological Chemistry. 280, 26, p. 25079 - 25086 8 p.

Research output: Contribution to journalArticleResearchpeer-review

78 Citations (Scopus)

PoPS: A computational tool for modeling and predicting protease specificity

Boyd, S. E., Pike, R. N., Rudy, G. B., Whisstock, J. & Garcia De La Banda, M. J., 2005, In : Journal of Bioinformatics and Computational Biology. 3, 3, p. 551 - 585 35 p.

Research output: Contribution to journalArticleResearchpeer-review

76 Citations (Scopus)