Ian Smith

Professor

1985 …2020
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Research Output 1985 2019

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2019

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 24 Apr 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz041.

Research output: Contribution to journalArticleResearchpeer-review

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 8 Aug 2019, (Accepted/In press) In : Bioinformatics. 8 p., btz629.

Research output: Contribution to journalArticleResearchpeer-review

Powering Amyloid Beta Degrading Enzymes: A Possible Therapy for Alzheimer’s Disease

Sikanyika, N. L., Parkington, H. C., Smith, A. I. & Kuruppu, S., 15 Jun 2019, In : Neurochemical Research. 44, 6, p. 1289-1296 8 p.

Research output: Contribution to journalArticleResearchpeer-review

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y., Smith, A. I., Webb, G. I., Liu, Q., Wei, L., Li, J. & Song, J., 4 Jun 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz050.

Research output: Contribution to journalArticleResearchpeer-review

2018

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences

Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T., Wang, Y., Webb, G. I., Smith, A. I., Daly, R. J., Chou, K-C. & Song, J., 15 Jul 2018, In : Bioinformatics. 34, 14, p. 2499-2502 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., Akutsu, T., Webb, G. I., Xu, D., Smith, A. I., Li, L., Chou, K-C. & Song, J., 4 Oct 2018, (Accepted/In press) In : Briefings in Bioinformatics. 24 p., bby089.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

Li, F., Li, C., Marquez-Lago, T. T., Leier, A., Akutsu, T., Purcell, A. W., Smith, A. I., Lithgow, T., Daly, R. J., Song, J. & Chou, K-C., 15 Dec 2018, In : Bioinformatics. 34, 24, p. 4223-4231 9 p., bty522.

Research output: Contribution to journalArticleResearchpeer-review

Serelaxin attenuates renal inflammation and fibrosis in a mouse model of dilated cardiomyopathy

Giam, B., Chu, P. Y., Kuruppu, S., Smith, A. I., Horlock, D., Murali, A., Kiriazis, H., Du, X-J., Kaye, D. M. & Rajapakse, N. W., 1 Dec 2018, In : Experimental Physiology. 103, 12, p. 1593-1602 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 2018, (Accepted/In press) In : Briefings in Bioinformatics. 17 p., bby077.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

N-Acetylcysteine Attenuates the Development of Renal Fibrosis in Transgenic Mice with Dilated Cardiomyopathy

Giam, B., Kuruppu, S., Chu, P. Y., Smith, A. I., Marques, F. Z., Fiedler, A., Horlock, D., Kiriazis, H., Du, X-J., Kaye, D. M. & Rajapakse, N. W., 18 Dec 2017, In : Scientific Reports. 7, 1, 12 p., 17718.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Proteomics Identification of Potential Candidates Involved in Cell Proliferation for Early Stage of Brain Regeneration in the Adult Zebrafish

Lim, F. T., Ogawa, S., Smith, A. I. & Parhar, I. S., 1 Feb 2017, In : Zebrafish. 14, 1, p. 10-22 13 p.

Research output: Contribution to journalArticleResearchpeer-review

2016

N-acetylcysteine attenuates the development of cardiac fibrosis and remodeling in a mouse model of heart failure

Giam, B., Chu, P. . Y., Kuruppu, S., Smith, A. I., Horlock, D., Kiriazis, H., Du, X-J., Kaye, D. M. & Rajapakse, N. W., 1 Apr 2016, In : Physiological Reports. 4, 7, 13 p., e12757.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2015

Changes in protein abundance are observed in bacterial isolates from a natural host

Rees, M. A., Stinear, T. P., Goode, R. J. A., Coppel, R. L., Smith, A. I. & Kleifeld, O., 2015, In : Frontiers in Cellular and Infection Microbiology. 5, 15 p., 71.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Proteomic characterization of a natural host-pathogen interaction: repertoire of in vivo expressed bacterial and host surface-associated proteins

Rees, M. A., Kleifeld, O., Crellin, P. K., Ho, B. K-C., Stinear, T. P., Smith, A. I. & Coppel, R. L., 2015, In : Journal of Proteome Research. 14, 1, p. 120 - 132 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Structural determinants for binding to angiotensin converting enzyme 2 (ACE2) and angiotensin receptors 1 and 2

Clayton, D. J., Hanchapola, I., Thomas, W. G., Widdop, R. E., Smith, A. I., Perlmutter, P. & Aguilar, M. M. I. . I., 2015, In : Frontiers in Pharmacology. 6, (Art. No: 5), p. 1 - 9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
2014

Inhibition of presynaptic neurotoxins in taipan venom by suramin

Kuruppu, D. M. S., Chaisakul, J., Smith, A. I. & Hodgson, W. C., 2014, In : Neurotoxicity Research. 25, 3, p. 305 - 310 6 p.

Research output: Contribution to journalArticleResearchpeer-review

In vitro toxic effects of puff adder (Bitis arietans) venom, and their neutralization by antivenom

Fernandez, S., Hodgson, W. C., Chaisakul, J., Kornhauser, R. S., Konstantakopoulos, N., Smith, A. I. & Kuruppu, D. M. S., 2014, In : Toxins. 6, 5, p. 1586 - 1597 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

Nitric oxide inhibits the production of soluble endothelin converting enzyme-1

Kuruppu, D. M. S., Rajapakse, N. W., Dunstan, R. A. & Smith, A. I., 2014, In : Molecular and Cellular Biochemistry. 396, 1-2, p. 49 - 54 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Production of soluble Neprilysin by endothelial cells

Kuruppu, D. M. S., Rajapakse, N. W., Minond, D. & Smith, A. I., 2014, In : Biochemical and Biophysical Research Communications. 446, 2, p. 423 - 427 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Soluble and catalytically active endothelin converting enzyme-1 is present in cerebrospinal fluid of subarachnoid hemorrhage patients

Kuruppu, D. M. S., Chou, S. H. Y., Feske, S. K., Suh, S., Hanchapola, I., Lo, E. H., Ning, M. & Smith, A. I., 2014, In : Molecular & Cellular Proteomics. 13, 4, p. 1091 - 1094 4 p.

Research output: Contribution to journalArticleResearchpeer-review

2013

Applicability of green fluorescence protein in the study of endothelin converting enzyme-1c trafficking

Kuruppu, DM. S., Tochon-Danguy, N. & Smith, A. I., 2013, In : Protein Science. 22, 3, p. 306 - 313 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Endothelin-converting enzyme-1 inhibition and renoprotection in end-stage renal disease

Kuruppu, D. M. S., Rajapakse, N. W. & Smith, A. I., 2013, In : Pflugers Archiv-European Journal of Physiology. 465, 7, p. 929 - 934 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Expression and cellular distribution of ubiquitin in response to injury in the developing spinal cord of Monodelphis domestica

Noor, N. M., Mollgard, K., Wheaton, B. J., Steer, D. L., Truettner, J. S., Dziegielewska, K. M., Dietrich, W. D., Smith, A. I. & Saunders, N. R., 2013, In : PLoS ONE. 8, 4, 15 p., e62120.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Structural and functional analysis of the pore-forming toxin NetB from clostridium perfringens

Yan, X., Porter, C. J., Hardy, S. P., Steer, D., Smith, A. I., Quinsey, N. S., Hughes, V., Cheung, J. K., Keyburn, A. L., Kaldhusdal, M., Moore, R. J., Bannam, T. L., Whisstock, J. C. & Rood, J. I., 2013, In : mBio. 4, 1, 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

The proteome browser web portal

Goode, R. JA., Yu, S. X., Kannan, A., Christiansen, J. H., Beitz, A., Hancock, W. S., Nice, E. C. & Smith, A. I., 2013, In : Journal of Proteome Research. 12, 1, p. 172 - 178 7 p.

Research output: Contribution to journalArticleResearchpeer-review

The x-ray crystal structure of mannose-binding lectin-associated serine proteinase-3 reveals the structural basis for enzyme inactivity associated with the Carnevale, Mingarelli, Malpuech, and Michels (3MC) syndrome

Yongqing, T., Wilmann, P. G., Reeve, S. B., Coetzer, T. H., Smith, A. I., Whisstock, J., Pike, R. N. & Wijeyewickrema, L. C., 2013, In : Journal of Biological Chemistry. 288, 31, p. 22399 - 22407 9 p.

Research output: Contribution to journalArticleResearchpeer-review

2012

Application of protein purification methods for the enrichment of a cytotoxin from Campylobacter jejuni

Gatsos, X., Steer, D. L., Junaid, T. A., Smith, A. I., Adler, B. & Albert, M. J., 2012, In : BMC Microbiology. 12, Art No.:303, p. 1 - 10 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

Endothelin converting Enzyme-1 phosphorylation and trafficking

Kuruppu, D. M. S. & Smith, A. I., 2012, In : FEBS Letters. 586, 16, p. 2212 - 2217 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Evidence that renal arginine transport is impaired in spontaneously hypertensive rats

Rajapakse, N. W., Kuruppu, D. M. S., Hanchapola, I., Venardos, K. M., Mattson, D. L., Smith, A. I., Kaye, D. M. & Evans, R. G., 2012, In : American Journal of Physiology - Renal Physiology. 302, 12, p. F1554 - F1562 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Protein Kinase C recognition sites in the cytoplasmic domain of Endothelin Converting Enzyme-1c

Kuruppu, DM. S., Tochon-Danguy, N. & Smith, A. I., 2012, In : Biochemical and Biophysical Research Communications. 427, 3, p. 606 - 610 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteomic changes in rat spermatogenesis in response to in vivo androgen manipulation; impact on meiotic cells

Stanton, P. G., Sluka, P., Foo, C. FH., Stephens, A. N., Smith, A. I., McLachlan, R. I. & O'Donnell, L., 2012, In : PLoS ONE. 7, 7, 19 p., e41718.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The AprV5 subtilase is required for the optimal processing of all three extracellular serine proteases from Dichelobacter nodosus

Han, X. Y., Kennan, R. M., Steer, D. L., Smith, A. I., Whisstock, J. C. & Rood, J. I., 2012, In : PLoS ONE. 7, 10, 8 p., e47932.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

The x-ray crystal structure of full-length human plasminogen

Law, R. HP., Caradoc-Davies, T. T., Cowieson, N. P., Horvath, A. J., Quek, A. J., Amarante Da Encarnacao, J., Steer, D. L., Cowan, A. D., Zhang, Q., Lu, B. GC., Pike, R. N., Smith, A. I., Coughlin, P. B. & Whisstock, J. C., 2012, In : Cell Reports. 1, 3, p. 185 - 190 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

Toxinology of venoms from five Australian lesser known elapid snakes

Pycroft, K., Fry, B. G., Isbister, G. K., Kuruppu, D. S. M., Lawrence, J. M., Smith, A. I. & Hodgson, W. C., 2012, In : Basic and Clinical Pharmacology and Toxicology. 111, 4, p. 268 - 274 7 p.

Research output: Contribution to journalArticleResearchpeer-review

2011

Age-dependent changes in the proteome following complete spinal cord transection in a postnatal South American Opossum (Monodelphis domestica)

Noor, N. M., Steer, D. L., Wheaton, B. J., Ek, C. J., Truettner, J. S., Dietrich, W. D., Dziegielewska, K. M., Richardson, S. J., Smith, A. I., VandeBerg, J. L. & Saunders, N. R., 2011, In : PLoS ONE. 6, 11, 16 p., e27465.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Angiotensin-converting enzyme 2 ectodomain shedding cleavage-site identification: Determinants and constraints

Lai, Z., Hanchapola, I., Steer, D. & Smith, A., 2011, In : Biochemistry. 50, 23, p. 5182 - 5194 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Beta-amino acid substitution to investigate the recognition of angiotensin II (AngII) by angiotensin converting enzyme 2 (ACE2)

Clayton, D., Hanchapola, I., Hausler, N., Unabia, S., Lew, R. A., Widdop, R. E., Smith, A. I., Perlmutter, P. & Aguilar, M. -I., 2011, In : Journal of Molecular Recognition. 24, 2, p. 235 - 244 10 p.

Research output: Contribution to journalArticleResearchpeer-review

S1 pocket of a bacterially derived subtilisin-like protease underpins effective tissue destruction

Wong, W., Wijeyewickrema, L. C., Kennan, R. M., Reeve, S. B., Steer, D. L., Reboul, C., Smith, A. I., Pike, R. N., Rood, J. I., Whisstock, J. C. & Porter, C. J., 2011, In : Journal of Biological Chemistry. 286, 49, p. 42180 - 42187 8 p.

Research output: Contribution to journalArticleResearchpeer-review

2010

Metabolic effects of low dose angiotensin converting enzyme inhibitor in dietary obesity in the rat

Velkoska, E., Warner, F. J., Cole, T. J., Smith, A. I. & Morris, M. J., 2010, In : Nutrition Metabolism and Cardiovascular Diseases. 20, p. 49 - 55 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Role of Protein Kinase C in Endothelin Converting Enzyme-1 trafficking and shedding from endothelial cells

Kuruppu, S., Tochon-Danguy, N. & Smith, A. I., 2010, In : Biochemical and Biophysical Research Communications. 398, 2, p. 173 - 177 5 p.

Research output: Contribution to journalArticleResearchpeer-review

The innate immune molecule, NOD1, regulates direct killing of Helicobacter pylori by antimicrobial peptides

Grubman, A., Liaskos, M., Viala, J., Allison, C. C., Badea, L., Karrar, A., Boneca, I. G., Le Bourhis, L., Reeve, S. B., Smith, A. I., Hartland, E. L., Philpott, D. J. & Ferrero, R. L., 2010, In : Cellular Microbiology. 12, 5, p. 626-639 13 p.

Research output: Contribution to journalArticleResearchpeer-review

The subtilisin-like protease AprV2 is required for virulence and uses a novel disulphide-tethered exosite to bind substrates

Kennan, R. M., Wong, W., Dhungyel, O., Han, X., Wong, D. M., Parker, D., Rosado, C. J., Law, R. HP., McGowan, S., Reeve, S. B., Levina, V., Powers, G. A., Pike, R. N., Bottomley, S. P., Smith, A. I., Marsh, I., Whittington, R. J., Whisstock, J., Porter, C. J. & Rood, J. I., 2010, In : PLoS Pathogens. 6, 11, p. 1 - 12 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Variations in the pharmacological profile of post-synaptic neurotoxins isolated from the venoms of the Papuan (Oxyuranus scutellatus canni) and coastal (Oxyuranus scutellatus scutellatus) taipans

Kornhauser, R., Hart, A. J., Reeve, S. B., Smith, A. I., Fry, B. G. & Hodgson, W. C., 2010, In : NeuroToxicology. 31, 2, p. 239 - 243 5 p.

Research output: Contribution to journalArticleResearchpeer-review

2009

Aberrant protein expression in plasma and kidney tissue during experimental obstructive nephropathy

Giannakis, E., Samuel, C., Hewitson, T. D., Boon, W. M., Macris, M., Reeve, S. B., Lawrence, J. M., Smith, A. I., Tregear, G. W. & Wade, J. D., 2009, In : Proteomics - Clinical Applications. 3, 10, p. 1211 - 1224 14 p.

Research output: Contribution to journalArticleResearchpeer-review

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

Membrane proteomics: The development of diagnostics based on protein shedding

Lai, Z. W., Steer, D. L. & Smith, A. I., 2009, In : Current Opinion in Molecular Therapeutics. 11, 6, p. 623 - 631 9 p.

Research output: Contribution to journalArticleResearchpeer-review

The identification of a calmodulin-binding domain within the cytoplasmic tail of angiotensin-converting enzyme-2

Lai, Z. W., Lew, R. A., Yarski, M. A., Mu, F-T., Andrews, R. K. & Smith, A. I., 2009, In : Endocrinology. 150, 5, p. 2376 - 2381 6 p.

Research output: Contribution to journalArticleResearchpeer-review

2008

Acute kidney injury in the rat causes cardiac remodelling and increases angiotensin-converting enzyme 2 expression

Burchill, L., Velkoska, E., Dean, R. G., Lew, R. A., Smith, A. I., Levidiotis, V. & Burrell, L. M., 2008, In : Experimental Physiology. 93, 5, p. 622 - 630 9 p.

Research output: Contribution to journalArticleResearchpeer-review