Ian Smith

Professor

1985 …2020
If you made any changes in Pure these will be visible here soon.

Research Output 1985 2019

2019

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

Mei, S., Li, F., Leier, A., Marquez-Lago, T. T., Giam, K., Croft, N. P., Akutsu, T., Smith, A. I., Li, J., Rossjohn, J., Purcell, A. W. & Song, J., 14 Jun 2019, (Accepted/In press) In : Briefings in Bioinformatics. 17 p., bbz051.

Research output: Contribution to journalReview ArticleResearchpeer-review

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

Chen, Z., Zhao, P., Li, F., Wang, Y., Smith, A. I., Webb, G. I., Akutsu, T., Baggag, A., Bensmail, H. & Song, J., 11 Nov 2019, (Accepted/In press) In : Briefings in Bioinformatics. 21 p., bbz112.

Research output: Contribution to journalArticleResearchpeer-review

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 30 Sep 2019, (Accepted/In press) In : Bioinformatics. 9 p., btz721.

Research output: Contribution to journalArticleResearchpeer-review

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

4 Citations (Scopus)

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

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., Nov 2019, In : Briefings in Bioinformatics. 20, 6, p. 2150-2166 17 p., bby077.

Research output: Contribution to journalArticleResearchpeer-review

2018
55 Citations (Scopus)

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

Open Access
File

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
File
37 Citations (Scopus)

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

1 Citation (Scopus)

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

2 Citations (Scopus)

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
File
3 Citations (Scopus)

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

Letter by Rajapakse et al Regarding Article, "Combined angiotensin receptor antagonism and neprilysin inhibition"

Rajapakse, N. W., Kuruppu, S. & Smith, A. I., 19 Jul 2016, In : Circulation. 134, 3, p. e9-e10 2 p.

Research output: Contribution to journalLetterOtherpeer-review

18 Citations (Scopus)

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
File
2015
2 Citations (Scopus)

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
File
8 Citations (Scopus)

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

4 Citations (Scopus)

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
1 Citation (Scopus)

Angiotensin (1-7) as a Therapy to Prevent Rupture of Intracranial Aneurysms?

Kuruppu, D. M. S., Smith, A. I., Drummond, G. R. & Sobey, C. G., 2014, In : Hypertension. 64, 2, p. 222 - 223 2 p.

Research output: Contribution to journalLetterOther

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

4 Citations (Scopus)

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
3 Citations (Scopus)

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

13 Citations (Scopus)

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

7 Citations (Scopus)

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

Acetylation

Li, Q., Clarke, I. J. & Smith, A. I., 2013, Handbook of Biologically Active Peptides. Kastin, A. J. (ed.). 2nd ed. San Diego CA USA: Elsevier, p. 1711 - 1714 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

2 Citations (Scopus)

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

3 Citations (Scopus)

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

8 Citations (Scopus)

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
File
34 Citations (Scopus)

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
24 Citations (Scopus)

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

17 Citations (Scopus)

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
2 Citations (Scopus)

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
18 Citations (Scopus)

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

7 Citations (Scopus)

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

6 Citations (Scopus)

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

31 Citations (Scopus)

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
File
5 Citations (Scopus)

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
107 Citations (Scopus)

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
11 Citations (Scopus)

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
12 Citations (Scopus)

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
File
16 Citations (Scopus)

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

4 Citations (Scopus)

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

12 Citations (Scopus)

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
17 Citations (Scopus)
19 Citations (Scopus)

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