Blackburn Publications | Division of Chemical & Systems Biology

2019
2018
1. Alula MT, Karamchand L, Hendricks NR and Blackburn JM. (2018). Citrate-capped silver nanoparticles as a probe for sensitive and selective colorimetric and spectrophotometric sensing of creatinine in human urine Analytica Chimica Acta (2018), https://doi.org/10.1016/j.aca.2017.12.016
2017
1. Ganief T, Gqamana P, Garnett S, Hoare J, Stein DJ, Joska J, Soares NC, Blackburn JM (2017) Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells.Proteomics (online) doi/10.1002/pmic.201600236[2017/01/23 11:07:10 AM]
2. Bell L, Peyper J, Garnett S, Tadokera R, Wilkinson R, Meintjes G & Blackburn JM (2017) Proteomic analysis of in vitro PBMC responses to Mycobacterium tuberculosis and response modulation by dexamethasone.Experimental & Molecular Pathology 102, 237-246.
3. 7:43858 | DOI: 10.1038/srep43858. (13 pgs)
4. Bordelon H, Ricks KM, Pask ME, Russ PK, Solinas F, Baglia M, Short PA, Nel A, Blackburn J, Dheda K, Zamundio C, Cáceres T, Wright DW, Haselton FR & Pettit A (2017) Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: application for transrenal Mycobacterium tuberculosis DNA detection. Journal of Microbiological Methods.2017 Mar; DOI 10.1016/j.mimet.2017.02.010.
5. Adeola HA, Blackburn JM, Rebbeck TR & Zerbini ZF (2017) Emerging proteomics biomarkers and prostate cancer burden in Africa:.Oncotarget, Advance Publications 2017.
6. Gurwitz KT, Ganief TA, Garnett S, Soares NC & Blackburn JM (2017) Time-dependent, HIV-Tat induced perturbation of human neurons In Vitro: towards a model for the molecular pathology of HIV-associated neurocognitive disorders. Frontiers in Molecular Neuroscience, Vol 10 Article 163. doi: 10.3389/fnmol.2017.00163
7. Duarte J & Blackburn JM (2017) Advances in the development of human protein microarrays. Expert Review of Proteomics, Vol 14 No 7, 627-641. DOI: 10.1080/14789450.2017.1347042.
8. Kalule JB, Fortuin S, Robberts L, Keddy KH, Nel A, Garnett S, Nicol M, Warner DF, Blackburn JM* & Soares NC* (2017) Proteomic comparison of three clinical diarrhoeagenic 1 drug-resistant Escherichia coli isolates grown on CHROMagar TM2 STEC media. J. Proteomics. http://dx.doi.org/10.1016/j.jprot.2017.09.003. online pulication.
9. Albeldas C, Ganief N, Calder B, Nakedi KC, Garnett S, Nel AJM, Blackburn JM* & Soares NC* (2017) Global proteome and phosphoproteome dynamics indicate novel mechanisms of vitamin C induced dormancy in Mycobacterium smegmati. Journal of Proteomics. http://dx.doi.org/10.1016/j.jprot.2017.10.006 . Online publication October, 2017
10. Smith M and Blackburn JM. (2017).Abstract A22: Identifying serum biomarkers for colorectal cancer using immunoproteomics.News Frontier 17-A22, November 2017.AACR International Conference: New Frontiers in Cancer Research; January 18-22, 2017; Cape Town, South Africa
2016
1. Soares NC, Blackburn JM and Bou G.(2017).Editorial: Proteomics of microbial human pathogens.Frontiers in Microbiology, Vol 7, Article 1742, 3pgs. ISSN 1664-8714, ISBN 978-2-88945-088-6, DOI 10.3389/978-2-88945-088-6
2. Soares NA and Blackburn JM (2016).Mass spectrometry targeted assays as a tool to improve our understanding of post-translational modifications in pathogenic bacteria. Frontiers in Microbiology, 7, Article 1216. doi: 10.3389/fmicb.2016.01216
3. Parev P, Qhanya LB, Mthakathi NT, Blackburn MJ, et al. (2016).Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. Scientific Reports 6, Art. 33099 (016), doi:10.1038/srep33099.
4. Alula MT, Krishnan S, Hendricks NR, Karamchand L & Blackburn J (2016) Identification and quantitation of pathogenic bacteria via in-situ formation of silver nanoparticles on cell walls, and detections via SERS.Microchimica Acta, 184, 219-227.
5. Lennard KS, Goosen RW & Blackburn JM (2016) Bacterially-associated transcriptional remodelling in a distinct molecular subtype of colorectal cancer provides a plausible mechanistic basis for disease development and progression. Submitted to PLoS One.
6. Peters JS, Calder B, Gionelli G, Degroeve S, Rajaonarifara E, Mulder N, Soares N, Martens L & Blackburn JM (2016) Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence. Frontiers in Microbiology. In the press.
7. Potgieter MG, Nakedi KC, Ambler J, Nel AJM, Garnett S, Soares NC, Mulder N* & Blackburn JM* (2016) Proteogenomic analysis of Mycobacterium smegmatis using high resolution mass spectrometry. Frontiers in Microbiology. April 2016, Vol 7, Article 427. doi: 10.3389/fmicb.2016.00427
8. Calder B, Albeldas C, Blackburn JM* & Soares NC* (2016) Mass spectrometry offers insight into the role of Ser/Thr/Tyr phosphorylation in the mycobacteria. Frontiers in Microbiology, February 2016 Vol 7 Article 141, doi:10.3389/fmicb.2016.00141
9. Adeola HA, Smith M, Kaestner L, Blackburn JM* & Zerbini ZF* (2016) Novel potential serological prostate cancer biomarkers using CT100+ cancer antigen microarray platform in a multi-cultural South African cohort. OncoTarget 7, 13945-13964.
10. Wood R, Morrow C, Barry III CE, Bryden WA, Call CJ, Hickey AJ, Rodes CE, Scriba TJ, Blackburn J, Issarow C, Mulder N, Woodward J, Moosa A, Singh V, Mizrahi V, Warner DF (2016) Real-time Investigation of Tuberculosis Transmission: Developing the Respiratory Aerosol Sampling Chamber (RASC). PLoS One. 11, e0146658.
11. Blackburn JM* & Martens L (2016) The challenge of metaproteomic analysis in human samples. Expert Review of Proteomics 13, 135-8.
12. Adeola HA, Calder B, Soares NC, Kaestner L, Blackburn JM* & Zerbini ZF* (2016) In-silico verification and PRM prevalidation of potential prostate cancer biomarkers. Future Oncology 12, 43-57
2015
1. Suereta Fortuin, Gisele G. Tomazella, Nagarjuna Nagaraj, Samantha L. Sampson, Nicolaas C. Gey van Pittius, Nelson C . Soares, Harald G. Wiker, Gustavo A. de Souza and Robin M. Warren. Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: expanding the mycobacterial phosphoproteome catalog. Frontiers in Biology, Volume 6, Article 6, 2015. doi: 10.3389/fmicb.2015.00006.
2. Kehilwe C. Nakedi, Andrew J. M.Nel, Shaun Garnett, Jonathan M. Blackburn and Nelson C. Soares. Comparative Ser/Thr/Tyr phosphoproteomics between two mycobacterial species: the fast growing Mycobacterium smegmatis and the slow growing Mycobacteriumbovis BCG. Frontiers in Microbiology, Volume 6, Article 237, 2015, 1-12. doi: 10.3389/fmicb.2015.00237.
3. Andrew J. M. Nel, Shaun Garnett, Jonathan M. Blackburn,* and Nelson C. Soares. Comparative Re-evaluation of FASP and Enhanced FASP Methods by LC−MS/MS. Journal of Proteome Research, 2015, 14, 1637−1642. DOI: 10.1021/pr501266c.
4. Bridget C, Soares NC, Elise de Kock & Blackburn JM. Mycobacterial proteomics: analysis of expressed proteomes and posttranslational modifications to identify candidate virulence factors. Expert Rev. Proteomics 12(1), 21–35 (2015).
5. Henry A. Adeola, Nelson C. Soares, Juliano D. Paccez, Lisa Kaestner, Jonathan M. Blackburn and Luiz F. Zerbini. Discovery of novel candidate urinary protein biomarkers for prostate cancer in a Multiethnic cohort of South African patients via label-free mass spectrometry. Proteomics Clin. Appl. 2015, 0, 1–13. DOI 10.1002/prca.201400197.
2014
1. Young BL, Mlamla Z, Gqamana P, Smit S, Roberts T, Peter J, Theron G, Govender U, Dheda K & Blackburn JM (2014) The Identification of Mycobacterium Tuberculosis-specific Biomarkers in Human Urine Samples From Patients with Active Tuberculosis. European Respiratory Journal 43, 1719–1729.
2. Beeton-Kempen N, Duarte J, Shoko A, Serufuri J-M, John T, Cebon J & Blackburn JM (2014) Quantitative determination of autoimmune profiles using a novel cancer-testis antigen microarray platform. International Journal of Cancer 135, 1842–1851.
3. Singh V, Brecik M, Mukherjee R, Evans JC, Svetlíková Z, Blackburn J, Warner DF, Mikušová K & Mizrahi V (2014) The Complex Mechanism of Antimycobacterial Action of 5-Fluorouracil. Chemistry & Biology. In the press.
4. Paruk F, Blackburn JM, Friedman IB & Mayosi BM (2014) National expenditure on health research in South Africa: What is the benchmark? S. Afr. Med. J. 104, 468-474.
5. Blackburn JM, Young-Gqamana & Dheda K (2014) Mycobacterium tuberculosis-specific biomarkers for diagnosing tuberculosis in a urine sample PCT application no. IB2014/063987.
6. Soares NC, Spat P, Mendez JA, Nakedi K, Aranda J, Bou G. (2014) Ser/Thr/Tyr phosphoproteome characterization of Acinetobacter baumannii: comparison between a reference strain and a highly invasive multidrug-resistant clinical isolate. J Proteomics. May 6;102:113-24.
7. Adeola H, Goosen RW, Goldberg P & Blackburn J (2014) Prospects of 'Omics Based Molecular Approaches in Colorectal Cancer Diagnosis & Treatment in the Developing World: A Case Study in Cape Town, South Africa. Chapter 15, pp363- 401. In Colorectal Cancer - Surgery, Diagnostics and Treatment (Ed. Khan J). InTech, Rijeka, Croatia. ISBN 980-953-307-958-0
2013
1. Arendse L, Blundell T & Blackburn J (2013) Combining in silico protein stability calculations with structure-function relationships to explore the effect of polymorphic variation on cytochrome P450 drug metabolism. Current Drug Metabolism 14, 745-763.
2. Soares NC, Spat P, Krug K & Macek B. (2013) Global dynamics of Escherichia coli proteome and phosphoproteome during growth in minimal medium. J Proteome Res. Jun 7;12(6):2611-21.
3. Viljoen KS & Blackburn JM (2013) Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity. BMC Genomics 14, 14.
4. Muth T, Peters J, Blackburn J, Rapp E & Martens L (2013) ProteoCloud: a full-featured open source proteomics cloud computing pipeline. J. Proteomics. http://dx.doi.org/10.1016/j.jprot.2012.12.02
2012
1. Mendez JA, Soares NC, Mateos J, Gayoso C, Rumbo C, Aranda J, Tomas M & Bou G (2012) Extracellular proteome of highly invasive multidrug-resistant clinical strain of Acinetobacter baumannii. J Proteome Res Dec 7;11(12):5678-94. (#) Both author contributed equally to this work.
2. Soufi B, Soares NC, Ravickumar V, Macek B (2012) Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation. Curr Opin Microbiol. Jun;15(3):357-63. (#) Both author contributed equally to this work.
3. Duarte J, Serufuri J-M, Mulder N & Blackburn J (2012) Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation. In Bioinformatics of Human Proteomics: Translational Bioinformatics (Wang X, ed). Springer, NY. ISBN 978-94-007-5811-7.
4. Ramautar A, Mabandla M, Blackburn J & Daniels WMU (2012) Inhibition of HIV-1 tat-induced transactivation and apoptosis by the divalent metal chelators, fusaric acid and picolinic acid - Implications for HIV-1 dementia. Neuroscience Research 74, 59-63.
2011
1. Mayosi BM, Mekwa NJ, Blackburn J, Coovadia H, Friedman IB, Jeenah M, Madela-Mntla EN, Magwaza AS, Makatini Z, Mkize DL, Mokgatle-Makwakwa C, Mokwena K, Nevhutalu K & Paruk F (2011) Strengthening research for health, innovation and development in South Africa. Department of Health, South Africa. http://www.nhrc.org.za.
2. Zawaira A, Coulson L, Gallotta M, Karimanzira O & Blackburn J (2011) On the deduction and analysis of singlet and two-state gating-models from the static structures of mammalian CYP450. J. Struct. Biol. 282-293.
3. Zawaira A, Ching LY, Coulson L, Blackburn J & Yap CW (2011) An expanded, unified Substrate Recognition Site map for mammalian Cytochrome P450s: analysis of molecular interactions between 15 mammalian CYP450 isoforms and 868 substrates. Current Drug Metabolism 12, 684-700.
4. Otto DME, Campanero-Rhodes MA, Karamanska R, Powell AK, Bovin N, Turnbull JE, Field R, Blackburn J, Feizi T & Crocker PR (2011) A versatile expression system for genome-wide screening of secreted and type 1 membrane proteins for glycan and protein interactions. Anal. Biochem. 411, 261-270.
5. Blackburn JM, Shoko A & Beeton-Kempen N (2011) Miniaturised, microarray-based assays for chemical proteomic studies of protein function. In Chemical Genomics: Reviews and Protocols (Zanders E, ed) The Humana Press, Springer, NY. ISBN 978-1-61779-348-6.
6. Blackburn JM & Shoko A (2011) Protein function microarrays for systems-oriented proteomic analysis. In Protein Microarrays: Methods in Molecular Biology (Korf U, Ed). The Humana Press, Springer, NY. ISBN 978-1-61779-285-4.
2010
1. Zawaira A, Gallotta M, Beeton-Kempen N, Coulson L, Marais P, Kuttel M & Blackburn J (2010) Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins. Computational Biology and Chemistry, 34, 42–52.
2. Dheda K, Lenders L, Davids V, Roberts V, Meldau R, Ling D, Brunet L, van Zyl Smit R, Peters J, Badri M , Sechi L, Sharma S, Hoelscher M, Dawson R, Whitelaw A, Blackburn J, Pai M & Zumla A (2010) Clinical utility of a commercial LAM-ELISA assay for TB diagnosis in HIV-infected patients using urine and sputum samples. Plos One, 5, e9848 (pp1-8).
2009
1. Blackburn JM, Serufuri J-MS & Kumuthini J (2009) An in vitro method of cancer diagnosis. RSA patent 2009/05150.
2008
1. Dakshinamurthy A, Ramesar R, Goldberg P & Blackburn JM (2008) Infrequent and Low Expression of Cancer-Testis Antigens Located on the X Chromosome in Colorectal Cancer: Implications for Immunotherapy in South African Populations. Biotechnology Journal 3, 1417-1423.
2. Beeton-Kempen N, Shoko A, Blackburn J (2008) Personalising protein-drug interactions. Pure & Applied Chemistry 80, 1793–1802.
3. Zhi, Z-L, Laurent, N, Powell, AK, Karamanska, R, Fais, M, Voglmeir, J, Wright, A, Blackburn, JM, Crocker, PR, Russell, DA, Flitsch, S, Field, RA, & Turnbull, JE (2008) A Versatile Gold Surface Approach for Fabrication and Interrogation of Glycoarrays. ChemBioChem 9, 1568-1575.
4. Laurent N, Voglmeir J, Wright A, Blackburn J, Pham NT, Wong S, Gaskell SJ & Flitsch SL (2008) Enzymatic glycosylation of peptide arrays on gold surfaces. ChemBioChem 9, 883-887.