Rhodes>BM>People>Academic Staff>Tastan Bishop>Publications

Publications

A. Theses:

  • A.O. Tastan, "How lazy are the tRNAs on the ribosome? New insights for the alpha–epsilon model," Ph.D. Thesis, Biochemistry Dept., the Free University, Berlin, Germany, May 2003.

  • A.O. Tastan,  "The Molecular Basis of Alpha-Thalassemia in Turkey: Establishment and Application of PCR-Based Methods," M.Sc. Thesis, Dept. of Molecular Biology and Genetics, Bosphorous University, Istanbul, Turkey, Feb. 1996.

B. Book Chapter:

  • A. Özlem Tastan Bishop, Ulrich Stelzl, Markus Pech and Knud H. Nierhaus, “Characterization of RNA-protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome,” Chapter 9 in: RNA-Protein Interaction Protocols, Methods in Molecular Biology, Vol. 488, 129-151, 2008.

C. Book:

Özlem Tastan Bishop (Editor) “Bioinformatics and Data Analysis in Microbiology”, Horizon/Caister Press (April 2014) ISBN: 978-1-908230-39-3. http://www.horizonpress.com/bioinformatics

D. Journal Papers:

  • Thommas M Musyoka, Aquillah M Kanzi, Kevin Loob and Özlem Tastan Bishop “Analysis of Non-Peptidic Compounds as Potential Malarial Inhibitors against Plasmodial Cysteine Proteases via Integrated Virtual Screening Workflow”  Journal of Biomolecular Structure and Dynamics  Accepted, DOI: 10.1080/07391102.2015.1108231, 2015.

  • Nicola J Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S. Pillay, Jacky L Snoep, Özlem Tastan Bishop, Nicki Tiffin “The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt”  PLOS Computational Biology  In Press, 2015.

  • David K Brown, David L Penkler, Thommas M Musyoka, and Özlem Tastan Bishop "JMS: An open source workflow management system and web-based cluster front-end for high performance computing"  PLOS One  2015 Aug 17;10(8):e0134273. doi: 10.1371/journal.pone.0134273. eCollection 2015.

  • Rowan Hatherley, David K Brown, Thommas M Musyoka, David L Penkler, Ngonidzashe Faya, Kevin A Lobb and Özlem Tastan Bishop "SANCDB: A South African Natural Compound Database" Journal of Cheminformatics, 7 (29), 2015. doi: 10.1186/s13321-015-0080-8. 

  • Rowan Hatherley, Crystal-Leigh Clitheroe, Ngonidzashe Faya and Özlem Tastan Bishop "Plasmodium falciparum Hop: Detailed analysis on complex formation with Hsp70 and Hsp90" Biochemical and Biophysical Research Communications, 2015, 456: 440-445. doi: 10.1016/j.bbrc.2014.11.103. Epub 2014 Dec 4. pii: S0006-291X(14)02144-5 

  • H3Africa Consortium “Enabling Genomic Revolution in Africa” Science, 2014, vol 344 (6190) pp 1346-1348.

  • Özlem Tastan Bishop, Ezekiel F. Adebiyi, Ahmed M. Alzohairy, Dean Everett, Kais Ghedira, Amel Ghouila, Judit Kumuthini, Nicola J. Mulder, Sumir Panji, Hugh-G. Patterton (for the H3ABioNet Consortium, as members of The H3Africa Consortium)“Bioinformatics Education -  Perspectives and Challenges out of Africa” Briefings in Bioinformatics 2015 Mar;16(2):355-64. doi: 10.1093/bib/bbu022. Epub 2014 Jul 2.

  • P Machanick and Ö Tastan Bishop, "How to establish a bioinformatics postgraduate degree programme - a case study from South Africa" Briefings in Bioinformatics 2015 Mar;16(2):346-54. doi: 10.1093/bib/bbu014. Epub 2014 May 2.

  • Hatherley, R., Blatch, G.L., Tastan Bishop, Ö. “Plasmodium falciparum Hsp70-x: An atypical cytosolic heat shock protein” Journal of Biomolecular Structure and Dynamics 2014 Nov;32(11):1766-79. doi: 10.1080/07391102.2013.834849. Epub 2013 Sep 13; Arxiv number: 1307.3446

  • Tastan Bishop, Ö., Edkins, A., Blatch, G.L., “Sequence and domain conservation of the coelacanth Hsp40 and Hsp90 chaperones suggests conservation of function” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2014 Sep;322(6):359-78. doi: 10.1002/jez.b.22541. Epub 2013 Sep 17.

  • Kumwenda, B., Litthauer, D., Tastan Bishop, Ö. and Reva, O. “Analysis of Protein Thermostability in Industrially Important Thermus Bacteria Species” Evolutionary Bioinformatics 9: 327–342, 2013.

  • Yssel, A., Reva O., Tastan Bishop, Ö. “Comparative Structural Bioinformatics Analysis of Bacillus amyloliquefaciens Chemotaxis Proteins within Bacillus subtilis Group” Applied Microbiology and Biotechnology 92(5):997-1008, 2011.

  • Tastan Bishop, Ö. and Kroon, M. “Study of protein complexes via homology modeling, applied to cysteine proteases and their protein inhibitors” Journal of Molecular Modeling 17(12):3163-72, 2011.

  • Mautsa, N., Prinsloo, E., Tastan Bishop, Ö. and Blatch, G.L. “Characterization of the PINIT domain of PIAS3: In vitro interaction with STAT3” Journal of Molecular Recognition 24: 795-803, 2011.

  • Tastan Bishop, A.Ö., De Beer, T.A.P. and Joubert, F. “Protein homology modeling and its use in South Africa”, South African Journal of Science, 104 (1 & 2): 2-6, 2008.

  • A. Özlem Tastan Bishop and Trevor Sewell “A new approach to possible substrate binding mechanisms for nitrile hydratase”, Biochemical and Biophysical Research Communications, 343: 319-325, 2006.

  • Srinivas Mullapudi, Lee Pullan, Ozlem T. Bishop, Hassan Khalil, James K. Stoops, Roland Beckmann, Peter M. Kloetzel, Elke Kruger and Pawel A. Penczek “Rearrangement of the 16S Precursor Subunits Is Essential for the Formation of the Active 20S Proteasome”, Biophysical Journal, 87: 1-8, 2004.

  • Markus A. Schäfer*, A. Özlem Tastan*, Sebastian Patzke, Gregor Blaha, Christian M. T. Spahn, Daniel N. Wilson, and Knud H. Nierhaus, “Codon-Anticodon Interaction at the P Site Is a Prerequisite for tRNA Interaction with the Small Ribosomal Subunit“, Journal of Biological Chemistry, 277: 19095-19105, 2002. (* Equally contributed first authorship)

  • A.O. Tastan, D. Canatan, A.N. Basak, “A Search For The a-Thal-2 Determinants –a3.7and –a4.2 in the Newborns from Antalya District of Turkey: Cord Blood Study Using the PCR Method”, Balkan Journal of Medical Genetics, 2(1), pp. 23-25, 1999.

  • David J. Picketts, Ayse O. Tastan, Douglas R. Higgs, and Richard J. Gibbons, “Comparison of the human and murine ATRX gene identifies highly conserved, functionally important domains”, Mammalian Genome, 9, pp. 400-403, 1998.

E. Conference Papers:

  • Vorster BJ, Tastan Bishop Ö, Schlüter U, Coetzer N and Michaud D. “New insights towards phytocystatin – papain interactions”, Annals of Applied Biology 96: 403 – 408, 2010.

  • A. Özlem Tastan Bishop, Gordon Wells, Fourie Joubert, Carsten Wrenger, Rolf D. Walter and Abraham I. Louw “Progress towards Determining the Structure of Plasmodium falciparum Pyridoxal Kinase”, Proceedings of First Southern African Bioinformatics Workshop, 2007, 41-44.

F. Recent Conference Abstracts:

  • CN Ryan, S Lapa, L Avdeeva, R Borriss, O Reva, Ö Tastan Bishop “A-domain binding pocketof nonribosomal peptidesynthetases of B. atrophaeus UCMB5137(63Z)” 3DSIG 2013, Structural Bioinformatics and Computational Biophysics, ISMB Satellite Meeting, Berlin Germany, July 2013.
  • Ö Tastan Bishop, AL Edkins and GL Blatch “Coelecanth chaperon machinery” 21th Annual International Conference on Intelligent Systems for Molecular Biology & 12th European Conference on Computational Biology (ISMB-ECCB), Berlin, Germany, July 2013.
  • Ö Tastan Bishop, A Kanzi and K Lobb “Non-peptide compoundsof South African natural origin as potential malarial inhibitors” 3DSIG 2013, Structural Bioinformatics and Computational Biophysics, ISMB Satellite Meeting, Berlin Germany, July 2013.
  • C-L Clitheroe and O Tastan Bishop “Structural analysis of malarial Hop protein and its interactions with several Hsp70s and Hsp90s under various simulated conditions applicable to the trophozoite (infectious) stage”  Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • J Njuguna and O Tastan Bishop “Structural analysis of prodomain inhibition of cysteine proteases in Plasmodium species” Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • S Adeyemi, O Tastan Bishop and A Edkins “Analysis of the interactions between type III Hsp40 and Hsp70 molecular chaperones from humans” Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • A Kanzi, K Lobb and O Tastan Bishop “Falcipains as malarial drug targets” Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • E Kihara and O Tastan Bishop “Structural bioinformatics analysis of Plasmodium Hsp40 proteins and their interactions with Plasmodium Hsp70s” Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • R Hatherley, G Blatch and O Tastan Bishop “Plasmodium falciparum Hsp70-x: An atypical cytosolic heat shock protein” Joint SAGS / SASBCB Conference, Stellenbosch, September 2012.
  • Hatherley, R.A., Pesce E. R., Tastan Bishop, Ö. and Blatch, G. L. “Comparative Analysis of two Malarial Heat Shock Proteins, PfHsp70-1 and PfHsp70-x” ISCB Africa ASBCB Conference on Bioinformatics, Cape Town, South Africa, 9-11 March 2011.
  • Mathu, A., Kaye, P., Lobb, K., Tastan Bishop, Ö. “The influence of mutations on the molecular architecture of the sub-type C HIV-1 protease receptor site” ISCB Africa ASBCB Conference on Bioinformatics, Cape Town, South Africa, 9-11 March 2011.
  • Tastan Bishop, Ö. and Kroon, M. “A Homology Based Study of the Complexes of Cysteine Proteases and Their Protein Inhibitors” ISCB Africa ASBCB Conference on Bioinformatics, Cape Town, South Africa, 9-11 March 2011.
  • Yssel A., Reva, O., Tastan Bishop, Ö. “The spatial evolution of the bacterial chemotaxis pathway” SAICSIT WITS conference 2009, 11-12 October 2009. (http://www.bioinf.wits.ac.za/sabioinf2009/biopapers.html)
  • Mokoena, F., Vorster, J., Tastan Bishop, Ö. “Malarial drug targets: cysteine proteases as hemoglobinases” SAICSIT WITS conference 2009, 11-12 October 2009. (http://www.bioinf.wits.ac.za/sabioinf2009/biopapers.html)
  • Kroon, M., Joubert, F., and Tastan Bishop, Ö. “Large Scale Sequence and Structural Analysis of Papain-like Cysteine Proteases” SAICSIT WITS conference 2009, 11-12 October 2009. (http://www.bioinf.wits.ac.za/sabioinf2009/biopapers.html)
  • Tastan Bishop, A.Ö. and Kroon, M. “Identification and Analysis of Common Features of Cysteine Proteases of Malaria Parasites for the Development of Novel Parasitic Protease Inhibitors” 17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology (ISMB-ECCB), Stockholm, Sweden. June 2009.
  • Vorster BJ, Tastan Bishop Ö, Schlüter U, Michaud D. “Understanding phytocystatin structure / function relationships through homology modeling”, 17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology (ISMB-ECCB), Stockholm, Sweden. June 2009.
  • Vorster, B.J., Tastan Bishop, Ö., Schlüter, U., Coetzer, N. and Michaud, D. “New insights towards phytocystatin – papain interactions. Agriculture: Africa’s “engine for growth” – Plant science & biotechnology hold the key. Rothamstead Research, Harpenden, UK. October 2009
  • B.J. Vorster, Ö. Tastan Bishop, U. Schlüter, K. Kunert, D. Michaud, Understanding plants cystatin structure/function relationships through homology modelingSouth African Journal of Botany, Volume 75, Issue 2, April 2009, Page 426
  • U. Schlüter, B.J. Vorster, Ö. Tastan Bishop, K.J. Kunert, D. Michaud,Phytocystatins: A comparative analysis of cysteine protease inhibitors in plants South African Journal of Botany, Volume 75, Issue 2, April 2009, Page 419

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Last Modified: Tue, 13 Oct 2015 10:14:16 SAST