Tastan Bishop Ö (Editor) "Bioinformatics and Data Analysis in Microbiology" Horizon/Caister Academic Press (April 2014) ISBN: 978-1-908230-39-3.
N’tji Diallo B, Glenister M, Musyoka TM, Lobb K, Tastan Bishop Ö "SANCDB: an update on South African natural compounds and their readily available analogs" Journal of Cheminformatics 2021 May 5 doi: 10.1186/s13321-021-00514-2.
Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa BT, Samtal C, Sallam RM, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedire K, Fadlelmola FM, Mulder N, Kassim SK "Human OMICs and Computational Biology research in Africa: Current challenges and prospects" PubMed 2021 April 1doi: 10.1089/omi.2021.0004.
LT Sigauke,Tastan Bishop Ö, Lobb K "Introducing derivatizeME and its application in the augmentation of a natural product library" Journal of Computational Biophysics and Chemistry 2021 March 20 doi: 10.1142/s2737416521500101.
Manyumwa CV, Tastan Bishop Ö "In Silico investigation of potential applications of gamma carbonic anhydrases as catalysts of CO2 biomineralization processes: A visit to the thermophilic bacteria Persephonella hydeogeniphila, Persephonella marina, Thermosulfidebacter takaii, and Thermus thermophilus" International Journal of Moleculars Sciences 2021 March 11 doi: 10.3390/ijms22062861.
Chebon-Bore L, Sanyanga TA, Manyumwa CV, Khairallah A, Tastan Bishop Ö "Decoding the molecular effects of Atovaquone linked resistant mutations on plasmodium falciparum Cytb-ISP complex in the phospholipid bilayer membrane" International Journal of Moleculars Sciences 2021 February 21 doi: 10.3390/ijms22042138.
N’tji Diallo B, Swart T, Hoppe HC, Tastan Bishop Ö, Lobb K "Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay" Nature Scientific Reports 2021 January 14 doi: 10.1038/s41598-020-80722-2.
Boateng RA, Tastan Bishop Ö, Musyoka TM "Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study" Malaria Journal 2020 November 30 doi: 10.1186/s12936-020-03512-1.
Veldman W, Liberato MV, Almeida VM, Souza VP, Frutuoso MA, Marana SR, Moses V, Tastan Bishop Ö, Polikarpov I "X-ray Structure, Bioinformatics Analysis, and Substrate Specificity of a 6-Phospho-β-glucosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis" Journal of Chemical Information and Modeling 2020 November 9 doi: 10.1021/acs.jcim.0c00759.
Manyumwa CV, Emameh RZ, Tastan Bishop Ö "Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses" Int J Mol Sci 2020 October 29 doi: 10.3390/ijms21218066.
Khairallah A, Ross C, Tastan Bishop Ö "Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites" Frontiers in Molecular Biosciences 2020 September 25 doi: 10.3389/fmolb.2020.575196.
Sheik Amamuddy O, Verkhivker GM, Tastan Bishop Ö "Impact of early pandemic stage mutations on molecular dynamics of SARS-CoV-2 Mpro" Journal of Chemical Information and Modeling 2020 August 27 doi: 10.1021/acs.jcim.0c00634.
Subramaniyam S, Yang S, N'tji Diallo B, Fanshu X, Lei L, Li C, et al. "Oral Phyto-thymol ameliorates the stress induced IBS symptoms" Nature Scientific Reports 2020 August 17 doi: 10.1038/s41598-020-70420-4.
Khairallah A, Tastan Bishop Ö, Moses V "AMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6‐pyruvoyl tetrahydropterin synthase" Journal of Biomolecular Structure and Dynamics 2020 July 28 doi: 10.1080/07391102.2020.1796800.
Nyamai DW, Tastan Bishop Ö "Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using In Silico Approaches" Int J Mol Sci 2020 May 27 doi: 10.3390/ijms21113803.
Sheik Amamuddy O, Musyoka TM, Boateng RA, Zabo S, Tastan Bishop Ö "Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase" Computational and Structural Biotechnology Journal 2020 May 18 doi: 10.1016/j.csbj.2020.05.009.
Sanyanga A, Tastan Bishop Ö. "Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function" Int J Mol Sci 2020 April 16 doi: 10.3390/ijms21082764.
Upfold N, Ross C, Tastan Bishop Ö, Knox C. "The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid" Viruses 2020 March 31 doi: 10.3390/v12040387.
Amusengeri A, Tata RB, Tastan Bishop Ö. "Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis" Molecules 2020 Feb 18 doi: 10.3390/molecules25040904.
Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker G, Tastan Bishop Ö. "Integrated Computational Approaches and Tools forAllosteric Drug Discovery" Int J Mol Sci 2020 Jan 28 doi: 10.3390/ijms21030847.
Amusengeri A, Astl L, Lobb K, Verkhivker GM, Tastan Bishop Ö "Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s" Int J Mol Sci 2019 November 8 doi: 10.3390/ijms20225574.
Musyoka TM, Bishop ÖT "South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches" Molecules 2019 November 7 doi: 10.3390/molecules24224036.
Sanyanga A, Nizami B, Tastan Bishop Ö "Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency" Molecules 2019 November doi: 10.3390/molecules24213987.
Musyoka TM, Njuguna JN, Tastan Bishop Ö "Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide based inhibitor design" Malaria Journal 2019 April doi: 10.1186/s12936-019-2790-2.
Siwe-Noundou X, Musyoka TM, Moses V, Ndinteh DT, Mnkandhla D, Hoppe H, Tastan Bishop Ö, Krause RWM "Anti-HIV-1 integrase potency of methylgallate from Alchornea cordifolia using in vitro and in silico approaches" Nature Scientific Reports 2019 March doi: 10.1038/s41598-019-41403-x.
Penkler DL, Tastan Bishop Ö "Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain" Nature Scientific Reports 2019 February doi: 10.1038/s41598-018-35835-0.
Nyamai DW, Tastan Bishop Ö "Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study" Malaria Journal 2019 February doi: 10.1186/s12936-019-2665-6.
Amusengeri A, Tastan Bishop Ö "Discorhabdin N, a South African Natural Compound, for Hsp72 and Hsc70 Allosteric Modulation: Combined Study of Molecular Modeling and Dynamic Residue Network Analysis" Molecules 2019 January doi: 10.3390/molecules24010188.
Kimuda MP, Laming D, Hoppe HC, Tastan Bishop Ö "Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays" Molecules 2019 January doi: 10.3390/molecules24010142.
Amamuddy OS, Bishop N, Tastan Bishop Ö "Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics" Nature Scientific Reports 2018 December doi: 10.1038/s41598-018-36041-8.
Musyoka T, Tastan Bishop Ö, Lobb K, Moses V "The determination of CHARMM force field parameters for the Mg2+ containing HIV-1 integrase" Chemical Physics Letters 2018 November doi: 10.1016/j.cplett.2018.09.019.
Penkler D, Tastan Bishop Ö "Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain" Preprint 2018 August doi: 10.1101/386755.
Musyoka T, Njuguna JN, Tastan Bishop Ö "Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide-based inhibitor design" Preprint 2018 August doi: 10.1101/381566.
Sheik Amamuddy O, Bishop N, Tastan Bishop Ö "Characterizing drug resistance using geometric ensembles from HIV protease dynamics" Preprint 2018 July doi: 10.1101/379958.
Ross CJ, Nizami B, Glenister M, Sheik Amamuddy O, Atilgan AR, Atilgan C, Tastan Bishop Ö "MODE-TASK: Large-scale protein motion tools" Bioinformatics 2018 May 29 doi: 10.1093/bioinformatics/bty427.
Ross CJ, Atilgan AR, Tastan Bishop Ö, Atilgan C "Unraveling the Motions behind Enterovirus 71 Uncoating" Biophysical Journal 2018 February 27 doi: 10.1016/j.bpj.2017.12.021. PMID: 29490244.
Penkler DL, Atilgan C, Tastan Bishop Ö "Allosteric Modulation of Human Hsp90α Conformational Dynamics" Journal of Chemical Information and Modeling 2018 February 12 doi: 10.1021/acs.jcim.7b00630.
Kimuda MP, Noyes H, Mulindwa J, Enyaru J, Alibu VP, Sidibe I, Ngoyi DM, Hertz-Fowler C, MacLeod A, Tastan Bishop Ö, Matovu E "No evidence for association between APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations" PLoS Neglected Tropical Diseases 2018 February 22 doi: doi.org/10.1371/journal.pntd.0006300.
Ksouri A, Ghedira K, Abderrazek RB, Gowri Shankar BA, Benkahla A, Tastan Bishop Ö, Bouhaouala-Zahar B "Homology modeling and docking of AahII-Nanobody complexes reveal the epitope binding site on AahII scorpion toxin" Biochemical and Biophysical Research Communications 2018 February 19 doi: 10.1016/j.bbrc.2018.01.036.
Penkler DL, Atilgan C, Tastan Bishop Ö "Allosteric Modulation of Human Hsp90α Conformational Dynamics" Journal of Chemical Information and Modeling 2018 January 29 doi: 10.1021/acs.jcim.7b00630.
Rafael CN, Ambler J, Niehaus A, Ross J, Tastan Bishop Ö "Establishment of "The South African Bioinformatics Student Council" and Activity Highlights" EMBnet 2018 January 26 doi: 10.14806/ej.23.0.903.
Brown DK, Tastan Bishop Ö. "HUMA: A platform for the analysis of genetic variation in humans" Human Mutation 2018 January 1 doi: 10.1002/humu.23334. PMID: 28967693
Sheik Amamuddy O, Bishop NT, Tastan Bishop Ö. "Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks" BMC Bioinformatics 2017 August 15 doi: 10.1186/s12859-017-1782-x.
Jongeneel CV, Achinike-Oduaran O, Adebiyi E, Adebiyi M, Adeyemi S, Akanle B, et al. "Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network" PLoS Computational Biology 2017 June 1 doi: 10.1371/journal.pcbi.1005419. PMID: 28570565
Ilboudo H, Noyes H, Mulindwa J, Kimuda MP, Koffi M, Kaboré JW, et al. "Introducing the TrypanoGEN biobank: A valuable resource for the elimination of human African trypanosomiasis" PLoS Neglected Tropical Diseases 2017 June 1 doi: 10.1371/journal.pntd.0005438. PMID: 28570558
Brown DK, Penkler DL, Sheik Amamuddy O, Ross C, Atilgan AR, Atilgan C, Tastan Bishop Ö. "MD-TASK: a software suite for analyzing molecular dynamics trajectories." Bioinformatics 2017 May 31 doi: 10.1093/bioinformatics/btx349. PMID: 28575169
Ross C, Knox C, & Tastan Bishop Ö. "Interacting motif networks located in hotspots associated with RNA release are conserved in Enterovirus capsids." FEBS letters 2017 May 22. doi: 10.1002/1873-3468.12663. PMID: 28471477
Penkler D, Sensoy O, Atilgan C, & Tastan Bishop Ö. "Perturbation Response Scanning Reveals Key Residues for Allosteric Control in Hsp70." Journal of Chemical Information and Modeling 2017 May 15. doi: 10.1021/acs.jcim.6b00775. PMID: 28505454
Moses V, Tastan Bishop Ö, & Lobb KA. "The evaluation and validation of copper (II) force field parameters of the Auxiliary Activity family 9 enzymes." Chemical Physics Letters 2017 April 8; 678, 91-97. doi: 10.1016/j.cplett.2017.04.022.
Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, et al. "Development of Bioinformatics Infrastructure for Genomics Research in H3Africa." Global Heart 2017 Mar 13. pii: S2211-8160(17)30005-4. doi: 10.1016/j.gheart.2017.01.005. PMID: 28302555
Brown DK, Sheik Amamuddy O, Tastan Bishop Ö. "Structure-Based Analysis of Single Nucleotide Variants in the Renin-Angiotensinogen Complex." Global Heart 2017 Mar 13. pii: S2211-8160(17)30006-6. doi: 10.1016/j.gheart.2017.01.006. PMID: 28302554
Brown DK, Tastan Bishop Ö. "Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: A Proposed Protocol for Analyzing Variation at the Protein Level." Global Heart 2017 Mar 13. pii: S2211-8160(17)30009-1. doi: 10.1016/j.gheart.2017.01.009. PMID: 28302551
Cornick JE, Tastan Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, et al. "The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1." Vaccine 2017 Feb 7;35(6):972-980. doi: 10.1016/j.vaccine.2016.12.037. PMID: 28081968
Hatherley R, Brown DK, Glenister M, Tastan Bishop Ö. "PRIMO: An Interactive Homology Modeling Pipeline" PLoS One 2016, Nov 17;11(11):e0166698. doi: 10.1371/journal.pone.0166698. PMID: 27855192
Moses V, Hatherley R, Tastan Bishop Ö. "Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins." Biotechnol Biofuels 2016, Nov 9;9:239. doi: 10.1186/s13068-016-0655-2. PMID: 27833654
Ross C, Upfold N, Luke GA, Tastan Bishop Ö, Knox C "Subcellular localisation of Theiler's Murine Encephalomyelitis Virus (TMEV) capsid subunit VP1 vis-á-vis host protein Hsp90" Virus Research 2016, Aug 15;222:53-63. doi: 10.1016/j.virusres.2016.06.003.
Musyoka TM, Kanzi AM, Lobb K, Tastan Bishop Ö "Structure Based Docking and Molecular Dynamic Studies of Plasmodial Cysteine Proteases against a South African Natural Compound and its Analogs" Nature Scientific Reports 2016, Mar 31;6:23690. doi: 10.1038/srep23690.
Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop Ö, Tiffin N. "The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt" PLoS Computational Biology 2016, Feb 4;12(2):e1004395. doi: 10.1371/journal.pcbi.1004395.
Thommas M. Musyoka, Aquillah M. Kanzi, Kevin Lobb 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 2016, Jan 28:1-18 1. [Epub ahead of print], doi: 10.1080/07391102.2015.1108231.
Kibet CK and Machanick P. "Transcription factor motif quality assessment requires systematic comparative analysis" F1000Research 2016, 4(ISCB Comm J):1429 (doi: 10.12688/f1000research.7408.2)
Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Ibrahimi A, Hide W, Jaufeerally Fakim Y, Jongeneel V, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Alzohairy AM, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N, H3ABioNet Consortium. "H3ABioNet, a sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa." Genome Research 2015, Dec 1. pii: gr.196295.115. doi: 10.1101/gr.196295.115.
Ngonidzashe Faya, David Penkler and Özlem Tastan Bishop "Human, Vector and Parasite Hsp90 Proteins: A Comparative Bioinformatics Analysis" FEBS Open Bio 2015, 10.1016/j.fob.2015.11.003.
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 10(8): e0134273, 2015. doi: 10.1371/journal.pone.0134273.
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 456: 440-445, 2015. 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. DOI: 10.1126/science.1251546.
P Machanick and Ö Tastan Bishop, "How to establish a bioinformatics postgraduate degree programme - a case study from South Africa" Briefings in Bioinformatics 16 (2): 346 - 54, 2015. 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 at the host–parasite interface"
Journal of Biomolecular Structure and Dynamics 32(11): 1766 - 79, 2014 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 322 (6): 359 - 78, 2014. 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. https://doi.org/10.4137/EBO.S12539.
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. https://doi.org/10.1007/s00894-011-0990-y.
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. https://doi.org/10.1007/s00253-011-3582-y.
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. https://doi.org/10.1002/jmr.1111.
Vorster BJ, Tastan Bishop Ö, Schlüter U, Coetzer N, Michaud D "New insights towards phytocystatin – papain interactions" Annals of Applied Biology 96: 403 – 408, 2010.
