List

Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua BP, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa bioRxiv 2024.03.13.584859; doi: https://doi.org/10.1101/2024.03.13.584859.
Lekhuleni C, Ndlangisa K, Gladstone RA, Chochua S, Metcalf BJ, Li Y, Kleynhans J, de Gouveia L, Hazelhurst S, Ferreira ADS, Skosana H, Walaza S, Quan V, Meiring S, Hawkins PA, McGee L, Bentley SD, Cohen C, Lo SW, von Gottberg A, & du Plessis M (2024). Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children. Nature Communications, 15(1), 8401. https://doi.org/10.1038/s41467-024-52459-3
Hazelhurst, S., Boua, P., Choudhury, A., Madala, S., Sengupta, D., Tluway, F., and Ramsay, M. (2024). Computation of Socio-Economic Status in the AWI-Gen Project. medRχiv. https://doi.org/10.1101/2024.08.22.24312411
Ohene-Kwofie D and Hazelhurst S (2024) Single Matrix Block Shift (SMBS) Dense Matrix Multiplication Algorithm In SAICSIT 2024: South African Computer Science and Information Systems Research Trends -- Proceedings of the 45th Annual Conference of the South African Institute of Computer Scientists and Information Technologists, Gerber A(Ed), pp. 190-206, Published as Communications in Computer and Information Science, Springer-Verlag, doi:10.1007/978-3-031-64881-6_11.
Twesigomwe D, DrDrögemDrögemoller BI, Wright GEB, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S (2024). Characterization of CYP2B6 and CYP2A6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clinical Pharmacology and Therapeutics, 115(3):576-594. doi: 10.1002/cpt.3124. PMID: 38049200.
Kamp M, Achilonu O, Kisiangani I, Nderitu DM, Mpangase PT, Tadesse GA, Adetunji K, Iddi S, Speakman S, Hazelhurst S, Asiki G and Ramsay M. (2023). Multimorbidity in African ancestry populations: a scoping review. BMJ Global Health, 8(12), e013509. https://doi.org/10.1136/bmjgh-2023-013509
Singh S, Choudhury A, Hazelhurst S, Crowther N, Boua P, Sorgho H, Agongo G, Nonterah E, Micklesfield L, Norris S, Kisiangani I, Mohamed S, Gomez-Olive FX, Tollman S, Choma S, Brandenburg JT and Ramsay M. (2023) Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study. Nature Communications. 14:8376,
Booyse RP, Twesigomwe D and Hazelhurst S. (2023) Characterization of CYP2C19 pharmacogenetic variation in African populations and comparison with other global populations. Pharmacogenomics 24(16) do:10.2217/pgs-2023-0166.
Sengupta D, Botha G, Meintjes A, Mbiyavanga M, AWI-Gen Study, H3Africa Consortium, Hazelhurst S, Mulder N, Ramsay M, Choudhury A. (2023) Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations. Cell Genomics 3(10032), pp1-11., doi:10.1016/j.xgen.2023.100332
Twesigomwe D, Drögemoller B, Wright G, Adebamowo C, Agongo G, Boua RP, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza M, Tiemessen C, Lombard Z, and Hazelhurst S (2023). Characterisation of CYP2D6 pharmacogenetic variation in sub-Saharan African populations. Clinical Pharmacology & Therapeutics 113(3), pp 643-649. doi.org/10.1002/cpt.2749
Kanoni S. et al. [GLCG Consortium] (2022). Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis., Genome Biology 23(268), 1-42. doi:10.1186/s13059-022-02837-1.
Brandenburg JT, Clark L., Botha G., Panji S, Baichoo S, Fields C and Hazelhurst S (2022). H3AGWAS: a portable workflow for genome wide association studies. BMC Bioinformatics 23, 498.
Wang WY, Twesigomwe D, Nofziger C, Turner AJ, Helmecke LS, Broeckel U, Derezinski A, Hazelhurst S, and Gaedigk, A. (2022). Characterization of Novel CYP2D6 Alleles across Sub-Saharan African Populations. Journal of Personalized Medicine, 12, 1575. doi:10.3390/jpm12101575
Booyse RP, Twesigomwe D and Hazelhurst S. (2022). Characterization of POR haplotype distribution in African populations and comparison with other global populations. Pharmacogenomics 23(14). doi:10.2217/pgs-2022-0082. ISSN 1462-2416.
Maré IA, Kramer B, Hazelhurst S, Nhlapho MD, Zent R, Harris P, Klipin MJ (2022). Electronic Data Capture System (REDCap) for Healthcare Research and Training in a Resource-Constrained Environment: Technology Adoption Case Study. JMIR Medical Informatics, 10(8), e33402. doi:10.2196/33402. ISSN 2291-9694
Ramdas et al. [GLCG Consortium] (2022). A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. The American Journal of Human Genetics, 109(8), 1366-1387. doi:10.1016/j.ajhg.2022.06.012 ISSN0002-9297
Choudhury A, Brandenburg JT, Chikowore T , Sengupta D, Boua P, Crowther N, Agongo G, Asiki G, Gomez-Olive FX, Kisiangani I, Maimela E, Masemola-Maphuta M, Micklesfield L, Nonterah E, Norris S, Sorgho H, Tinto H, Tollman S, Graham S, Willer C, AWI-Gen Study, H3Africa Consortium, Hazelhurst S, and Ramsay M. (2022) Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits, Nature Communications 13(2578), pp. 1-13.
Nkera-Gutabara CK, Kerr R, Scholefield J, Hazelhurst S, Naidoo J. (2022) Microbiomics: The Next Pillar of Precision Medicine and Its Role in African Healthcare. Frontiers in Genetics 13, 869610, April. doi:10.3389/fgene.2022.869610, ISSN 1664-8021.
Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., Wade, A. N., Wafawanaka, F., Xavier Gómez-Olivé, F., Twine, R., Lombard, Z., AWI-Gen Collaborative Centre, Hazelhurst, S. and Bhatt, A. S. (2022). Short-and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nature Communications, 13(926), 1-18.https://doi.org/10.1038/s41467-021-27917-x
Batista da Rocha J, Othman H and Hazelhurst S. (2022) Molecular dynamics of G6PD variants from sub-Saharan Africa, Biochemistry and Biophysics Reports, 30(101236), pp. 1-7, ISSN 2405-5808.
Boua, P. R., Brandenburg, J.-T., Choudhury, A., Sorgho, H., Nonterah, E. A., Agongo, G., Asiki, G., Micklesfield, L., Choma, S., Gómez-Olivé, F. X., Hazelhurst, S., Tinto, H., Crowther, N. J., Mathew, C. G. and Ramsay, M. (2022). Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans Nature Communications, 13(855), 1-11. https://doi.org/10.1038/s41467-022-28276-x
Mpangase PT, Frost J, Tikly M, Ramsay M and Hazelhurst S. (2021) nf-rnsaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data. South African Computer Journal 33(2), doi:10.18489/sacj.v33i2.830
Graham S et al [GLCG Consortium] (2021) The power of genetic diversity in genome-wide association studies of lipids. Nature https://doi.org/10.1038/s41586-021-04064-3.
Twesigomwe D, Drögemöller BI, Wright GEB, Siddiqui A, da Rocha J, Lombard Z, Hazelhurst S. (2021) StellarPGx: A Nextflow pipeline for calling star alleles in cytochrome P450 genes. Clinical Pharmacology & Therapeutics 110(3) September, pp. 741-749 doi:10.1002/cpt.2173. ISSN: 1532-6535
Othman H, da Rocha J and Hazelhurst S. (2021) Single Nucleotide Polymorphism Induces Divergent Dynamic Patterns in CYP3A5: A Microsecond Scale Biomolecular Simulation of Variants Identified in Sub-Saharan African Populations. Internatioal Journal of Molecular Sciences 22(7786), July, doi.org/10.3390/ijms22157786 (EISSN 1422-0067)
da Rocha J, Othman H, Tiemessen GT, Botha G, Ramsay M, Masimirembwa C, Adebamowo C, Choudhury A, Brandenburg JT, Matshaba M, Simo G, Gamo FJ, Hazelhurst S as members of the H3Africa Consortium. (2021) G6PD variant distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. The Pharmacogenomics Journal, July, doi.org/10.1038/ s41397-021-00242-8.
da Rocha J, Othman H, Botha G, Twesigomwe D, Ahmed S, Cottino L, Drögemöller BI, Fadlelmola F, Machanick P, Mbiyavanga M, Panji S, Wright GEB, Adebamowo C, Matshaba M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Baldwin SJ, Chiano M, Cox C, Gross AS, Thomas P, Gamo F-J, Hazelhurst S as members of H3Africa Consortium (2021) The extent and impact of variation in ADME genes in sub-Saharan African populations. Frontiers in Pharmacology, 12(634016), doi: 10.3389/fphar.2021.634016, ISSN 1663-9812.
Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, Gunnink H, Chousou-Polydouri N, Delius P, Tollman S, Gómez-Olive Casas FX, Norris S, Mashinya F, Alberts M, Hazelhurst S, Schlebusch CM, Ramsay M. (2021) Genetic substructure and complex demographic history of South African Bantu speakers. Nature Communications 12(2080).
Pantanowitz L, Michelow P, Hazelhurst S, Kalra S, Choi C, Shah S, Babaie M, Tizhoosh HR. (2021) A Digital Pathology Solution to Resolve the Tissue Floater Conundrum. Archives of Pathology & Laboratory Medicine 145 (3): 359-364.
Pantanowitz L, Wu U, Seigh L, LoPresti E, Yeh F-C, Yeh J, Salgia P, Michelow P, Hazelhurst S, Chen W, Hartman D. (2021) Artificial Intelligence-Based Screening for Mycobacteria in Whole Slide Images of Tissue Samples. American Journal of Clinical Pathology, 156, July, pp. 117-128.
Choudhury et al. (2020) High-depth African genomes inform human migration and health. Nature 586, pp. 741-748. doi: 10.1038/s41586-020-2859-7
Oduaran OH, Tamburini. FB, Sahibdeen. V, Brewster. R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman S, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS and Hazelhurst S. (2020) Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition. BMC Microbiology 20:330.
Ceballos F, Hazelhurst S, Clark D, Agongo G, Asiki G, Boua P, Gómez-Olivé FX, Mashinya F, Norris S, Wilson J, and Ramsay M. (2020) Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study Nature Communications 11:5754.
Pantanowitz L, Quiroga-Garza GM, Bien L, Heled R, Laifenfeld D, Linhart C, Sandbank J, Shach A, Shalev V, Vecsler M, Michelow P, Hazelhurst S, Dhir R. (2020) An artificial intelligence algorithm for prostate cancer diagnosis in whole slide images of core needle biopsies: a blinded clinical validation and deployment study The Lancet Digital Health, 2(8), e407-e416, doi.org/10.1016/S2589-7500(20)30159-X. ISSN 2589-7500.
Pantanowitz L, Hartman D, Qi Y, Cho EY, Suh B, Paeng K, Dhir R, Michelow P, Hazelhurst S, Song SY and Cho SY (2020). Accuracy and efficiency of an artificial intelligence tool when counting breast mitoses Diagnositic Pathology 15:80, doi.org/10.1186/s13000-020-00995-z.
Twesigomwe D, Wright GEB, Drögemoller B, da Rocha J, Lombard Z and Hazelhurst S. (2020). A Systematic Comparison of Pharmacogene Star Allele Calling Bioinformatics Algorithms: a Focus on CYP2D6 Genotyping. npj Genomic Medicine 5(20), doi.org/10.1038/s41525-020-0135-2, ISSN 2056-7944
Othman O, Bouslama Z, Brandenburg JT, da Rocha J, Hamdi Y, Ghedira K, Srairi-Abid N and Hazelhurst S. (2020). Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochemical and Biophysical Research Communications, 527 702-708
Mpangase PR, Frost J, Hazelhurst S and Ramsay M. (2020). nf-rnaSeqMetagen: A Nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data. Medicine in Microecology 4
Boua PR, Brandenburg JT, Choudhury A, Hazelhurst S, Sengupta D, Agongo G, Nonterah EA, Oduro AR, Tinto H, Mathew CG, Sorgho H, Ramsay M. (2020). Novel and Known Gene-Smoking Interactions With cIMT Identified as Potential Drivers for Atherosclerosis Risk in West-African Populations of the AWI-Gen Study. Frontiers in Genetics. 2020 Feb 7;10:1354. doi: 10.3389/fgene.2019.01354. eCollection 2019.
Ahmed AE, Mpangase P, Panji S, Baichoo S, Botha G, Fadlelmola FM, Hazelhurst S, van Heusden P, Jongeneel CV, Joubert F,Sergeevna Mainzer L, Meintjes A, Armstrong D, Crusoe MR, O'Connor BD , Souilmi Y, Alghali M, Aron S, Bendou H, De Beste E, Mbiyavanga M, Souiai O, Yi L, Zermeno J, Mulder N. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience [version 2; peer review: 2 approved, 1 approved with reservations]. AAS Open Research 1(9), https://doi.org/10.12688/AASOPENRES.12847.2
Parker, Z, Maslamoney, S, Meintjes, A, Botha, G, Panji, S, Hazelhurst, S and Mulder, N. (2019). Building Infrastructure for African Human Genomic Data Management. Data Science Journal, 18: 47, pp. 1-8. DOI: https://doi.org/10.5334/dsj-2019-047. ISSN: 1683-1470
Ceballos FC, Hazelhurst S, Ramsay M. (2019), Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories . Human Genetics 138:1123-1142, doi.org/10.1007/s00439-019-02045-1. ISSN 1432-1203
Nonterah EA, Boua PR, Klipstein-Grobusch K, Asiki G, Micklesfield LK, Agongo G, Ali SA, Mashinya F, Sorgho H, Nakanabo-Diallo S, Debpuur C, Kyobutungi C, Alberts M, Norris S, Tollman S, Tinto H, Soo C, Mukomana F, Hazelhurst S, Wade A, Kahn K, Oduro AR, Grobbee DE, Sankoh O , Ramsay M, Bots ML, Crowther NJ as members and collaborators of AWI-Gen and as members of the H3Africa Consortium, Lombard Z, Gómez-Olivé Casas FX, Wagner R, Cook I, Ntuli S, Khayeka-Wandabwa C, Haregu T, Mohammed SF, Muthuri S, Rouamba T, Fato E, Anati I, Amega-Etego L , Baloyi N , Kagura J, Munthali R, Guman Y, and Choudhury A. (2019). Classical Cardiovascular Risk Factors and HIV are Associated With Carotid Intima-Media Thickness in Adults From Sub-Saharan Africa: Findings From H3Africa AWI-Gen Study. Journal of the American Heart Association 8(14), 2019, https://doi.org/10.1161/JAHA.118.011506. ISSN: 2047-9980
Brewster R, Tamburini FB, Asiimwe E, Oduaran O, Hazelhurst S and Bhatt AS (2019). Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends in Microbiology 27(10), 824-835. https://doi.org/10.1016/j.tim.2019.05.006. ISSN: 0966-842X.
Ramsay, M, Crowther N, Agongo G, Ali SA, Asiki G, Boua R, Gómez-Olivé FX, Kahn K, Khayeka-Wandabwa C, Mashinya F, Micklesfield L, Mukomana F, Nonterah EA, Soo C, Sorgho H, Wade A, Wagner R, Alberts M, Hazelhurst S, Kyobutungi C, Norris S, Oduro A, Sankoh O, Tinto H, Tollman S as members of AWI-Gen and the H3Africa Consortium. Regional and sex-specific variation in BMI distribution in four sub-Saharan African countries: The H3Africa AWI-Gen study. Global Health Action 11:sup2, 1556561, doi:10.1080/16549716.2018.1556561. ISSN 1654-9880.
Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, De Beste E, Mpangase P, Souiai O, Alghali M, Yi L, O'Connor B, Crusoe M, Armstrong D, Aron S, Joubert D, Ahmed A, Mbiyavanga M, Van Heusden P, Magosi, L, Zermeno, J, Mainzer L, Fadlelmola F, Jongeneel CV, and Mulder N. (2018) Developing reproducible bioinformatics analysis workflows for heterogenous computing environments to support African genomics , BMC Bioinformatics 19, 457, 13 pages, doi:10.1186/s12859-018-2446-1
Ali S, Soo C, Agongo G, Alberts M, Amenga-Etego L, Boua R, Choudhury A, Crowther N, Depuur C, Goómez-Olivé FX, Guiraud I, Haregu T, Hazelhurst S, Kahn K, Khayeka-Wandabwa C, Kyobutungi C, Lombard Z, Mashinya F, Micklesfield L, Mohamed S, Mukomana F, Nakanabo-Diallo S, Natama H, Ngomi N, Nonterah EA, Norris SA, Oduro A, Somé A, Sorgho H, Tindana P, Tinto H, Tollman S, Twine R, Wade A, Sankoh O and Ramsay M. Genomic and environmental risk factors for cardiometabolic diseases in Africa: methods used for Phase 1 of the AWI-Gen population cross-sectional study, Global Health Action, 11:sup2, 1507133, doi:10.1080/16549716.2018.150713.
Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Human Molecular Genetics, 27(R2), 1 August 2018, pp. R209-R218, doi:10.1093/hmg/ddy16.
Sahibdeen V, Crowther NJ, Soodyall H, Hendry LM, Munthali RJ, Hazelhurst S, Choudhury A, Norris SA, Ramsay M and Lombard Z. (2018) Genetic variants in SEC16B are associated with body composition in black South Africans. Nutrition and Diabetes 8:43. doi:10.1038/s41387-018-0050-0.
Ceballos FC, Hazelhurst S and Ramsay M. (2018) Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data. BMC Genomics19:106, https://doi.org/10.1186/s12864-018-4489-0.
Choudhury A, Ramsay M, Hazelhurst S, Aron S, Bardien S, Botha G, Chimusa ER, Christoffels A, Gamieldien J, Sefid-Dashti MJ, Joubert F, Meintjes F, Mulder N, Ramesar R, Rees J, Scholtz K, Sengupta D, Soodyall H, Venter P,Warnich L, Pepper MS. (2017) Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nature Communications 8(1), 2062. doi:10.1038/s41467-017-00663-9.
Soo CS, Mukomana F, Hazelhurst S, Ramsay M. Establishing an Academic Biobank in a Resource Challenged Environment. South African Medical Journal, 107(6), 486-492, 2017. doi:10.7196/SAMJ.2017.v107i6.12099
Jongeneel CV, Achinike-Oduaran O, Adebiyi R, Adebiyi M, Adeyemi S, Akanle B, Aron S, Ashano E, H Bendou, G Botha, E Chimusa, A Choudhury, R Donthu, J Drnevich, O Falola, Fields CJ, Hazelhurst S, Hendry L, Isewon I, Khetani RS, Kumuthini J, Kimuda MP, Magosi L, Sergeevna Mainzer L, Maslamoney S, Mbiyavanga M, Meintjes A, Mugutso D, Mpangase P, Munthali R, Nembaware V, Ndhlovu A, Odia T, Okafor A, Oladipo O, Panji S, Pillay V, Rendon G, Sengupta D, Mulder N, as members of the H3ABioNet Consortium. (2017) Assessing Computational Genomics Skills: Our Experience in the H3ABioNet African Bioinformatics Network. PLoS Computational Biology, June. doi:10.1371/journal.pcbi.1005419
Gómez-Olivé FX, Ali SA, Made F, Kyobutungi C, Nonterah E, Micklesfield L, Alberts M, Boua R, Hazelhurst S, Debpuur C, Mashinya F, Dikotope S, Sorgho H, Cook I, Muthuri S, Soo C, Mukomana F, Agongo G, Wandabwa C, Afolabi S, Oduro A, Tinto H, Wagner RG, Haregu T, Wade A, Kahn K, Norris SA, Crowther NJ, Tollman S, Sankoh O, Ramsay M. as members of AWI-Gen and the H3A Consortium. (2017) Stark Regional and Sex Differences in the Prevalence and Awareness of Hypertension. Global Heart, 12(2), pp. 81-90. doi: 10.1016/j.gheart.2017.01.007
Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, Akanle B, Alibi M, Armstrong DL, Aron S, Ashano E, Baichoo S, Benkahla A, Brown DK, Chimusa ER, Fadlelmola FM, Falola D, Fatumo S, Ghedira K, Ghouila A, Hazelhurst S, Isewon I, Jung S, Kassim SK, Kayondo JK, Mbiyavanga M, Meintjes A, Mohammed S, Mosaku A, Moussa A, Muhammd M, Mungloo-Dilmohamud Z, Nashiru O, Odia T, Okafor A, Oladipo O, Osamor V, Oyelade J, Sadki K, Salifu S, Soyemi J, Panji S, Radouani F, Souiai O, Tastan Bishop Ö and the H3ABionet Consortium as members of the H3A Consortium. (2017) Development of Bioinformatics Infrastructure for Genomics Research in H3Africa Global Heart, 12(2), pp 91-98. doi: 10.1016/j.gheart.2017.01.005.
Ramsay M, et al. (2016) H3Africa AWI-Gen Collaborative Centre: a resource to study the interplay between genomic and environmental risk factors for cardiometabolic diseases in four sub-Saharan African countries. . Global Health, Epidemiology and Genomics, 1(e20), November. doi:10.1017/gheg.2016.16.
Kench D, Hazelhurst S, Otulaja F. Grit and growth mindset among high school students in a computer programming project: A mixed methods study. In Proceedings of the South African Computer Lecturers' Association Conference, July 2016.
Mulder NJ, et al. H3ABioNet, a sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa. Genome Research 2016. 26: 271-277
Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J., Pilay C, Snoep JL, Ozlem Bishop T, Tiffin N. The Development of Computational Biology in South Africa: successes achieved and lessons learnt. PLoS Computational Biology 12(2), February 2016. doi:10.1371/journal.pcbi.1004395
Miteff S and Hazelhurst S. NFShunt: a Linux firewall with OpenFlow-enabled hardware bypass. Proceedings of the IEEE Conference on Network Function Virtualization and Software Defined Networks, San Francisco, November 2015, doi:10.1109/NFV-SDN.2015.7387413 .
Ndhlovu A, Hazelhurst S. and Durand PM. Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix. BMC Bioinformatics, 16(1):255, 2015, doi:10.1186/s12859-015-0688-8
Ndhlovu A, Durand PM and Hazelhurst S. EvoDB: A database of evolutionary and phylogenetic trees for PFAM-A. Database: The Journal of Databases and Curation, 2015, doi: 10.1093/database/bav065. ISSN: 1758-0463
Robillard DE, Mpangase PT, Hazelhurst S, and Dehne F. SpeeDB: Fast Structural Protein Searches , Bioinformatics ISSN 1460-2059, 31(18) 3027-3034, 2015.
Klipin M, Mare I, Hazelhurst S, and Kramer, B. The Process of Installing REDCap, a Web Based Database Supporting Biomedical Research: The First Year. Applied Clinical Informatics 5(4), pp. 916-929, 2014. DOI: 10.4338/ACI-2014-06-CR-0054, 2014.
The H3Africa Consortium. Enabling the genomic revolution in Africa. Science, 20 June 2014, pp. 1346-1348.
Govind N, Choudhury A, Hodkinson B, Ickinger C, Frost J, Lee A, Gregersen PK, Reynolds RJ, Bridges SL, Hazelhurst S, Ramsay M and Tikly M. Immunochip Identifies Novel, and Replicates Known, Genetic Risk Loci for Rheumatoid Arthritis in Black South Africans. Molecular Medicine 30:341-349, 2014. ISSN: 1528-3658
Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Jalali Sefid Dashti M, Mulder N, Tiffin N and Ramsay M. Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genomics 15:437, 2014. doi:10.1186/1471-2164-15-437 ISSN: 1471-2164.
Buchmann R and Hazelhurst. Genesis Manual: Software for visualising population admixture and PCA.
May A, Hazelhurst S, Li Y, Norris SA, Govind N, Tikly M, Hon C, Johnson KJ, Hartmann N, Staedtler F and Ramsay M. Genetic diversity in black South Africans from Soweto. BMC Genomics 14:644, 2013. doi:101186/1471-2164-14-644. Data.
Hazelhurst S and Lipták Z. KABOOM! A new suffix-array based algorithm for clustering expression data. Bioinformatics, 27(24):3348-55, December. 2011. doi: 10.1093/bioinformatics/btr560.
Hazelhurst S, Johnson Y, Sanders I. An empirical analysis of the relationship between web usage and academic performance in undergraduate students. Proceedings of the Annual Conference of the South African Computer Lecturer's Association, Ballito, South Africa, July 2011, pp. 29-37.
Hazelhurst S. Truth in advertising: Reporting performance of computer programs, algorithms and the impact of architecture. South African Computer Journal 46, December 2010, pp. 24-37
Hazelhurst S. PH2: An Hadoop-based framework for mining structural properties from the PDB Database. Proceedings of the Annual Research Symposium of the South African Institute of Computer Scientists and Information Technologists (SAICSIT 2010), ACM International Conference Publication Series, pp. 104-112
Durand PM, Hazelhurst S, and Coetzer TL. Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. BMC Bioinformatics 11:151, doi:10.1186/1471-2105-11-151, 2010.
Cohen J and Hazelhurst S (Eds). Proceedings of the Annual Research Symposium of the South African Institute of Computer Scientists and Information Technologists (SAICSIT 2009). ACM International Conferences Proceedings. 2009. ISBN 978-1-60558-643-4.
Araya S and Hazelhurst S. Support vector machine prediction of HIV-1 drug resistance using the viral nucleotide patterns. Transactions of the Royal Society of South Africa. 64(1), pp. 62-72, 2009.
Hazelhurst S. Scientific computing using virtual high-performance computing: a case study using the Amazon Elastic Computing Cloud. Proceedings of SAICSIT 2008, October 2008. ACM International Conference Proceedings
Hazelhurst S. Algorithms for clustering EST sequences: the wcd tool. South African Computer Journal, 40, June 2008. pp. 51-62.,
Hazelhurst S, Hide W, Liptak Z, Nogueira R, and Starfield R. An overview of the wcd EST clustering tool. Bioinformatics. 24(13), July 2008, pp. 1542-1546. doi: 10.1093/bioinformatics/btn203. PDF.
Hazelhurst S. The wcd 0.4 EST Clustering Tool Manual . Technical Report TR-Wits-CS-2007-3, August, 2007. Document PDF (35 pages)
Hazelhurst S and Ramsay M (Eds). Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January 2007, Johannesburg, South Africa. ISBN 978-0-620-38113-0.
Oni O and Hazelhurst S. A Scheme to Improve Internet Firewall Efficiency for IPv6. International Conference on Internet Technologies and Applications (ITA05), Wrexham, United Kingdom, September 2005.
Hazelhurst S. Semantics, implementation and performance of dynamic access lists for TCP/IP packet filtering. South African Computer Journal, Vol. 33 December 2004.
Hazelhurst S. An efficient implementation of the d2 distance function for EST clustering: preliminary investigations. Accepted for Proceedings of the Annual Conference of the South African Insitute of Computer Scientists and Information Technologists, Stellenbosch, 4--6 October 2004.
Hazelhurst S. Generating and model checking a hierarchy of abstract models. South African Computer Journal, Vol 32, July 2004, pp. 53-68.
Zimmermann J, Liptak Z, and Hazelhurst S. A Method for Evaluating the Quality of String Dissimilarity Measures and Clustering Algorithms for EST Clustering. In Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), May 2004, Taiwan, pp. 301--309.
Badimo A, Bergheim A, Hazelhurst S, Papathanasopolous M, Morris L. The stability of phylogenetic tree construction of the HIV-1 virus using genome-ordering data versus env} gene data. Proceedings of SAICSIT 2003, September 2003.
Hazelhurst S, Weissberg O, Kamhi G and Fix L. A Hybrid Verification Approach : Getting Deep into the Design. Proceedings of the 39th ACM/IEEE Design Automation Conference, New Orleans, United States, June 2002.
Hazelhurst S and Arlat J. Specifying and Verifying Fault Tolerant Hardware. Designing Correct Circuits, Grenoble, France, April 2002.
Lipson A and Hazelhurst S. DNA Pattern Matching with FPGAs. Proceedings of the Twelfth Symposium of the Pattern Recognition Association of South Africa, November 2001.
Hazelhurst S. Viewpoint: Developing IT skills internationally: who's developing whom? Communications of the ACM 44(7), July 2001, pp. 27-28.
Hazelhurst S. A Proposal for Dynamic Access Lists for TCP/IP Packet Filtering. Proceedings of the South African Institute of Computer Scientists and Information Technologists, September 2001.
Sinnappan R and Hazelhurst S. `A Reconfigurable Approach to Packet Filtering'. In Proceedings of FPL 2001: 11th International Conference on Field Programmable Logic and Applications, Belfast, United Kingdom, August 2001.
Hazelhurst S, Attar A, and Sinnappan R. Algorithms for Improving the Dependability of Firewall and Filter Rule Lists. Workshop on Dependability of IP Applications, Platforms and Networks. Published in Proc. Int Conf on Dependable Systems and Network, IEEE Computer Society Press, New York, June 2000.
Chen Y, Galpin V, Hazelhurst S, Mateer R and Mueller C. Development of a Decentralized Virtual Service Redirector for Internet Applications. Proceedings of the Seventh IEEE Workshop on Future Trends of Distributed Computing Systems, December 1999, pp. 235--241.
Hazelhurst S. Generalised Unification of Finite Temporal Logic Formulas. South African Computer Journal 24, November 1999, pp. 110-118. (Research Paper) (Previous version available as technical report TR-Wits-CS-1999-6, July 1999.
Galpin V, Hazelhurst S, Mueller C and Sanders I, Introducing Research Methods to Honours Students. South African Computer Journal, 24, November 1999. pp. 258-263. (Experience paper)
Report on experiences on web-based learning: Postscript version for printing; HTML version for on-line viewing.
Hazelhurst S and Seger C.-J.H. . Model Checking Lattices: Using and reasoning about information orders for abstraction. Logic Journal of the IGPL, 7(3), May 1999, pp 375-411.
Hazelhurst S. Generating and Model Checking a Hierarchy of Abstract Models. Technical Report TR-Wits-CS-1999-0, March, 1999.Abstract Document PostScript, gzip
Hazelhurst S and Seger C.J-H . Symbolic Trajectory Evaluation. In "Formal Hardware Verification: Methods and Systems in Comparison" (T. Kropf, Ed). Springer-Verlag State of the Art Survey. LNCS 1287.
Hazelhurst S. Compositional Model Checking of Partially Ordered State Spaces. PhD Thesis: Technical Report 96-02, Department of Computer Science, University of British Columbia.
Hazelhurst S and Seger C.-J.H. A Simple Theorem Prover Based on Symbolic Trajectory Evaluation and OBDDs. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 14(4), April 1995, pp. 413-422.
Hazelhurst S and Seger CJH. Composing Symbolic Trajectory Evaluation Results. In Proceedings of the Sixth International Conference on Computer-Aided Verification, (D. L. Dill, Ed), Stanford University, United States, 20--24 June 1994, pp. 273--285.
Hazelhurst S. A Linda Solution to the Evolving Philosophers Problem. South African Computer Journal 5, 1991, pp. 44--53.
Hazelhurst S. Modula-2 Muddles. SIGPLAN Notices 25(4), April 1990, pp. 9-11. [Unrefereed, appearing as a letter to the editor, but still I thought it made a point.]

List of papers and other work