Browsing Faculty of Natural Sciences by Author "Christoffels, Alan"
Now showing items 21-40 of 44
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A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads
Mbandi, Stanley K.; Hesse, Uljana; Rees, Jasper G.; Christoffels, Alan (Frontiers, 2014)Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base ... -
Gonad differentiation in zebrafish is regulated by the canonical Wnt signalling pathway
Sreenivasan, Rajini; Jiang, Junhai; Wang, Xingang; Bartfai, Richard; Kwan, Hsiao, Y.; Christoffels, Alan; Orban, Laszlo (Society for the Study of Reproduction, 2014)Zebrafish males undergo a ‘‘juvenile ovary-to-testis’’ gonadal transformation process. Several genes, including nuclear receptor subfamily 5, group A (nr5a) and anti-Mu¨ llerian hormone (amh), and pathways such as Tp53-mediated ... -
Human African trypanosomiasis research gets booost: unravelling the tsetse Genome
Aksoy, Serap; Attardo, Geoffrey; Berriman, Matthew; Christoffels, Alan; Lehane, Mike; Masiga, Daniel K.; Toure', Yeya (PLOS, 2014)Human African trypanosomiasis (HAT), also known as sleeping sickness, is a neglected disease that impacts 70 million people distributed over 1.55 million km2 in sub-Saharan Africa. Trypanosoma brucei gambiense accounts for ... -
Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a subset of 237 donors in the South African Bone Marrow Registry
Tshabalala, Mqondisi; Ingram, Charlotte; Schlaphoff, Terry; Borrill, Veronica; Christoffels, Alan; Pepper, Michael S. (Hindawi, 2018)Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry ... -
Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing
Allam, Mushal; Spillings, Belinda L.; Abdalla, Hiba; Mapiye, Darlington; Koekemoer, Lizette L.; Christoffels, Alan (BioMed Central, 2016)Background: Over the past several years, thousands of microRNAs (miRNAs) have been identified in the genomes of various insects through cloning and sequencing or even by computational prediction. However, the number of ... -
In silico repurposing of a Novobiocin derivative for activity against latency associated Mycobacterium tuberculosis drug target nicotinate-nucleotide adenylyl transferase (Rv2421c)
Cloete, Ruben; Shahbaaz, Mohd; Christoffels, Alan (Public Library of Science, 2021)Nicotinamide-nucleotide adenylyl transferase (Rv2421c) was selected as a potential drug target, because it has been shown, in vitro, to be essential for Mycobacterium tuberculosis growth. It is conserved between mycobacterium ... -
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms
Mbandi, Stanley K.; Hesse, Uljana; Van Heusden, Peter; Christoffels, Alan (BioMed Central, 2015)Background: De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially ... -
Information security at South African universities-Implications for biomedical research
Anderson, Dominique; Abiodun, Oluwafemi Peter; Christoffels, Alan (Oxford University Press, 2020)In South Africa, a similar regulation strategy to the European Union General Data Protection Regulation, called the Protection of Personal Information Act (No 4 of 2013) (POPIA), will be implemented, with a view to ... -
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
Woldesemayat, Adugna Abdi; Van Heusden, Peter; Ndimba, Bongani K.; Christoffels, Alan (BioMed Central, 2017)BACKGROUND: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth ... -
International Glossina Genome Initiative 2004-2014: a driver for post-genomic era research on the African continent
Christoffels, Alan; Masiga, Daniel K.; Berriman, Matthew; Lehane, Mike; Toure', Yeya; Aksoy, Serap (PLOS, 2014)Human African trypanosomiasis (HAT), also known as sleeping sickness, is a neglected disease that impacts 70 million people distributed over 1.55 million km2 in sub- Saharan Africa and includes at least 50% of the population ... -
Investigation of distinct gene expression profile patterns that can improve the classification of intermediate-risk prognosis in AML patients
Eshibona, Nasr; Livesey, Michelle; Christoffels, Alan (Frontiers Media, 2023)Acute myeloid leukemia (AML) is a heterogeneous type of blood cancer that generally affects the elderly. AML patients are categorized with favorable-, intermediate-, and adverse-risks based on an individual’s genomic ... -
Mice and men: Their promoter properties
Bajic, Vladimir B.; Tan, Sin lam; Christoffels, Alan; Schonbach, Christian; Lipovich, Leonard; Yang, Liang; Hofmann, Oliver; Kruger, Adele; Hide, Winston; Kai, Chikatoshi; Kawai, Jun; Hume, David, A.; Carninci, Piero; Hayashizaki, Yoshihide (PLoS Genetics, 2006)Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe the compositional landscape ... -
MicroRNA profile of Hermetia illucens (black soldier fly) and its implications on mass rearing
DeRaedt, Sarah; Christoffels, Alan (PloS one, 2022)The growing demands on protein producers and the dwindling available resources have made Hermetia illucens (the black soldier fly, BSF) an economically important species. Insights into the genome of this insect will better ... -
Molecular evolution of key receptor genes in primates and non-human primates
Picone, Barbara; Christoffels, Alan (Science Publishing Group, 2014)African primates remain an unexplored source of information required to complete the origin and evolution of many human pathogens. Current studies have shown the importance of several receptor human genes implicated in ... -
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans
Obiero, George F.; Nyanjom, Steven R. G.; Mireji, Paul O.; Christoffels, Alan; Robertson, Hugh M.; Masiga, Daniel K. (PLOS, 2014)Tsetse flies use olfactory and gustatory responses, through odorant and gustatory receptors (ORs and GRs), to interact with their environment. Glossina morsitans morsitans genome ORs and GRs were annotated using homologs ... -
A population model for the 2017/18 listeriosis outbreak in South Africa
Witbooi, Peter Joseph; Africa, Charlene Wilma Joyce; Christoffels, Alan; Ahmed, Ibrahim Hussin Ibrahim (PLoS One, 2020-03-12)We introduce a compartmental model of ordinary differential equations for the population dynamics of listeriosis, and we derive a model for analysing a listeriosis outbreak. The model explicitly accommodates neonatal ... -
Prediction of human-Bacillus anthracis protein–protein interactions using multi-layer neural network
Ahmed, Ibrahim; Witbooi, Peter; Christoffels, Alan (Oxford University Press, 2018)Triplet amino acids have successfully been included in feature selection to predict human-HPV protein-protein interactions (PPI). The utility of supervised learning methods is curtailed due to experimental data not being ... -
Predictive classifier models built from natural products with antimalarial bioactivity using machine learning approach
Egieyeh, Samuel; Syce, James; Malan, Sarel F.; Christoffels, Alan (Public Library of Science, 2018)In view of the vast number of natural products with potential antiplasmodial bioactivity and cost of conducting antiplasmodial bioactivity assays, it may be judicious to learn from previous antiplasmodial bioassays and ... -
Structure based identification of novel inhibitors against ATP synthase of Mycobacterium tuberculosis: A combined in silico and in vitro study
Cloete, Ruben; Grobbelaar, Melanie; Sampson, Samantha; Christoffels, Alan (International Journal of Biological Macromolecules, 2019)The shortcomings of conventional tuberculosis treatments resulting from the development of drug resistance in Mycobacteriumtuberculosis drive a need for the formulation of novel therapeutic agents. The diarylquinoline ... -
Taste and odorant receptors of the coelecanth- a gene repertoire in transition
Picone, Barbara; Hesse, Uljana; Panji, Sumir; Van Heusden, Peter; Jonas, Mario; Christoffels, Alan (Wiley, 2014)G-protein coupled chemosensory receptors (GPCR-CRs) aid in the perception of odors and tastes in vertebrates. So far, six GPCR-CR families have been identified that are conserved in most vertebrate species. Phylogenetic ...