Browsing South African National Bioinformatics Institute (SANBI) by Author "Christoffels, Alan"
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The African Coelecanth genome provides insights into tetrapod evolution
Christoffels, Alan; Hesse, Uljana; Gamieldien, Junaid; Panji, Sumir; Picone, Barbara; Van Heusden, Peter (Macmillan Publishers, 2013)The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of ... -
Challenges of biobanking in South Africa to facilitate indigenous research in an environment burdened with human immunodeficiency virus, tuberculosis, and emerging non-communicable diseases
Abayomi, Akin; Christoffels, Alan; Grewal, Ravnit; Karam, Locunda A.; Rossouw, Catherine; Staunton, Ciara; Swanepoel, Carmen; van Rooyen, Beverley (Mary Ann Liebert, Inc., 2013)The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth ... -
Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
Vij, Shubha; Van Heusden, Peter; Christoffels, Alan; Mbandi, Stanley K.; Mwangi, Sarah (Public Library of Science, 2016)We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared ... -
Comparative analysis of testis and ovary transcriptomes in zebrafish by combining experimental and computational tools
Li, Yang; Chia, Jer, M; Bartfai, Richard; Christoffels, Alan; Yue, Gen, H; Ding, Ke; Ho, Mei, Y; Hill, James, A; Stupka, Elia; Orban, Laszlo (Wiley, 2004)Studies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, knowledge on late events such as gonad ... -
Computational characterization of iron metabolism in the tsetse disease vector, glossina morsitans: Ire stem-loops
Dashti, Zahra Jalali Sefid; Gamieldien, Junaid; Christoffels, Alan (BMC, 2016)Iron metabolism and regulation is an indispensable part of species survival, most importantly for blood feeding insects. Iron regulatory proteins are central regulators of iron homeostasis, whose binding to iron response ... -
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species
Woldesemayat, Adugna Abdi; Modise, David M.; Gemeildien, Junaid; Ndimba, Bongani K.; Christoffels, Alan (Public Library of Science, 2018)BACKGROUND Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major ... -
DAMPD: a manually curated antimicrobial peptide database
Sundararajan, Vijayaraghava S.; Gabere, Musa N.; Pretorius, Ashley; Adam, Saleem; Christoffels, Alan; Minna, Lehvaslaiho; Archer, John A.C.; Bajic, Vladimir B. (Oxford University Press, 2012)The demand for antimicrobial peptides (AMPs) is rising because of the increased occurrence of pathogens that are tolerant or resistant to conventional antibiotics. Since naturally occurring AMPs could serve as templates ... -
Database for exploration of functional context of genes implicated in ovarian cancer
Kaur, Mandeer; Radovanovic, Aleksander; Essack, Magbubah; Schaefer, Ulf; Maqungo, Monique; Kibler, Tracey; Schmeier, Sebastian; Christoffels, Alan; Narasimhan, Kothandaraman; Choolani, Mahesh; Bajic, Vladimir B. (Oxford Journals, 2009)Ovarian cancer (OC) is becoming the most common gynecological cancer in developed countries and the most lethal gynecological malignancy. It is also the fifth leading cause of all cancer-related deaths in women. The ... -
DDEC: Dragon databaseof genes implicated in esophageal cancer
Essack, Magbubah; Radovanovic, Aleksander; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V.; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B. (BioMed Central, 2009)Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage ... -
DDESC: Dragon database for exploration of sodium channels in human
Sagar, Sunil; Kaur, Mandeep; Dawe, Adam; Seshadri, Sundararajan V.; Christoffels, Alan; Schaefer, Ulf; Radovanovic, Aleksander; Bajic, Vladimir B. (BMC Cancer, 2008)Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic ... -
DDPC: Dragon database of genes associated with prostate cancer
Maqungo, Monique; Kaur, Mandeep; Kwofie, Samuel K.; Radovanovic, Aleksander; Schaefer, Ulf; Schmeier, Sebastian; Oppon, Ekow; Christoffels, Alan; Bajic, Vladimir B. (Oxford Journals, 2011)Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount ... -
Designing novel possible kinase inhibitor derivatives as therapeutics against Mycobacterium tuberculosis: An in silico study
Shahbaaz, Mohd; Nkaule, Anati; Christoffels, Alan (Scientific Reports, 2019)Rv2984 is one of the polyphosphate kinases present in Mycobacterium tuberculosis involved in the catalytic synthesis of inorganic polyphosphate, which plays an essential role in bacterial virulence and drug resistance. ... -
Evolution and structural analysis of Glossina morsitans (Diptera; Glossinidae) Tetraspanins
Murungi, Edwin, K.; Kariithi, Henry, M.; Adunga, Vincent; Obonya, Meshack; Christoffels, Alan (MDPI, Basel, Switzerland, 2014)Tetraspanins are important conserved integral membrane proteins expressed in many organisms. Although there is limited knowledge about the full repertoire, evolution and structural characteristics of individual members ... -
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Tegally, Houriiyah; San, James E.; Christoffels, Alan (American Association for the Advancement of Science, 2022)Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the ... -
Genome sequence of the tsetse fly (glossina morsitans): vector of African trypanosomiasis
Christoffels, Alan; Obiero, George F.; Harkins, Gordon William (American Association for the Advancement of Science, 2014)Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between ... -
Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map
Celton, Jean M.; Christoffels, Alan; Sargant, Daniel J.; Xu, Xiangming; Rees, Jasper G. (BioMed Central, 2010)Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies ... -
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 ...