Browsing Researchers in 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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Transcriptomic analysis reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain
Sreenivasan, Rajini; Cai, Minnie; Bartfai, Richard; Wang, Xingang; Orban, Laszlo; Christoffels, Alan (Plosone, 2008)Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. We have ... -
A uniquely African focus: bioinformatics is a field that has grown exponentially in the past few years, and it is becoming increasingly important to collaborate as the field continues to gather momentum
Christoffels, Alan (2015)Bioinformatics is a field that has grown exponentially in the past few years, and it is becoming increasingly important to collaborate as the field continues to gather momentum. -
Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans
Choudhury, Ananyo; Christoffels, Alan; Gamieldien, Junaid; Sefid-Dashti, Mahjoubeh J. (Nature Publishing Group, 2017)The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot ...