Research Articles (SANBI): Recent submissions

Now showing items 101-120 of 127

    • Virome assembly and annotation: A surprise in the Namib Desert 

      Hesse, Uljana; Van Heusden, Peter; Kirby, Bronwyn; Olonade, Israel; van Zyl, Leonardo Joaquim; Trindade, Marla (Frontiers Research Foundation, 2017)
      Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further ...

    • Blood pressure gradients and cardiovascular risk factors in urban and rural populations in Abia State South Eastern Nigeria using the WHO STEPwise approach 

      Okpechi, Ikechi Gareth; Chukwuonye, Innocent Ijezie; Tiffin, Nicki; Madukwe, Okechukwu Ojoemelam; Onyeonoro, Ugochukwu Uchenna; Umeizudike, Theophilus Ifeanyichukwu; Ogah, Okechukwu Samuel; Onyeonoro, Ugochukwu Uchenna (Public Library of Science, 2013)
      Background: Developing countries of sub-Saharan Africa (SSA) face a double burden of non-communicable diseases (NCDs) and communicable diseases. As high blood pressure (BP) is a common global cardiovascular (CV) disorder ...

    • Trends in Genotypic HIV-1 Antiretroviral resistance between 2006 and 2012 in South African Patients receiving first- and second line antiretroviral treatment regimens 

      Van Zyl, Gert U.; Liu, Tommy F.; Claassen, Mathilda; Engelbrecht, Susan; de Oliveira, Tulio; Preiser, Wolfgang; Wood, Natasha T.; Travers, Simon A.; Shafer, Robert W. (University of the Western CapePublic Library of Science -- PLoS, 2013)
      South Africa's national antiretroviral (ARV) treatment program expanded in 2010 to include the nucleoside reverse transcriptase (RT) inhibitors (NRTI) tenofovir (TDF) for adults and abacavir (ABC) for children. We ...

    • A diverse array of genetic factors contribute to the pathogenesis of Systemic Lupus Erythematosus 

      Tiffin, Nicki; Adeyemo, Adebowale A.; Okpechi, Ikechi (Biomed Central, 2013)
      Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease with variable clinical presentation frequently affecting the skin, joints, haemopoietic system, kidneys, lungs and central nervous system. It can ...

    • The Influence of N-Linked Glycans on the MolecularDynamics of the HIV-1 gp120 V3 Loop 

      Wood, Natasha T.; Fadda, Elisa; Davis, Robert; Grant, Oliver C.; Martin, Joanne C.; Woods, Robert J.; Travers, Simon A. (PLoS ONE, 2013)
      N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising ...

    • Opportunities in Africa for training in genome science 

      Masiga, Daniel K.; Isokpehi, Raphael D. (Academic Journals, 2004)
      Genome science is a new type of biology that unites genetics, molecular biology, computational biology and bioinformatics. The availability of the human genome sequence, as well as the genome sequences of several other ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • Self-similarity of human protein interaction networks: a novel strategy of distinguishing proteins 

      Fadhal, Emad; Gamieldien, Junaid; Mwambene, Eric (2015)
      The successful determination of reliable protein interaction networks (PINs) in several species in the post-genomic era has hitherto facilitated the quest to understanding systems and structural properties of such networks. ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...