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Browsing by Author "Mulder, Nicola"

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Accumulation of splice variants and transcripts in response to PI3K inhibition in T cells

Author: Riedel, Alice ; Mofolo, Boitumelo ; Avota, Elita ; Schneider-Schaulies, Sibylle ; Meintjes, Ayton ; Mulder, Nicola ; Kneitz, Susanne Date: 2013 BACKGROUND: Measles virus (MV) causes T cell suppression by interference with phosphatidylinositol-3-kinase (PI3K) activation. We previously found that this interference affected the activity of splice regulatory proteins and a T cell inhibitory ... Read more c b
African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Author: Othman, Houcemeddine ; Zass, Lyndon ; da Rocha, Jorge E B ; Radouani, Fouzia ; Samtal, Chaimae ; Benamri, Ichrak ; Kumuthini, Judit ; Fakim, Yasmina J ; Hamdi, Yosr ; Mezzi, Nessrine ; Boujemaa, Maroua ; Okeke, Chiamaka Jessica ; Tendwa, Maureen B ; Sanak, Kholoud ; Chaouch, Melek ; Panji, Sumir ; Kefi, Rym ; Sallam, Reem M ; Ghoorah, Anisah W ; Romdhane, Lilia ; Kiran, Anmol ; Meintjes, Ayton P ; Maturure, Perceval ; Jmel, Haifa ; Ksouri, Ayoub ; Azzouzi, Maryame ; Farahat, Mohammed A ; Ahmed, Samah ; Sibira, Rania ; Turkson, Michael E E ; Ssekagiri, Alfred ; Parker, Ziyaad ; Fadlelmola, Faisal M ; Ghedira, Kais ; Mulder, Nicola ; Kamal Kassim, Samar Date: 11 Feb 2022 Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains ... Read more c b
An African Genome Variation Database and its applications in human diversity and health

Author: Todt, Davis Date: 2021 African genomes exhibit the highest levels of sequence and haplotype diversity of all extant human populations. A combination of historical as well as geographical factors have contributed toward the high level of genetic diversity in Ancestral ... Read more
Analysis of within-host evolution of Plasmodium Falciparum during treatment

Author: Okendo, Javan Ochieng Date: 2018 Antimalarial drugs impose strong selective pressure on Plasmodium falciparum parasite genomes and leave signatures of selection. The evolutionary basis of drug resistant malaria in endemic and epidemic settings continues to remain an ongoing ... Read more
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee)

Author: Welch, Lonnie ; Brooksbank, Cath ; Schwartz, Russell ; Morgan, Sarah L ; Gaeta, Bruno ; Kilpatrick, Alastair M ; Mietchen, Daniel ; Moore, Benjamin L ; Mulder, Nicola ; Pauley, Mark ; Pearson, William ; Radivojac, Predrag ; Rosenberg, Naomi ; Rosenwald, Anne ; Rustici, Gabriella ; Warnow, Tandy Date: 2016 Read more c b
A bioinformatic study on the feasibility of a cross-species proteomics analyses of mycobacteria

Author: Rajaonarifara, Elinambinina Date: 2013 Includes abstract. Includes bibliographical references. Read more
Characterisation of the metabolome of Mycobacterium tuberculosis to identify new pathways and pathway holes

Author: Wolfenden, Kristen Marie Date: 2014 Due to high incidence rates and the development of new drug-resistant or multidrug-resistant strains of TB, the development of new medicines and treatments for tuberculosis is a necessity. In order to develop these drugs, Mycobacterium ... Read more
Creating and analysing an African pan-genome

Author: Bourn, Jessica Jean Date: 2022 The human reference genome is currently a core resource for understanding the role of genetics in human health, disease, and variation, and has been invaluable in the development of clinical and computational tools for these purposes. However, ... Read more
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures

Author: Mazandu, Gaston ; Mulder, Nicola Date: 2013 BACKGROUND: The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow ... Read more c b
DAS Writeback: A Collaborative Annotation System

Author: Salazar, Gustavo ; Jimenez, Rafael ; Garcia, Alexander ; Hermjakob, Henning ; Mulder, Nicola ; Blake, Edwin Date: 2011 BACKGROUND: Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources ... Read more c b
Data integration for the analysis of uncharacterized proteins in Mycobacterium tuberculosis

Author: Mazandu, Gaston Kuzamunu Date: 2010 Mycobacterium tuberculosis is a bacterial pathogen that causes tuberculosis, a leading cause of human death worldwide from infectious diseases, especially in Africa. Despite enormous advances achieved in recent years in controlling the disease, ... Read more
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Author: Baichoo, Shakuntala ; Souilmi, Yassine ; Panji, Sumir ; Botha, Gerrit ; Meintjes, Ayton ; Hazelhurst, Scott ; Bendou, Hocine ; Beste, Eugene d ; Mpangase, Phelelani T ; Souiai, Oussema ; Alghali, Mustafa ; Yi, Long ; O’Connor, Brian D ; Crusoe, Michael ; Armstrong, Don ; Aron, Shaun ; Joubert, Fourie ; Ahmed, Azza E ; Mbiyavanga, Mamana ; Heusden, Peter v ; Magosi, Lerato E ; Zermeno, Jennie ; Mainzer, Liudmila S ; Fadlelmola, Faisal M ; Jongeneel, C. V ; Mulder, Nicola Date: 29 Nov 2018 Abstract Background The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa ... Read more
Development of computational methods for custom protein arrays analysis : a case study on a 100-protein ("CT100") cancer/testis antigen array

Author: Safari Serufuri, Jean-Michel Date: 2010 Custom antigen arrays offer a platform to assay the serological response of cancer patients to at set of selected cancer testis antigens in order to infer a diagnosis value or to assess the patient responses to particular treatments. However, ... Read more
Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity

Author: Nyangahu, Donald D ; Lennard, Katie S ; Brown, Bryan P ; Darby, Matthew G ; Wendoh, Jerome M ; Havyarimana, Enock ; Smith, Peter ; Butcher, James ; Stintzi, Alain ; Mulder, Nicola ; Horsnell, William ; Jaspan, Heather B Date: 07 Jul 2018 Background: Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining infant gut microbiota. ... Read more
Genetic characteristics of Plasmodium vivax from Northern Mali

Author: Djimde, Moussa Date: 2018 Introduction: The surprising presence of P. vivax in West Africa and their ability to infect a Duffy negative population is one more threat to public health. In order to contribute to malaria elimination efforts, there is a need to investigate ... Read more
Genetic dating and pattern of admixture in modern human evolution

Author: Defo, Joel Date: 2017 Genetic variation is shaped by admixture between populations in an evolutionary process. The mixture dynamic between groups of populations results in a mosaic of chromosomal segments inherited from multiple ancestral populations. The distribution ... Read more
GenGraph: a python module for the simple generation and manipulation of genome graphs

Author: Ambler, Jon M ; Mulaudzi, Shandukani ; Mulder, Nicola Date: 25 Oct 2019 Abstract Background As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often ... Read more
A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

Author: Chimusa, Emile R ; Meintjies, Ayton ; Tchanga, Milaine ; Mulder, Nicola ; Seoighe, Cathal ; Soodyall, Himla ; Ramesar, Rajkumar Date: 2015 We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between ... Read more c b
Identification of the virulence gene of Mycobacterium tuberculosis

Author: Rabiu, Halimah Adenike Date: 2007 The major thrust of this project is to identify and characterize potential virulence genes from M. tuberculosis. To this end, we have compiled and integrated information from various public databases to catalogue 246573 microbial genes from ... Read more
Impact of the mycobiome on the health of the female genital tract

Author: Gangiah, Tamlyn Kirstey Date: 2022 The female genital tract microbiome comprises a community of microorganisms. Imbalances in the microbiome are associated with vaginal diseases such as bacterial vaginosis (BV) and sexually transmitted infections (STIs). These diseases greatly ... Read more

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