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2. The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Author

Kiran, Anmol, primary, Hanachi, Mariem, additional, Alsayed, Nihad, additional, Fassatoui, Meriem, additional, Oduaran, Ovokeraye H, additional, Allali, Imane, additional, Maslamoney, Suresh, additional, Meintjes, Ayton, additional, Zass, Lyndon, additional, Rocha, Jorge Da, additional, Kefi, Rym, additional, Benkahla, Alia, additional, Ghedira, Kais, additional, Panji, Sumir, additional, Mulder, Nicola, additional, Fadlelmola, Faisal M, additional, and Souiai, Oussema, additional

Published
2024
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3. African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Author

Othman, Houcemeddine, primary, Zass, Lyndon, additional, da Rocha, Jorge E. B., additional, Radouani, Fouzia, additional, Samtal, Chaimae, additional, Benamri, Ichrak, additional, Kumuthini, Judit, additional, Fakim, Yasmina J., additional, Hamdi, Yosr, additional, Mezzi, Nessrine, additional, Boujemaa, Maroua, additional, Okeke, Chiamaka Jessica, additional, Tendwa, Maureen B., additional, Sanak, Kholoud, additional, Chaouch, Melek, additional, Panji, Sumir, additional, Kefi, Rym, additional, Sallam, Reem M., additional, Ghoorah, Anisah W., additional, Romdhane, Lilia, additional, Kiran, Anmol, additional, Meintjes, Ayton P., additional, Maturure, Perceval, additional, Jmel, Haifa, additional, Ksouri, Ayoub, additional, Azzouzi, Maryame, additional, Farahat, Mohammed A., additional, Ahmed, Samah, additional, Sibira, Rania, additional, Turkson, Michael E. E., additional, Ssekagiri, Alfred, additional, Parker, Ziyaad, additional, Fadlelmola, Faisal M., additional, Ghedira, Kais, additional, Mulder, Nicola, additional, and Kamal Kassim, Samar, additional

Published
2022
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5. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

Author

Ahmed, Azza E., primary, Mpangase, Phelelani T., additional, Panji, Sumir, additional, Baichoo, Shakuntala, additional, Souilmi, Yassine, additional, Fadlelmola, Faisal M., additional, Alghali, Mustafa, additional, Aron, Shaun, additional, Bendou, Hocine, additional, De Beste, Eugene, additional, Mbiyavanga, Mamana, additional, Souiai, Oussema, additional, Yi, Long, additional, Zermeno, Jennie, additional, Armstrong, Don, additional, O'Connor, Brian D., additional, Mainzer, Liudmila Sergeevna, additional, Crusoe, Michael R., additional, Meintjes, Ayton, additional, Van Heusden, Peter, additional, Botha, Gerrit, additional, Joubert, Fourie, additional, Jongeneel, C. Victor, additional, Hazelhurst, Scott, additional, and Mulder, Nicola, additional

Published
2019
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7. Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Author

Mulder, Nicola J, Adebiyi, Ezekiel, Adebiyi, Marion, Adeyemi, Seun, Ahmed, Azza, Ahmed, Rehab, Akanle, Bola, Alibi, Mohamed, Armstrong, Don L, Aron, Shaun, Ashano, Efejiro, Baichoo, Shakuntala, Benkahla, Alia, Brown, David K, Chimusa, Emile R., Fadlelmola, Faisal M., Falola, Dare, Fatumo, Segun, Ghedira, Kais, Ghouila, Amel, Hazelhurst, Scott, Isewon, Iunu, Jung, Segun, Kassim, Samar Kamal, Kayondo, Jonathan K, Mbiyavanga, Mamana, Meintjes, Ayton, Mohammed, Somia, Mosaku, Abayomi, Moussa, Ahmed, Muhammd, Mustafa, Mungloo-Dilmohamud, Zahra, Nashiru, Oyekanmi, Odia, Trust, Okafor, Adaobi, Oladipo, Olaleye, Osamor, Victor, Oyelade, Jellili, Sadki, Khalid, Salifu, Samson Pandam, Soyemi, Jumoke, Panji, Sumir, Radouani, Fouzia, Souiai, Oussama, and Tastan Bishop, Özlem

Subjects
Biomedical Research, Africa, Computational Biology, Humans, Genomics, Article
Abstract

Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community.H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training.For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.

Published
2017

8. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Author

Jongeneel, C Victor, Bendou, Hocine, Chimusa, Emile, Drnevich, Jenny, Falola, Oluwadamila, Fields, Christopher J, Hazelhurst, Scott, Hendry, Liesl, Isewon, Itunuoluwa, Kimuda, Magambo Phillip, Mainzer, Liudmila Sergeevna, Maslamoney, Suresh, Meintjes, Ayton, Munthali, Richard, Odia, Trust, Pillay, Venesa, Mulder, Nicola, Institute of Infectious Disease and Molecular Medicine, and Faculty of Health Sciences

Subjects
South Africa, Databases, Genetic, Database Management Systems, Humans, Nigeria, Genomics, Developing Countries, African Continental Ancestry Group
Abstract

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

Published
2017
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9. Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Author

Baichoo, Shakuntala, primary, Souilmi, Yassine, additional, Panji, Sumir, additional, Botha, Gerrit, additional, Meintjes, Ayton, additional, Hazelhurst, Scott, additional, Bendou, Hocine, additional, Beste, Eugene de, additional, Mpangase, Phelelani T., additional, Souiai, Oussema, additional, Alghali, Mustafa, additional, Yi, Long, additional, O’Connor, Brian D., additional, Crusoe, Michael, additional, Armstrong, Don, additional, Aron, Shaun, additional, Joubert, Fourie, additional, Ahmed, Azza E., additional, Mbiyavanga, Mamana, additional, Heusden, Peter van, additional, Magosi, Lerato E., additional, Zermeno, Jennie, additional, Mainzer, Liudmila Sergeevna, additional, Fadlelmola, Faisal M., additional, Jongeneel, C. Victor, additional, and Mulder, Nicola, additional

Published
2018
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10. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

Author

Ahmed, Azza E., primary, Mpangase, Phelelani T., additional, Panji, Sumir, additional, Baichoo, Shakuntala, additional, Souilmi, Yassine, additional, Fadlelmola, Faisal M., additional, Alghali, Mustafa, additional, Aron, Shaun, additional, Bendou, Hocine, additional, De Beste, Eugene, additional, Mbiyavanga, Mamana, additional, Souiai, Oussema, additional, Yi, Long, additional, Zermeno, Jennie, additional, Armstrong, Don, additional, O'Connor, Brian D., additional, Mainzer, Liudmila Sergeevna, additional, Crusoe, Michael R., additional, Meintjes, Ayton, additional, Van Heusden, Peter, additional, Botha, Gerrit, additional, Joubert, Fourie, additional, Jongeneel, C. Victor, additional, Hazelhurst, Scott, additional, and Mulder, Nicola, additional

Published
2018
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11. Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

Author

Choudhury, Ananyo, primary, Ramsay, Michèle, additional, Hazelhurst, Scott, additional, Aron, Shaun, additional, Bardien, Soraya, additional, Botha, Gerrit, additional, Chimusa, Emile R., additional, Christoffels, Alan, additional, Gamieldien, Junaid, additional, Sefid-Dashti, Mahjoubeh J., additional, Joubert, Fourie, additional, Meintjes, Ayton, additional, Mulder, Nicola, additional, Ramesar, Raj, additional, Rees, Jasper, additional, Scholtz, Kathrine, additional, Sengupta, Dhriti, additional, Soodyall, Himla, additional, Venter, Philip, additional, Warnich, Louise, additional, and Pepper, Michael S., additional

Published
2017
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12. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Author

Jongeneel, C. Victor, primary, Achinike-Oduaran, Ovokeraye, additional, Adebiyi, Ezekiel, additional, Adebiyi, Marion, additional, Adeyemi, Seun, additional, Akanle, Bola, additional, Aron, Shaun, additional, Ashano, Efejiro, additional, Bendou, Hocine, additional, Botha, Gerrit, additional, Chimusa, Emile, additional, Choudhury, Ananyo, additional, Donthu, Ravikiran, additional, Drnevich, Jenny, additional, Falola, Oluwadamila, additional, Fields, Christopher J., additional, Hazelhurst, Scott, additional, Hendry, Liesl, additional, Isewon, Itunuoluwa, additional, Khetani, Radhika S., additional, Kumuthini, Judit, additional, Kimuda, Magambo Phillip, additional, Magosi, Lerato, additional, Mainzer, Liudmila Sergeevna, additional, Maslamoney, Suresh, additional, Mbiyavanga, Mamana, additional, Meintjes, Ayton, additional, Mugutso, Danny, additional, Mpangase, Phelelani, additional, Munthali, Richard, additional, Nembaware, Victoria, additional, Ndhlovu, Andrew, additional, Odia, Trust, additional, Okafor, Adaobi, additional, Oladipo, Olaleye, additional, Panji, Sumir, additional, Pillay, Venesa, additional, Rendon, Gloria, additional, Sengupta, Dhriti, additional, and Mulder, Nicola, additional

Published
2017
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13. Development of Bioinformatics Infrastructure for Genomics Research

Author

Mulder, Nicola J., primary, Adebiyi, Ezekiel, additional, Adebiyi, Marion, additional, Adeyemi, Seun, additional, Ahmed, Azza, additional, Ahmed, Rehab, additional, Akanle, Bola, additional, Alibi, Mohamed, additional, Armstrong, Don L., additional, Aron, Shaun, additional, Ashano, Efejiro, additional, Baichoo, Shakuntala, additional, Benkahla, Alia, additional, Brown, David K., additional, Chimusa, Emile R., additional, Fadlelmola, Faisal M., additional, Falola, Dare, additional, Fatumo, Segun, additional, Ghedira, Kais, additional, Ghouila, Amel, additional, Hazelhurst, Scott, additional, Isewon, Itunuoluwa, additional, Jung, Segun, additional, Kassim, Samar Kamal, additional, Kayondo, Jonathan K., additional, Mbiyavanga, Mamana, additional, Meintjes, Ayton, additional, Mohammed, Somia, additional, Mosaku, Abayomi, additional, Moussa, Ahmed, additional, Muhammd, Mustafa, additional, Mungloo-Dilmohamud, Zahra, additional, Nashiru, Oyekanmi, additional, Odia, Trust, additional, Okafor, Adaobi, additional, Oladipo, Olaleye, additional, Osamor, Victor, additional, Oyelade, Jellili, additional, Sadki, Khalid, additional, Salifu, Samson Pandam, additional, Soyemi, Jumoke, additional, Panji, Sumir, additional, Radouani, Fouzia, additional, Souiai, Oussama, additional, Tastan Bishop, Özlem, additional, and Members of the HAfrica Consortium, The HABioNet Consortium, as, additional

Published
2017
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14. 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, Institute of Infectious Disease and Molecular Medicine, and Faculty of Health Sciences

Subjects
Immune Cells, T-Lymphocytes, Immunology, lcsh:Medicine, Phosphoinositide Signal Transduction, T cell receptors, Signaling Pathways, Phosphatidylinositol 3-Kinases, Molecular cell biology, Suppressor Factors, Immunologic, Humans, Protein Isoforms, ddc:610, lcsh:Science, Biology, Immune Response, Cytoskeleton, DNA Primers, Oligonucleotide Array Sequence Analysis, Phosphoinositide-3 Kinase Inhibitors, Reverse transcriptase-polymerase chain reaction, TCR signaling cascade, T Cells, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, lcsh:R, Cellular Structures, Gene regulation, Cell cycle and cell division, RNA processing, Gene Expression Regulation, Measles virus, lcsh:Q, Gene expression, Biologie, Cell Division, Algorithms, Alternative splicing, Research Article, Signal Transduction
Abstract

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 protein isoform was produced from an alternatively spliced pre-mRNA. Hypothesis: Differentially regulated and alternatively splice variant transcripts accumulating in response to PI3K abrogation in T cells potentially encode proteins involved in T cell silencing. Methods: To test this hypothesis at the cellular level, we performed a Human Exon 1.0 ST Array on RNAs isolated from T cells stimulated only or stimulated after PI3K inhibition. We developed a simple algorithm based on a splicing index to detect genes that undergo alternative splicing (AS) or are differentially regulated (RG) upon T cell suppression. Results: Applying our algorithm to the data, 9% of the genes were assigned as AS, while only 3% were attributed to RG. Though there are overlaps, AS and RG genes differed with regard to functional regulation, and were found to be enriched in different functional groups. AS genes targeted extracellular matrix (ECM)-receptor interaction and focal adhesion pathways, while RG genes were mainly enriched in cytokine-receptor interaction and Jak-STAT. When combined, AS/RG dependent alterations targeted pathways essential for T cell receptor signaling, cytoskeletal dynamics and cell cycle entry. Conclusions: PI3K abrogation interferes with key T cell activation processes through both differential expression and alternative splicing, which together actively contribute to T cell suppression.

Published
2013

15. A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study.

Author

Ben Hamda, Cherif, Sangeda, Raphael, Mwita, Liberata, Meintjes, Ayton, Nkya, Siana, Panji, Sumir, Mulder, Nicola, Guizani-Tabbane, Lamia, Benkahla, Alia, Makani, Julie, Ghedira, Kais, and null, null

Subjects
SICKLE cell anemia diagnosis, SICKLE cell anemia, MICROARRAY technology, CHRONIC diseases, PATHOLOGICAL physiology, GENE expression, GENETICS
Abstract

A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2018
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16. The Generation Challenge Programme Platform: Semantic Standards andWorkbench for Crop Science

Author

Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswa, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and Hintum, Theo van

Subjects
Bioinformatics, Comparative genomics, Genome annotation
Abstract

Made available in DSpace on 2016-10-10T03:52:58Z (GMT). No. of bitstreams: 5 The Generation Challenge Programme Platform_Semantic Standards and Workbench for Crop Science.pdf: 583382 bytes, checksum: c43dff314e03cd75dcf5453f02c182fa (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24372 bytes, checksum: 94b0a37ff5ec51de8c55507bff4a7ff9 (MD5) license_rdf: 24623 bytes, checksum: 378d22d8fe50e084ee2f354be78cbe62 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2008 The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. Sim Publicado

Published
2008

17. Development of data templates for data collection, storage and database submission

Author

Davenport, Guy, Anducho, Miguel, Braak, Kyle, Bruskiewich, Richard, Carollo Blake, Victoria, Hazekamp, Tom, Farmer, Andrew, Matthews, Dave, Meintjes, Ayton, Metz, Thomas, Morris, Jane, Manuel Ruiz, Schaeffer, Mary, Hintum, Theo, and Mccouch, Susan

Subjects
C30 - Documentation et information, U30 - Méthodes de recherche, F30 - Génétique et amélioration des plantes
Abstract

A large amount of data is generated each year by the scientific community. These data must be collected with sufficient metadata and controls and have an adequate level of completeness and accuracy that allow it to be utilized and analyzed accurately. The data must also be stored in a machine readable format that allows it to be easily validated and loaded into a database. We are developing machine readable templates for data captured manually, which provides guidelines on capturing the data, metadata and available controls and defines the level completeness and accuracy required. We are also providing similar guidelines for data captured automatically by scientific equipment, such as genotyping systems, or data generated by analytical software. We have developed data templates for plant accession passports and genotyping data produced in work by the Generation Challenge Program (GCP, www.generationcp.org) and its partners, and are developing additional templates for mapping, QTL, SNP genotyping and plant phenotypic (evaluation) data in collaboration with GrainGenes (wheat.pw.usda.gov/), MaizeGDB (www.maizegdb.org/) and Gramene (www.gramene.org/). The templates are provided in both Excel and text formats, which are validated and converted to XML for storage. The software is generic enough to support a range of formats and can conform to most XML schemas. The XML form of the data is then transformed using XSL (Extensible Stylesheet Language) to the various formats required for database submission, visualization and analysis. The templates and software are available on the GCP bioinformatics portal (www.generationcp.org/bioinformatics). (Texte intégral)

Published
2007

18. Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

Author

Choudhury, Ananyo, primary, Hazelhurst, Scott, additional, Meintjes, Ayton, additional, Achinike-Oduaran, Ovokeraye, additional, Aron, Shaun, additional, Gamieldien, Junaid, additional, Jalali Sefid Dashti, Mahjoubeh, additional, Mulder, Nicola, additional, Tiffin, Nicki, additional, and Ramsay, Michèle, additional

Published
2014
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21. Computational analysis of candidate disease genes and variants for Salt-sensitive hypertension in indigenous Southern Africans

Author

Tiffin, Nicki, Meintjes, Ayton, Ramesar, Rajkumar, Bajic, Vladimir B., Rayner, Brian, Tiffin, Nicki, Meintjes, Ayton, Ramesar, Rajkumar, Bajic, Vladimir B., and Rayner, Brian

Abstract

Multiple factors underlie susceptibility to essential hypertension, including a significant genetic and ethnic component, and environmental effects. Blood pressure response of hypertensive individuals to salt is heterogeneous, but salt sensitivity appears more prevalent in people of indigenous African origin. The underlying genetics of salt-sensitive hypertension, however, are poorly understood. In this study, computational methods including text- and data-mining have been used to select and prioritize candidate aetiological genes for salt-sensitive hypertension. Additionally, we have compared allele frequencies and copy number variation for single nucleotide polymorphisms in candidate genes between indigenous Southern African and Caucasian populations, with the aim of identifying candidate genes with significant variability between the population groups: identifying genetic variability between population groups can exploit ethnic differences in disease prevalence to aid with prioritisation of good candidate genes. Our top-ranking candidate genes include parathyroid hormone precursor (PTH) and type-1angiotensin II receptor (AGTR1). We propose that the candidate genes identified in this study warrant further investigation as potential aetiological genes for salt-sensitive hypertension. © 2010 Tiffin et al.

Published
2010

23. The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Author

Bruskiewich, Richard, primary, Senger, Martin, additional, Davenport, Guy, additional, Ruiz, Manuel, additional, Rouard, Mathieu, additional, Hazekamp, Tom, additional, Takeya, Masaru, additional, Doi, Koji, additional, Satoh, Kouji, additional, Costa, Marcos, additional, Simon, Reinhard, additional, Balaji, Jayashree, additional, Akintunde, Akinnola, additional, Mauleon, Ramil, additional, Wanchana, Samart, additional, Shah, Trushar, additional, Anacleto, Mylah, additional, Portugal, Arllet, additional, Ulat, Victor Jun, additional, Thongjuea, Supat, additional, Braak, Kyle, additional, Ritter, Sebastian, additional, Dereeper, Alexis, additional, Skofic, Milko, additional, Rojas, Edwin, additional, Martins, Natalia, additional, Pappas, Georgios, additional, Alamban, Ryan, additional, Almodiel, Roque, additional, Barboza, Lord Hendrix, additional, Detras, Jeffrey, additional, Manansala, Kevin, additional, Mendoza, Michael Jonathan, additional, Morales, Jeffrey, additional, Peralta, Barry, additional, Valerio, Rowena, additional, Zhang, Yi, additional, Gregorio, Sergio, additional, Hermocilla, Joseph, additional, Echavez, Michael, additional, Yap, Jan Michael, additional, Farmer, Andrew, additional, Schiltz, Gary, additional, Lee, Jennifer, additional, Casstevens, Terry, additional, Jaiswal, Pankaj, additional, Meintjes, Ayton, additional, Wilkinson, Mark, additional, Good, Benjamin, additional, Wagner, James, additional, Morris, Jane, additional, Marshall, David, additional, Collins, Anthony, additional, Kikuchi, Shoshi, additional, Metz, Thomas, additional, McLaren, Graham, additional, and van Hintum, Theo, additional

Published
2008
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24. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Author

Mulder, Nicola J., Adebiyi, Ezekiel, Alami, Raouf, Benkahla, Alia, Brandful, James, Doumbia, Seydou, Everett, Dean, Fadlelmola, Faisal M., Gaboun, Fatima, Gaseitsiwe, Simani, Ghazal, Hassan, Hazelhurst, Scott, Hide, Winston, Ibrahimi, Azeddine, Jaufeerally Fakim, Yasmina, Jongeneel, C. Victor, Joubert, Fourie, Kassim, Samar, Kayondo, Jonathan, Kumuthini, Judit, Lyantagaye, Sylvester, Makani, Julie, Mansour Alzohairy, Ahmed, Masiga, Daniel, Moussa, Ahmed, Nash, Oyekanmi, Ouwe Missi Oukem-Boyer, Odile, Owusu-Dabo, Ellis, Panji, Sumir, Patterton, Hugh, Radouani, Fouzia, Sadki, Khalid, Seghrouchni, Fouad, Tastan Bishop, Ozlem, Tiffin, Nicki, Ulenga, Nzovu, Adebiyi, Marion, Ahmed, Azza E., Ahmed, Rehab I., Alearts, Maaike, Alibi, Mohamed, Aron, Shaun, Baichoo, Shakuntala, Bendou, Hocine, Botha, Gerrit, Brown, David, Chimusa, Emile, Christoffels, Alan, Cornick, Jennifer, Entfellner, Jean-Baka Domelevo, Fields, Chris, Fischer, Anne, Gamieldien, Junaid, Ghedira, Kais, Ghouila, Amel, Sui, Shannan Ho, Isewon, Itunuoluwa, Isokpehi, Raphael, Dashti, Mahjoubeh Jalali Sefid, Kamng'ona, Arox, Khetani, Radhika S., Kiran, Anmol, Kulohoma, Benard, Kumwenda, Benjamin, Lapine, Dan, Mainzer, Liudmila Sergeevna, Maslamoney, Suresh, Mbiyavanga, Mamana, Meintjes, Ayton, Mlyango, Flora Elias, Mmbando, Bruno, Mohammed, Somia A., Mpangase, Phelelani, Msefula, Chisomo, Mtatiro, Siana Nkya, Mugutso, Dunfunk, Mungloo-Dilmohammud, Zahra, Musicha, Patrick, Nembaware, Victoria, Osamor, Victor Chukwudi, Oyelade, Jelili, Rendon, Gloria, Salazar, Gustavo A., Salifu, Samson Pandam, Sangeda, Raphael, Souiai, Oussema, Van Heusden, Peter, and Wele, Mamadou

Abstract

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Published
2016
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