Development of Bioinformatics Infrastructure for Genomics Research

Global Heart

Volumn 12, Issue 2, 2017, Pages 91-98

  Mulder, Nicola J ^a   Adebiyi, Ezekiel ^b   Adebiyi, Marion ^b   Adeyemi, Seun ^b   Ahmed, Azza ^c   Ahmed, Rehab ^c   Akanle, Bola ^b   Alibi, Mohamed ^d   Armstrong, Don L ^e   Aron, Shaun ^f   Ashano, Efejiro ^b,g   Baichoo, Shakuntala ^h   Benkahla, Alia ^d   Brown, David K ⁱ   Chimusa, Emile R ^a,j   Fadlelmola, Faisal M ^c,k   Falola, Dare ^b   Fatumo, Segun ^g   Ghedira, Kais ^d   Ghouila, Amel ^d   Hazelhurst, Scott ^f   Isewon, Itunuoluwa ^b   Jung, Segun ^l   Kassim, Samar Kamal ^m   Kayondo, Jonathan K ⁿ   Mbiyavanga, Mamana ^a   Meintjes, Ayton ^a   Mohammed, Somia ^c   Mosaku, Abayomi ^b   Moussa, Ahmed ^o   Muhammd, Mustafa ^c   Mungloo Dilmohamud, Zahra ^h   Nashiru, Oyekanmi ^g   Odia, Trust ^b   Okafor, Adaobi ^b   Oladipo, Olaleye ^b,p   Osamor, Victor ^b   Oyelade, Jellili ^b   Sadki, Khalid ^q   Salifu, Samson Pandam ^r,s   Soyemi, Jumoke ^t   Panji, Sumir ^a   Radouani, Fouzia ^u   Souiai, Oussama ^d   Tastan Bishop, Özlem ⁱ   more..

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b Centre for Economic Policy and Development Research   (Nigeria)

^c UNIVERSITY OF KHARTOUM   (Sudan)

^d PASTEUR INSTITUTE OF TUNIS   (Tunisia)

^e UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^f UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^g Federal Ministry of Science and Technology   (Nigeria)

^h UNIVERSITY OF MAURITIUS   (Mauritius)

ⁱ RHODES UNIVERSITY   (South Africa)

^j UNIVERSITY OF CAPE TOWN   (South Africa)

^k Sudan University   (Sudan)

^l UNIVERSITY OF CHICAGO   (United States)

^m AIN SHAMS UNIVERSITY   (Egypt)

ⁿ UGANDA VIRUS RESEARCH INSTITUTE   (Uganda)

^o Abdelmalek Essaadi University   (Morocco)

^p LANDMARK UNIVERSITY   (Nigeria)

^q MOHAMMED V UNIVERSITY   (Morocco)

^r KWAME NKRUMAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Ghana)

^s KUMASI CENTRE FOR COLLABORATIVE RESEARCH IN TROPICAL MEDICINE   (Ghana)

^t Department of Computer Science   (Nigeria)

^u Institut Pasteur du Maroc   (Morocco)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; BIOINFORMATICS; CLINICAL RESEARCH; CLOUD COMPUTING; CONTROLLED VOCABULARY; DATA ANALYSIS; GENETIC VARIABILITY; GENOMICS; HUMAN; INFORMATION PROCESSING; INFORMATION SERVICE; INFORMATION STORAGE; INTERNET; MEDICAL EDUCATION; METAGENOMICS; ONTOLOGY; PRIORITY JOURNAL; BIOLOGY; MEDICAL RESEARCH; PROCEDURES; TRENDS;

AFRICA; BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; GENOMICS; HUMANS;

EID: 85019725242     PISSN: 22118160     EISSN: 22118179     Source Type: Journal    
DOI: 10.1016/j.gheart.2017.01.005     Document Type: Article

References (32)

1. Muir, P., Li, S., Lou, S., et al. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol, 17, 2016, 53.
2. The H3Africa Consortium. Enabling African scientists to engage fully in the genomic revolution. Science 344 (2014), 1346–1348.
3. Mulder, N.J., Adebiyi, E., Alami, R., et al. H3ABioNet, a sustainable pan African bioinformatics network for human heredity and health in Africa. Genome Res 26 (2015), 271–277.
4. Thorvaldsdottir, H., Robinson, J.T., Mesirov, J.P., Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14 (2013), 178–192.
5. Foster, I., Globus Online: accelerating and democratizing science through cloud-based services. IEEE Internet Comput 15 (2011), 70–73.
6. Lappalainen, I., Almeida-King, J., Kumanduri, V., et al. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet 47 (2015), 692–695.
7. Harris, P.A., Taylor, R., Thielke, R., Payne, J., Gonzalez, N., Conde, J.G., Research electronic data capture (REDCap)—a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform 42 (2009), 377–381.
8. Mulder, N., Nembaware, V., Adekile, A., Inusa, B., Brown, B., Campbell, A., Proceedings of a Sickle Cell Disease Ontology Workshop–towards the first comprehensive Ontology for Sickle Cell Disease. Appll Trans Gen 9 (2016), 23–29.
9. Horridge, M., Tudorache, T., Nuylas, C., Vendetti, J., Noy, N.F., Musen, M.A., WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. Bioinformatics 30 (2014), 2384–2385.
10. UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res 43 (2015), D204–D212.
11. Sherry, S.T., Ward, M.H., Kholodov, M., et al. dbSNP: the NCBI database of genetic variation. Nucl Acids Res 29 (2001), 308–311.
12. Hubbard, T., Barker, D., Birney, E., et al. The Ensembl genome database project. Nucl Acids Res 30 (2002), 38–41.
13. Berman, H.M., Westbrook, J., Feng, Z., et al. The Protein Data Bank. Nucl Acids Res 28 (2000), 235–242.
14. Gray, K.A., Yates, B., Seal, R.L., Wright, M.W., Bruford, E.A., Genenames.org: the HGNC resources in 2015. Nucl Acids Res 43 (2015), D1079–D1085.
15. Landrum, M.J., Lee, J.M., Riley, G.R., et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucl Acids Res 42 (2014), D980–D985.
16. Hamosh, A., Scott, A.F., Amberger, J., Valle, D., McKusick, V.A., Online Mendelian Inheritance in Man (OMIM). Hum Mut 15 (2000), 57–61.
17. Afgan, E., Baker, D., van den Beek, M., et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44 (2016), W3–W10.
18. Brown, D.K., Penkler, D.L., Musyoka, T.M., Tastan Bishop, Ö., JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing. PLoS One, 10, 2015, e0134273.
19. Howie, B.N., Donnelly, P., Marchini, J., A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet, 5, 2009, e1000529.
20. Delaneau, O., Marchini, J., Zagury, J.F., A linear complexity phasing method for thousands of genomes. Nat Methods 9 (2012), 179–181.
21. Chimusa, E.R., Daya, M., Möller, M., et al. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel Proxy Ancestry Selection Method. PLoS One, 8, 2013, e73971.
22. Chimusa, E.R., Mbiyavanga, M., Mazandu, G.K., Mulder, N.J., ancGWAS: a post genome-wide association study method for interaction, pathway, and ancestry analysis in homogeneous and admixed populations. Bioinformatics 32 (2016), 549–556.
23. Choi, Y., Sims, G.E., Murphy, S., Miller, J.R., Chan, A.P., Predicting the functional effect of amino acid substitutions and indels. PLoS ONE, 7, 2012, e46688.
24. Adzhubei, I., Jordan, D.M., Sunyaev, S.R., Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Gen 76 (2013), 7.20.1–7.20.41.
25. Capriotti, E., Calabrese, R., Casadio, R., Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinform 22 (2006), 2729–2734.
26. Shihab, H.A., Gough, J., Cooper, D.N., et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using Hidden Markov Models. Hum Mut 34 (2013), 57–65.
27. Masso, M., Vaisman, I.I., AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements. Prot Eng Des Sel 23 (2010), 683–687.
28. Cheng, J., Randall, A., Baldi, P., Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62 (2006), 1125–1132.
29. Hatherley, R., Brown, D.K., Glenister, M., Tastan Bishop, Ö., PRIMO: An Interactive Homology Modeling Pipeline. PLoS One, 11, 2016, e0166698.
30. Campbell, M.C., Tishkoff, S.A., African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 9 (2008), 403–433.
31. Chimusa, E.R., Meintjies, A., Tchanga, M., et al. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations. PLoS Genet, 11, 2015, e1005052.
32. Tastan Bishop, Ö.T., Adebiyi, E.F., Alzohairy, A.M., et al. Bioinformatics education—perspectives and challenges out of Africa. Brief Bioinf 16 (2014), 355–364.