The extent and impact of variation in ADME genes in sub-Saharan African populations
- da Rocha, Jorge E B, Othman, Houcemeddine, Botha, Gerrit, Cottino, Laura, Twesigomwe, David, Ahmed, Samah, Drögemöller, Britt I, Fadlelmola, Faisal M, Machanick, Philip, Mbiyavanga, Mamana, Panji, Sumir, Wright, Galen E B, Adebamowo, Clement, Matshaba, Mogomotsi, Ramsay, Michéle, Simo, Gustave, Simuunza, Martin C, Tiemessen, Caroline T, Baldwin, Sandra, Chiano, Mathias, Cox, Charles, Gross, Annette S, Thomas, Pamela, Gamo, Francisco-Javier, Scott Hazelhurst
- Authors: da Rocha, Jorge E B , Othman, Houcemeddine , Botha, Gerrit , Cottino, Laura , Twesigomwe, David , Ahmed, Samah , Drögemöller, Britt I , Fadlelmola, Faisal M , Machanick, Philip , Mbiyavanga, Mamana , Panji, Sumir , Wright, Galen E B , Adebamowo, Clement , Matshaba, Mogomotsi , Ramsay, Michéle , Simo, Gustave , Simuunza, Martin C , Tiemessen, Caroline T , Baldwin, Sandra , Chiano, Mathias , Cox, Charles , Gross, Annette S , Thomas, Pamela , Gamo, Francisco-Javier , Scott Hazelhurst
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439202 , vital:73555 , https://homes.cs.ru.ac.za/philip/Courses/CSHonsArch/HonsArchNotes2022.pdf
- Description: Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterized in European and Asian populations, but data from African populations are under-studied—which has implications for drug safety and effective use in Africa.
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- Authors: da Rocha, Jorge E B , Othman, Houcemeddine , Botha, Gerrit , Cottino, Laura , Twesigomwe, David , Ahmed, Samah , Drögemöller, Britt I , Fadlelmola, Faisal M , Machanick, Philip , Mbiyavanga, Mamana , Panji, Sumir , Wright, Galen E B , Adebamowo, Clement , Matshaba, Mogomotsi , Ramsay, Michéle , Simo, Gustave , Simuunza, Martin C , Tiemessen, Caroline T , Baldwin, Sandra , Chiano, Mathias , Cox, Charles , Gross, Annette S , Thomas, Pamela , Gamo, Francisco-Javier , Scott Hazelhurst
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439202 , vital:73555 , https://homes.cs.ru.ac.za/philip/Courses/CSHonsArch/HonsArchNotes2022.pdf
- Description: Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterized in European and Asian populations, but data from African populations are under-studied—which has implications for drug safety and effective use in Africa.
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Development of Bioinformatics Infrastructure for Genomics Research:
- 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 Rugamika, Fadlelmola, Faisal M, Falola, Dare, Fatumo, Segun, Ghedira, Kais, Ghouila, Amel, Hazelhurst, Scott, Itunuoluwa Isewon, Segun Jung, 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, Tastan Bishop, Özlem
- Authors: 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 Rugamika , Fadlelmola, Faisal M , Falola, Dare , Fatumo, Segun , Ghedira, Kais , Ghouila, Amel , Hazelhurst, Scott , Itunuoluwa Isewon , Segun Jung , 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 , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148239 , vital:38722 , DOI: 10.1016/j.gheart.2017.01.005
- Description: 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.
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- Authors: 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 Rugamika , Fadlelmola, Faisal M , Falola, Dare , Fatumo, Segun , Ghedira, Kais , Ghouila, Amel , Hazelhurst, Scott , Itunuoluwa Isewon , Segun Jung , 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 , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148239 , vital:38722 , DOI: 10.1016/j.gheart.2017.01.005
- Description: 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.
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Bioinformatics education—perspectives and challenges out of Africa
- Tastan Bishop, Özlem, Adebiyi, Ezekiel F, Alzohairy, Ahmed M, Everett, Dean B, Ghedira, Kais, Ghouila, Amel, Kumuthini, Judit, Mulder, Nicola J, Panji, Sumir, Patterton, Hugh-G
- Authors: Tastan Bishop, Özlem , Adebiyi, Ezekiel F , Alzohairy, Ahmed M , Everett, Dean B , Ghedira, Kais , Ghouila, Amel , Kumuthini, Judit , Mulder, Nicola J , Panji, Sumir , Patterton, Hugh-G
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123244 , vital:35420 , https://doi.10.1093/bib/bbu022
- Description: The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s.The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming.This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and theWellcomeTrust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations.
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- Authors: Tastan Bishop, Özlem , Adebiyi, Ezekiel F , Alzohairy, Ahmed M , Everett, Dean B , Ghedira, Kais , Ghouila, Amel , Kumuthini, Judit , Mulder, Nicola J , Panji, Sumir , Patterton, Hugh-G
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123244 , vital:35420 , https://doi.10.1093/bib/bbu022
- Description: The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s.The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming.This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and theWellcomeTrust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations.
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The African coelacanth genome provides insights into tetrapod evolution:
- Amemiya, Chris T, Alföldi, Jessica, Lee, Alison P, Fan, Shaohua, Philippe, Herve´, MacCallum, Iain, Braasch, Ingo, Manousaki, Tereza, Schneider, Igor, Rohner, Nicolas, Organ, Chris, Chalopin, Domitille, Smith, Jeramiah J, Robinson, Mark, Dorrington, Rosemary A, Gerdol, Marco, Aken, Bronwen, Biscotti, Maria Assunta, Barucca, Marco, Baurain, Denis, Berlin, Aaron, Blatch, Gregory L, Buonocore, Francesco, Burmester, Thorsten, Campbell, Michael S, Canapa, Adriana, Cannon, John P, Christoffels, Alan, De Moro, Gianluca, Edkins, Adrienne L, Fan, Lin, Fausto, Anna Maria, Feiner, Nathalie, Forconi, Mariko, Gamieldien, Junaid, Gnerre, Sante, Gnirke, Andreas, Goldstone, Jared V, Haerty, Wilfried, Hahn, Mark E, Hesse, Uljana, Hoffmann, Steve, Johnson, Jeremy, Karchner, Sibel I, Kuraku, Shigehiro, Lara, Marcia, Levin, Joshua Z, Litman, Gary W, Mauceli, Evan, Miyake, Tsutomu, Mueller, M Gail, Nelson, David R, Nitsche, Anne, Olmo, Ettore, Ota, Tatsuya, Pallavicini, Alberto, Panji, Sumir, Picone, Barbara, Ponting, Chris P, Prohaska, Sonja J, Przybylski, Dariusz, Ratan Saha, Nil, Ravi, Vydianathan, Ribeiro, Filipe J, Sauka-Spengler, Tatjana, Scapigliati, Giuseppe, Searle, Stephen M J, Sharpe, Ted, Simakov, Oleg, Stadler, Peter F, Stegeman, John J, Sumiyama, Kenta, Tabbaa, Diana, Tafer, Hakim, Turner-Maier, Jason, van Heusden, Peter, White, Simon, Williams, Louise, Yandell, Mark, Brinkmann, Henner, Volff, Jean-Nicolas, Tabin, Clifford J, Shubin, Neil, Schartl, Manfred, Jaffe, David B, Postlethwait, John H, Venkatesh, Byrappa, Di Palma, Frederica, Lander, Eric S, Meyer, Axel, Lindblad-Toh, Kerstin
- Authors: Amemiya, Chris T , Alföldi, Jessica , Lee, Alison P , Fan, Shaohua , Philippe, Herve´ , MacCallum, Iain , Braasch, Ingo , Manousaki, Tereza , Schneider, Igor , Rohner, Nicolas , Organ, Chris , Chalopin, Domitille , Smith, Jeramiah J , Robinson, Mark , Dorrington, Rosemary A , Gerdol, Marco , Aken, Bronwen , Biscotti, Maria Assunta , Barucca, Marco , Baurain, Denis , Berlin, Aaron , Blatch, Gregory L , Buonocore, Francesco , Burmester, Thorsten , Campbell, Michael S , Canapa, Adriana , Cannon, John P , Christoffels, Alan , De Moro, Gianluca , Edkins, Adrienne L , Fan, Lin , Fausto, Anna Maria , Feiner, Nathalie , Forconi, Mariko , Gamieldien, Junaid , Gnerre, Sante , Gnirke, Andreas , Goldstone, Jared V , Haerty, Wilfried , Hahn, Mark E , Hesse, Uljana , Hoffmann, Steve , Johnson, Jeremy , Karchner, Sibel I , Kuraku, Shigehiro , Lara, Marcia , Levin, Joshua Z , Litman, Gary W , Mauceli, Evan , Miyake, Tsutomu , Mueller, M Gail , Nelson, David R , Nitsche, Anne , Olmo, Ettore , Ota, Tatsuya , Pallavicini, Alberto , Panji, Sumir , Picone, Barbara , Ponting, Chris P , Prohaska, Sonja J , Przybylski, Dariusz , Ratan Saha, Nil , Ravi, Vydianathan , Ribeiro, Filipe J , Sauka-Spengler, Tatjana , Scapigliati, Giuseppe , Searle, Stephen M J , Sharpe, Ted , Simakov, Oleg , Stadler, Peter F , Stegeman, John J , Sumiyama, Kenta , Tabbaa, Diana , Tafer, Hakim , Turner-Maier, Jason , van Heusden, Peter , White, Simon , Williams, Louise , Yandell, Mark , Brinkmann, Henner , Volff, Jean-Nicolas , Tabin, Clifford J , Shubin, Neil , Schartl, Manfred , Jaffe, David B , Postlethwait, John H , Venkatesh, Byrappa , Di Palma, Frederica , Lander, Eric S , Meyer, Axel , Lindblad-Toh, Kerstin
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/165030 , vital:41202 , DOI: 10.1038/nature12027
- Description: 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 its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
- Full Text:
- Authors: Amemiya, Chris T , Alföldi, Jessica , Lee, Alison P , Fan, Shaohua , Philippe, Herve´ , MacCallum, Iain , Braasch, Ingo , Manousaki, Tereza , Schneider, Igor , Rohner, Nicolas , Organ, Chris , Chalopin, Domitille , Smith, Jeramiah J , Robinson, Mark , Dorrington, Rosemary A , Gerdol, Marco , Aken, Bronwen , Biscotti, Maria Assunta , Barucca, Marco , Baurain, Denis , Berlin, Aaron , Blatch, Gregory L , Buonocore, Francesco , Burmester, Thorsten , Campbell, Michael S , Canapa, Adriana , Cannon, John P , Christoffels, Alan , De Moro, Gianluca , Edkins, Adrienne L , Fan, Lin , Fausto, Anna Maria , Feiner, Nathalie , Forconi, Mariko , Gamieldien, Junaid , Gnerre, Sante , Gnirke, Andreas , Goldstone, Jared V , Haerty, Wilfried , Hahn, Mark E , Hesse, Uljana , Hoffmann, Steve , Johnson, Jeremy , Karchner, Sibel I , Kuraku, Shigehiro , Lara, Marcia , Levin, Joshua Z , Litman, Gary W , Mauceli, Evan , Miyake, Tsutomu , Mueller, M Gail , Nelson, David R , Nitsche, Anne , Olmo, Ettore , Ota, Tatsuya , Pallavicini, Alberto , Panji, Sumir , Picone, Barbara , Ponting, Chris P , Prohaska, Sonja J , Przybylski, Dariusz , Ratan Saha, Nil , Ravi, Vydianathan , Ribeiro, Filipe J , Sauka-Spengler, Tatjana , Scapigliati, Giuseppe , Searle, Stephen M J , Sharpe, Ted , Simakov, Oleg , Stadler, Peter F , Stegeman, John J , Sumiyama, Kenta , Tabbaa, Diana , Tafer, Hakim , Turner-Maier, Jason , van Heusden, Peter , White, Simon , Williams, Louise , Yandell, Mark , Brinkmann, Henner , Volff, Jean-Nicolas , Tabin, Clifford J , Shubin, Neil , Schartl, Manfred , Jaffe, David B , Postlethwait, John H , Venkatesh, Byrappa , Di Palma, Frederica , Lander, Eric S , Meyer, Axel , Lindblad-Toh, Kerstin
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/165030 , vital:41202 , DOI: 10.1038/nature12027
- Description: 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 its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
- Full Text:
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