H3Africa Publications for 2014

1. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC.Genome Biol. 2014;15(11):519.
   PMID: 25403361

2. Clinical illness and outcomes in patients with Ebola in Sierra Leone. Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RS, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki S, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JL, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF; KGH Lassa Fever Program; Viral Hemorrhagic Fever Consortium; WHO Clinical Response Team. N Engl J Med. 2014 Nov 27;371(22):2092-100. PMID: 25353969 

3. Empowering African genomics for infectious disease control. Folarin OA, Happi AN, Happi CT. Genome Biol. 2014 Nov 7;15(11):515 PMID: 25417758

4. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O. Microbiol Insights. 2014 Nov 11;7:25-34. doi: 10.4137/MBI.S18076. eCollection 2014. PMID: 25452698

5. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants. Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE, Ritchie GR, Southam L, Gilly A, Tachmazidou I, Fatumo S, Matchan A, Rayner NW, Ntalla I, Mezzavilla M, Chen Y, Kiagiadaki C, Zengini E, Mamakou V, Athanasiadis A, Giannakopoulou M, Kariakli VE, Nsubuga RN, Karabarinde A, Sandhu M, McVean G, Tyler-Smith C, Tsafantakis E, Karaleftheri M, Xue Y, Dedoussis G, Zeggini E. Nat Commun. 2014 Nov 6;5:5345.PMID: 25373335
6. Informed consent and ethical re-use of African genomic data. Wright GE, Adeyemo AA, Tiffin N. Hum Genomics. 2014 Oct 22;8:18. doi: 10.1186/s40246-014-0018-7.PMID: 25339190
7. Epilepsy genetics in Africa: challenges and future perspectives.Landouré G, Maiga Y, Samassékou O, Nimaga K, Traoré M, Fischbeck KH.North Afr Middle East Epilepsy J. 2014 Sep-Oct;3(5):5-7.PMID: 26413584
8. Global clinical neuroscience: journey of a thousand miles begins with a single step. Owolabi MO, Ovbiagele B. J Neurol Sci. 2014 Sep 15;344(1-2):223. PMID: 24972817
9. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Science. 2014 Sep 12;345(6202):1369-72. PMID: 25214632
10. The epigenome of Trypanosoma brucei: a regulatory interface to an unconventional transcriptional machine. Maree JP, Patterton HG.Biochim Biophys Acta. 2014 Sep; 1839 (9):743-50.PMID: 24942804
11. Challenges in the detection, prevention, and treatment of HIV-associated malignancies in low- and middle-income countries in Africa. Adebamowo CA, Casper C, Bhatia K, Mbulaiteye SM, Sasco AJ, Phipps W, Vermund SH, Krown SE. J Acquir Immune Defic Syndr. 2014 Sep 1;67 Suppl 1:S17-26.PMID: 25117957
12. Lowering of blood pressure for recurrent stroke prevention.Boan AD, Lackland DT, Ovbiagele B. Stroke. 2014 Aug;45(8):2506-13.PMID: 24984744
13. Ethical issues in genomic research on the African continent: experiences and challenges to ethics review committees Michèle Ramsay, Jantina de Vries, Himla Soodyall, Shane A Norris, Osman Sankoh Hum Genomics. 2014; 8(1): 15. Published online 2014 August 21. doi: 10.1186/s40246-014-0015
14. A perpetual source of DNA or something really different: ethical issues in the creation of cell lines for African genomics research. de Vries J, Abayomi A, Brandful J, Littler K, Madden E, Marshall P, Ouwe Missi Oukem-Boyer O, Seeley J. BMC Med Ethics. 2014 Aug 7;15:60. PMID: 25104115
15. Bioinformatics Education-Perspectives and Challenges out of Africa. Tastan Bishop O, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton HG; (for the H3ABioNet Consortium, as members of The H3Africa Consortium). Brief Bioinform. 2014 Jul 2. PMID: 24990350
16. A call for policy action in sub-Saharan Africa to rethink diagnostics for pregnancy affected by sickle cell disease: differential views of medical doctors, parents and adult patients predict value conflicts in Cameroon. Wonkam A, Hurst S. OMICS. 2014 Jul;18(7):472-80. PMID: 24754796
17. Research capacity. Enabling the genomic revolution in Africa. H3Africa Consortium, Rotimi C, Abayomi A, Abimiku A, Adabayeri VM, Adebamowo C, Adebiyi E, Ademola AD, Adeyemo A, Adu D, Affolabi D, Agongo G, Ajayi S, Akarolo-Anthony S, Akinyemi R, Akpalu A, Alberts M, Alonso Betancourt O, Alzohairy AM, Ameni G, Amodu O, Anabwani G, Andersen K, Arogundade F, Arulogun O, Asogun D, Bakare R, Balde N, Baniecki ML, Beiswanger C, Benkahla A, Bethke L, Boehnke M, Boima V, Brandful J, Brooks AI, Brosius FC, Brown C, Bucheton B, Burke DT, Burnett BG, Carrington-Lawrence S, Carstens N, Chisi J, Christoffels A, Cooper R, Cordell H, Crowther N, Croxton T, de Vries J, Derr L, Donkor P, Doumbia S, Duncanson A, Ekem I, El Sayed A, Engel ME, Enyaru JC, Everett D, Fadlelmola FM, Fakunle E, Fischbeck KH, Fischer A, Folarin O, Gamieldien J, Garry RF, Gaseitsiwe S, Gbadegesin R, Ghansah A, Giovanni M, Goesbeck P, Gomez-Olive FX, Grant DS, Grewal R, Guyer M, Hanchard NA, Happi CT, Hazelhurst S, Hennig BJ, Hertz- C, Fowler, Hide W , Hilderbrandt F, Hugo-Hamman C, Ibrahim ME, James R, Jaufeerally-Fakim Y, Jenkins C, Jentsch U, Jiang PP, Joloba M, Jongeneel V, Joubert F, Kader M, Kahn K, Kaleebu P, Kapiga SH, Kassim SK, Kasvosve I, Kayondo J, Keavney B, Kekitiinwa A, Khan SH, Kimmel P, King MC, Kleta R, Koffi M, Kopp J, Kretzler M, Kumuthini J, Kyobe S, Kyobutungi C, Lackland DT, Lacourciere KA, Landouré G, Lawlor R, Lehner T, Lesosky M, Levitt N, Littler K, Lombard Z, Loring JF, Lyantagaye S, Macleod A, Madden EB, Mahomva CR, Makani J, Mamven M, Marape M, Mardon G, Marshall P, Martin DP, Masiga D, Mason R, Mate-Kole M, Matovu E, Mayige M, Mayosi BM, Mbanya JC, McCurdy SA, McCarthy MI, McIlleron H, Mc'Ligeyo SO, Merle C, Mocumbi AO, Mondo C, Moran JV, Motala A, Moxey-Mims M, Mpoloka WS, Msefula CL, Mthiyane T, Mulder N, Mulugeta Gh, Mumba D, Musuku J, Nagdee M, Nash O, Ndiaye D, Nguyen AQ, Nicol M, Nkomazana O, Norris S, Nsangi B, Nyarko A, Nyirenda M, Obe E, Obiakor R, Oduro A, Ofori-Acquah SF, Ogah O, Ogendo S, Ohene-Frempong K, Ojo A , Olanrewaju T, Oli J, Osafo C, Ouwe Missi Oukem-Boyer O, Ovbiagele B, Owen A, Owolabi MO, Owolabi L, Owusu-Dabo E, Pare G, Parekh R, Patterton HG, Penno MB, Peterson J, Pieper R, Plange-Rhule J, Pollak M, Puzak J, Ramesar RS, Ramsay M, Rasooly R, Reddy S, Sabeti PC, Sagoe K, Salako T, Samassékou O, Sandhu MS, Sankoh O, Sarfo FS, Sarr M, Shaboodien G, Sidibe I, Simo G, Simuunza M, Smeeth L, Sobngwi E, Soodyall H, Sorgho H, Sow Bah O, Srinivasan S, Stein DJ, Susser ES, Swanepoel C, Tangwa G, Tareila A, Tastan Bishop O, Tayo B, Tiffin N, Tinto H, Tobin E, Tollman SM, Traoré M, Treadwell MJ, Troyer J, Tsimako-Johnstone M, Tukei V, Ulasi I, Ulenga N, van Rooyen B, Wachinou AP, Waddy SP, Wade A, Wayengera M, Whitworth J, Wideroff L, Winkler CA, Winnicki S, Wonkam A, Yewondwos M, sen T, Yozwiak N, Zar H. Science. 2014 Jun 20;344(6190):1346-8.PMID: 24948725
18. Understanding the rise in cardiovascular diseases in Africa: harmonising H3Africa genomic epidemiological teams and tools. Owolabi MO, Mensah GA, Kimmel PL, Adu D, Ramsay M, Waddy SP, Ovbiagele B, Rabada-Diehl C, Rasooly R, Akarolo-Anthony SN, Rotimi C; H3Africa Consortium. Cardiovasc J Afr. 2014 May-Jun;25(3):134-6.PMID: 24878536
19. Computational biology and bioinformatics in Nigeria.Fatumo SA, Adoga MP, Ojo OO, Oluwagbemi O, Adeoye T, Ewejobi I, Adebiyi M, Adebiyi E, Bewaji C, Nashiru O. PLoS Comput Biol. 2014 Apr 24;10(4):e1003516. PMID: 24763310

20. Genetics of low spinal muscular atrophy carrier frequency in sub-Saharan Africa. Sangaré M, et al.Ann Neurol. 2014 Apr;75(4):525-32. doi: 10.1002/ana.24114. Epub 2014 Apr 2.PMID: 24515897

21. Tailored Hospital-based Risk Reduction to Impede Vascular Events After Stroke (THRIVES) study: qualitative phase protocol. Owolabi MO, Akinyemi RO, Hurst S, Arulogun O, Olaniyan O, Gebregziabher M, Salako BL, Ovbiagele B. Crit Pathw Cardiol. 2014 Mar;13(1):29-35. PMID: 24526149
22. Challenges of biobanking in South Africa to facilitate indigenous research in an environment burdened with human immunodeficiency virus, tuberculosis, and emerging noncommunicable diseases. Abayomi A, Christoffels A, Grewal R, Karam LA, Rossouw C, Staunton C, Swanepoel C, van Rooyen B. Biopreserv Biobank. 2013 Dec;11(6):347-54. PMID: 24835364

 Publications

H3Africa Publications for 2016

H3Africa Publications for 2015

H3Africa Publications for 2014

 Related Articles

H3ABioNet Monthly Newsletters

H3ABioNet aims to build and develop bioinformatics capacity and retention of African scientists through education and training. In order to stay up to date with H3ABioNet activities, monthly H3ABioNet newsletters are published.

H3Africa Publications for 2015

1. African partnerships through the H3Africa Consortium bring a genomic dimension to longitudinal population studies on the continent.Ramsay M, Sankoh O; as members of the AWI-Gen study and the H3Africa Consortium.Int J Epidemiol. 2015 Dec 10. pii: dyv187. [Epub ahead of print] No abstract available.PMID: 26659658

2. Human Heredity and Health (H3) in Africa Kidney Disease Research Network: A Focus on Methods in Sub-Saharan Africa. Osafo C, Raji YR, Burke D, Tayo BO, Tiffin N, Moxey-Mims MM, Rasooly RS, Kimmel PL, Ojo A, Adu D, Parekh RS; H3Africa Kidney Disease Research Network Investigators as members of The H3Africa Consortium. Clin J Am Soc Nephrol. 2015 Dec 7;10(12):2279-87. doi: 10.2215/CJN.11951214. Epub 2015 Jul 2.PMID: 26138261

3. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development.Chimusa ER, Mbiyavanga M, Masilela V, Kumuthini J.PLoS Comput Biol. 2015 Nov 19;11(11):e1004512. doi: 10.1371/journal.pcbi.1004512. eCollection 2015 Nov.PMID: 26583922

4. Artocarpus altilis CG-901 alters critical nodes in the JH1-kinase domain of Janus kinase 2 affecting upstream JAK/STAT3 signaling.Nash O, Omotuyi O, Lee J, Kwon BM, Ogbadu L.J Mol Model. 2015 Nov;21(11):280. doi: 10.1007/s00894-015-2821-z. Epub 2015 Oct 7.PMID: 26442513

5. A systematic review of known mechanisms of hydroxyurea-induced fetal hemoglobin for treatment of sickle cell disease. Pule GD, Mowla S, Novitzky N, Wiysonge CS, Wonkam A.Expert Rev Hematol. 2015 Oct;8(5):669-79. doi: 10.1586/17474086.2015.1078235. Epub 2015 Sep 1.PMID:26327494

6. Association between Variants at BCL11A Erythroid-Specific Enhancer and Fetal Hemoglobin Levels among Sickle Cell Disease Patients in Cameroon: Implications for Future Therapeutic Interventions. Pule GD, Ngo Bitoungui VJ, Chetcha Chemegni B, Kengne AP, Antonarakis S, Wonkam A.OMICS. 2015 Oct;19(10):627-31. doi: 10.1089/omi.2015.0124. Epub 2015 Sep 22. PMID:26393293

7. Genetic Diversity of Mycobacterium tuberculosis Complex Isolated from Tuberculosis Patients in Bahir Dar City and Its Surroundings, Northwest Ethiopia. Anwar Nuru,1,2 Gezahegne Mamo,3 Adane Worku,1 Aschalew Admasu,4 Girmay Medhin,1 Rembert Pieper,5 and Gobena Ameni1. BioMed Research International BioMed Research International 2015;2015:174732. doi: 10.1155/2015/174732. Epub 2015 Sep 28. PMID:26491657

8. JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.Brown DK, Penkler DL, Musyoka TM, Bishop ÖT.PLoS One. 2015 Aug 17;10(8):e0134273. doi: 10.1371/journal.pone.0134273. eCollection 2015.PMID: 26280450

9. Phenotyping Stroke in Sub-Saharan Africa: Stroke Investigative Research and Education Network (SIREN) Phenomics Protocol. Akpalu A, Sarfo FS, Ovbiagele B, Akinyemi R, Gebregziabher M, Obiako R, Owolabi L, Sagoe K, Jenkins C, Arulogun O, Adamu S, Appiah LT, Adadey MA, Agyekum F, Quansah JA, Mensah YB, Adeoye AM, Singh A, Tosin AO, Ohifemen O, Sani AA, Tabi-Ajayi E, Phillip IO, Isah SY, Tabari NA, Mande A, Agunloye AM, Ogbole GI, Akinyemi JO, Akpa OM, Laryea R, Melikam SE, Adinku D, Uvere E, Burkett NS, Adekunle GF, Kehinde SI, Azuh PC, Dambatta AH, Ishaq NA, Arnett D, Tiwari HK, Lackland D, Owolabi M.Neuroepidemiology. 2015 Aug 19;45(2):73-82. [Epub ahead of print] PMID: 26304844

10. Exploring researchers’ experiences of working with a researcher-driven, population-specific community advisory board in a South African schizophrenia genomics study. Megan M. Campbell, Ezra Susser, Jantina de Vries, Adam Baldinger, Goodman Sibeko, Michael M. Mndini, Sibonile G. Mqulwana, Odwa A. Ntola, Raj S. Ramesar, Dan J. Stein. BMC Med Ethics. 2015; 16: 45. Published online 2015 July 2. doi: 10.1186/s12910-015-0037-5 PMCID: PMC4487967

11. Perspectives in Genetics and Sickle Cell Disease Prevention in Africa: Beyond the Preliminary Data from Cameroon.Wonkam A, Ngo Bitoungui VJ, Ngogang J.Public Health Genomics. 2015;18(4):237-41. doi: 10.1159/000431020. Epub 2015 Jun 4. PMID:26044545

12. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Park DJ et al.Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.PMID: 26091036
13. Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women. Dareng EO, Ma B, Famooto AO, Akarolo-Anthony SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J, Adebamowo CA.Epidemiol Infect. 2015 Jun 11:1-15. [Epub ahead of print] PMID: 26062721
14. Negative Epistasis between Sickle and Foetal Haemoglobin Suggests a Reduction in Protection against Malaria. Mmbando BP, Mgaya J, Cox SE, Mtatiro SN, Soka D, Rwezaula S, Meda E, Msaki E, Snow RW, Jeffries N, Geller NL, Makani J.PLoS One. 2015 May 12;10(5):e0125929. doi: 10.1371/journal.pone.0125929. eCollection 2015. PMID: 25965586

15. The burden of stroke in Africa: a glance at the present and a glimpse into the future. Owolabi MO, Akarolo-Anthony S, Akinyemi R, Arnett D, Gebregziabher M, Jenkins C, Tiwari H, Arulogun O, Akpalu A, Sarfo FS, Obiako R, Owolabi L, Sagoe K, Melikam S, Adeoye AM, Lackland D, Ovbiagele B; Members of the H3Africa Consortium.Cardiovasc J Afr. 2015 Mar-Apr;26(2 Suppl 1):S27-38. doi: 10.5830/CVJA-2015-038. PMID: 25962945

16. Stroke genomics in people of African ancestry: charting new paths. Akinyemi RO, Ovbiagele B, Akpalu A, Jenkins C, Sagoe K, Owolabi L, Sarfo F, Obiako R, Gebreziabher M, Melikam E, Warth S, Arulogun O, Lackland D, Ogunniyi A, Tiwari H, Kalaria RN, Arnett D, Owolabi MO; SIREN Investigators as Members of the H3Africa Consortium. Cardiovasc J Afr. 2015 Mar-Apr;26(2 Suppl 1):S39-49. doi: 10.5830/CVJA-2015-039. PMID: 25962947

17. Sickle cell disease and H3Africa: enhancing genomic research on cardiovascular diseases in African patients. Wonkam A, Makani J, Ofori-Aquah S, Nnodu OE, Treadwell M, Royal C, Ohene-Frempong K; Members of the H3Africa Consortium. Cardiovasc J Afr. 2015 Mar-Apr;26 (2 Suppl 1):S50-5. doi: 10.5830/CVJA-2015-040. Review.PMID:25962948

18. Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa. Stremlau MH, Andersen KG, Folarin OA, Grove JN, Odia I, Ehiane PE, Omoniwa O, Omoregie O, Jiang PP, Yozwiak NL, Matranga CB, Yang X, Gire SK, Winnicki S, Tariyal R, Schaffner SF, Okokhere PO, Okogbenin S, Akpede GO, Asogun DA, Agbonlahor DE, Walker PJ, Tesh RB, Levin JZ, Garry RF, Sabeti PC, Happi CT. PLoS Negl Trop Dis. 2015 Mar 17;9(3):e0003631. doi: 10.1371/journal.pntd.0003631. eCollection 2015 Mar.PMID: 25781465

19. Welcome to eNeurologicalSci (eNS)!Ovbiagele B. eNeurologicalSci. 2015 Mar;1(1):10-11. No abstract available.PMID: 26366441 Free PMC Article
20. The H3Africa policy framework: negotiating fairness in genomics.Jantina de Vries, Paulina Tindana, Katherine Littler, Michèle Ramsay, Charles Rotimi, Akin Abayomi, Nicola Mulder, Bongani M. Mayosi. 2015 Mar; 31(3):11

21. A quick guide for building a successful bioinformatics community. Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N. PLoS Comput Biol. 2015 Feb 5;11(2):e1003972. PMID: 25654371 

Terms of reference for the Genome Analysis Working Group

Purpose

• Standardization and harmonization of genomic data with respect to analysis platforms; imputation; data cleaning and quality control
• Access desirability and feasibility of using standardized array platforms across the consortium
• Analysis of population structure and phenotypes across the consortium