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Global approaches to infectious disease surveillance and modeling.
Khurana MP, Tsui JL, Gutierrez B, Chopra A, Scheidwasser N, Zhu HBH, Chang SY, Duchêne DA, Mills C, Inward RPD, Reddy B, Brittain J, Dasgupta A, Sheldon J, Githinji G, Brownstein JS, Monod M, Ferretti L, Bershan S, Tietze S, Ferres L, Argimón S, Dallman TJ, Koua E, Ratmann O, Cauchemez S, Meyers LA, Su L, Vespignani A, Pronyk P, O'Toole Á, Rambaut A, Loman NJ, Holmes EC, Flaxman S, Mulder N, Morgan OW, Tegally H, Gomez-Rodriguez M, Shadbolt N, Happi C, Chand M, Tessema SK, Mbala-Kingebeni P, Suchard MA, Pybus OG, Scarpino SV, Bhatt S, Kraemer MUG.
Nat Med 2026 May;32(5)
Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.
Baker B, Baz Lomba JA, Bitilinyu-Bangoh J, Berglöf A, Bombaywala S, Calvert-Joshua T, Kaboré B, Kingpriest P, Lang T, Levy JI, Lompo P, Lyimo E, Martens L, Mavoko HM, Mesuere B, Moremi N, Mulder N, Ndure SL, Rameto MA, Rinke de Wit TF, Sebukoto H, Smith E, Tahita MC, Tevuzula VM, Tippett Barr BA, Tiwari A, Tran T, Ubomba-Jaswa E, Van Den Bossche T, Wolday D, Krolicka A, Baraka V, Pitkänen T, Lood R.
Epub ahead of print. PMID: 42208954.2026 May 28:101426
Unleashing potential: assessing Africa's readiness for the data science revolution to impact health.
Panji S, Ras V, Gichoya J, Julius R, Maslamoney S, Motshegwa T, Sharaf A, Skelton M, Tunga M, Mulder N.
Nat Commun17(1):5138
Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa
Jjingo D, Walakira A, Hashim S, Cheickna C, Galiwango R, Kibet C, Kivunike FN, Mboowa G, Kakembo FE, Ayodele B, Entfellner JD, de Villiers S, Wambui K, Fatumo S, Chikowore T, Mukisa J, Ssekagiri A, Bbosa N, Mulindwa J, Kyobe S, Nsubuga M, Kebirungi G, Katagirya E, Mwesigwa S, Lujumba I, Kamulegeya R, Kirimunda S, Kanyerezi S, Kiyaga S, Sserwadda I, Kiberu D, Bagaya BS, Okwir J, Nabisubi P, Nabakooza G, Atwine MT, Sserunjogi R, Julius R, Quiñones M, McCarthy M, Cruz P, Noble K, Whalen CJ, Hurt D, Giovanni MY, Tartakovsky M, Ssemwanga D, Kitayimbwa JM, Reynolds SJ, Whalen CC, Kambugu A, Hanchard NA, Jian L, Amoako-Yirenkyi P, Mardon G, Jordan IK, Salifu SP, Wele M, Adebiyi E, Shaffer JG, Doumbia S, Kateete DP, Skelton M, Mulder N, Kayondo JK, Masiga D; H3Africa Consortium.
Brief Bioinform9(1):27(1)
Challenges and recommendations in establishing national human diversity genomic projects.
Oleksyk TK, Wolfsberger WW, Chhugani K, Huang YN, Pokrytiuk V, Shchubelka K, Zelikovsky A, Pasaniuc B, Jinga V, Bucur O, Edmunds SC, Guio H, Lombard Z, Henn BM, Lobiuc A, Levitchi A, Ciorba D, Bostan V, Munteanu V, Gordeev V, Schaaf CP, Hoh BP, Moreno Estrada A, Covasa M, Dimian M, Kairov U, Pak VM, Seow SW, Chiang CWK, Nepolo E, Pellegrini M, Hamdi Y, Abedalthagafi MS, Mulder NJ, Mooney J, Sanchez-Galan JE, de Souza SJ, Raventós H, Muzzio M, Chavarria-Soley G, Mangul S.
Nat Methods23(7):1261-1266
Harnessing data science for health discovery and innovation in Africa (DS-I Africa).
Xiong C, Nakatumba Nabende J, Skelton M, Retshabile G, Wonkam A, Winters A, Kateete DP, Thaldar D, Agamah F, Amegah KA, Munung NS, Mulder N, Julius R, Chunara R, Fatumo S, Owolabi M.
Commun Med (Lond)6(1):128
Imagining Genomics and Population Health in 2050: Anticipating Future Research, Policy, and Governance Needs.
Knoppers BM, Joly Y, Zawati MANH, Alsafar H, Barrett JC, Blackburn L, Chung BH, Cornel MC, Dove ES, Glazer D, Ho CW, Khoury MJ, Lewis ACF, Lucassen A, Mills PFR, Mitchell C, Mulder N, Newson AJ, Ng A, Pharoah PDP, Rahimzadeh V, Roberts MC, Sanderson SC, Skopek JM, Zimmern R, Meslin EM.
Public Health Genomics29(1):140-148
Mapping pathogen genomics training provision: a structured analysis within a global consortium network.
Matimba A, Garson KL, Trovão NS, George S, Li YT, Evans D, Batista da Rocha J, Otieno J, Mokaya J, Calvert-Joshua T, Blankenship HM, Mulder N
Front Public Health29;14:1768827
Multi-trait GWAS reveals divergent local and polygenic architecture of cardiovascular traits across African and European ancestries in the UK Biobank.
Sinkala M, Elsheikh S, Mbiyavanga M, Cullinan J, Mulder N.
Commun Biol9(1):918
A scalable HPC framework for bioinformatics in resource-limited settings: design principles, implementation, and sustainability from the UVRI experience. Bioinformatics
Lukyamuzi E, Kimbowa Wamala T, Ssekagiri A, Galiwango R, Kebirungi G, Mugume A, Nsubuga M, Maslamoney S, Panji S, Mulder NJ, Jjingo D, Kayondo J.
Bioinformatics42(4)
The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training.
Wonkam A, Munung NS, Jonas M, Mupfurirwa W, Nguweneza A, Esoh K, Oosterwyk-Liu C, Magangana Z, Mnika K, Bitoungui VN, Kamkuemah M, Banda K, Samie N, Hotchkis J, Nembaware V, Kengne AP, Mulder N.
Database (Oxford)PMID: 41719582
Uncovering genetic variation in humoral inborn errors of immunity in African populations: insights from the African genome variation database.
Hlongwa L, Meintjes A, Mulder N, Mayne E.
Sci Rep16(1):9148
Mapping epigenetic gene variant dynamics: comparative analysis of frequency, functional impact and trait associations in African and European populations
Sinkala M, Retshabile G, Mpangase PT, Bamba S, Goita MK, Nembaware V, Elsheikh SSM, Heckmann J, Esoh K, Matshaba M, Adebamowo CA, Adebamowo SN, Amih OE, Landoure G, Wonkam A, Ramsay M, Mulder N
Sci Rep16(1):13378
2025 |
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FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries
Wonkam A, Esoh K, Levine RM, Ngo Bitoungui VJ, Mnika K, Nimmagadda N, Dempsey EAD, Nkya S, Sangeda RZ, Nembaware V, Morrice J, Osman F, Beer MA, Makani J, Mulder N, Lettre G, Steinberg MH, Latanich R, Casella JF, Drehmer D, Arking DE, Chimusa ER, Yen JS, Newby GA, Antonarakis SE.
Nat Commun 16(1):2092
Workforce Development in Genomic Data Science for Health: A Worldview
Lukhele ST, Ras V, Mulder N.
Epub ahead of print PMID:40203237
Exploring the female genital tract mycobiome in young South African women using metaproteomics. Microbiome
Gangiah TK, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, McDonald Z, Allali I, Dabee S, Barnabas S, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JS, Mulder N, Masson L.
PMID: 40108637 13(1):76
The evolution of health data ecosystems: An international survey
Lerner-Ellis JP, Price EM, Subhani S, Boughtwood T, Brion MJ, Rendon A, Cividanes L, Gemmer J, Ciofani D, Bertin N, Wee SS, Robertson S, Baz B, Crameri K, Österle S, Wirta V, Sikora P, Lindstrand A, Nowak F, Amado I, Mulder NJ, Ganna A, Goodhand P, Smith LD, Marshall CR, Zawati M, Ferretti V, Michaud JL, Bulman D, Bernier F, Boycott KM.
Am J Hum Genet Epub 2025 Jul 21. PMID: 40695271
Vaginal Microbiome Research Consortium for Africa: study protocol of a multicentre prospective clinical study to evaluate temporal vaginal microbial composition associated with maintenance of reproductive health in women in South Africa and Kenya
Kullin BR, Gitome S, Happel AU, Pidwell T, Lefevre M, Madikida A, Wekesa P, Mahlangu K, Ochieng J, Awili L, Agolla W, Otieno R, Mutharimi A, Ganief Y, Daniels R, Chicken A, Welp K, Livingstone H, Swanepoel C, Claassen-Weitz S, Kanyoka P, Ravel J, Humphrys M, Bilski L, Mulder N, Bekker LG, Gill K, Jaspan H, Bukusi EA, Passmore JS.
MID: 39987010 PMCID: PMC11848679
How to sustain a public-health genomics and bioinformatics workforce in Africa
Onywera H, Mulder N, Kebede Y, Tessema SK.
Epub ahead of print PMID: 40442296
Data simulation to optimize frameworks for genome-wide association studies in diverse populations
Mugo JW, Mulder N, Chimusa ER.
PMID: 40606669 PMCID: PMC12213643
Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity
Iranzadeh A, Alisoltani A, Kiran AM, Breiman RF, Chaguza C, Peno C, Cornick JE, Everett DB, Mulder N.
Sickle Cell Disease in Africa: SickleInAfrica Registry in Ghana, Nigeria and Tanzania
Morrice J, Mupfururirwa W, Chianumba RI, Amuzu EX, Kandonga D, Nembaware V, Jonas M, Hotchkiss J, Masamu U, Nguweneza A, Mmbando BP, Minja I, Jonathan A, Mulder N, Balandya E, Osei-Akoto A, Paintsil V, Makani J, Nnodu O; Members of SPARCO Nigeria; Sangeda RZ, Kengne AP, Kuzamunu G, Wonkam A.
EJHaem 6(3):e70044
Molecular markers of reduced behavioral sensitivity to transfluthrin in Anopheles gambiae s.s. from Western Kenya
Okeyo S, Derilus D, Impoinvil LM, Dada N, Omoke D, Saizonou H, Odhiambo CA, Mulder N, Juma G, Kulohoma BW, Gimnig JE, Djogbénou LS, Lenhart A, Ochomo E.
BMC Genomics 26(1):565
Strengthening global partnerships for sustainable sickle cell disease care: insights from SickleInAfrica at the 77th United Nations General Assembly and the US-Africa Leaders' Summit. BMJ Glob Health
Minja IK, Nkya S, Bukini D, Mahenge N, Masamu U, Manongi J, Mgaya J, Mtiiye F, Nkanyemka M, Kisali EP, Mwinchande Mahawi I, Rifai A, Jonathan A, Nembaware V, Jonas M, Mulder N, Namazi R, Munube D, Paintsil V, Sangeda RZ, Ackerman H, Parker R, Sarfo FS, Guindo A, Nnodu OE, Balandya E, Kiguli S, Chunda-Liyoka C, Kuona P, Peprah E, Kamuhabwa A, Makani J.
BMJ Glob Health10(3):e017154
Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection
Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S.
Epub 138:91-96
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata
Kiran A, Hanachi M, Alsayed N, Fassatoui M, Oduaran OH, Allali I, Maslamoney S, Meintjes A, Zass L, Rocha JD, Kefi R, Benkahla A, Ghedira K, Panji S, Mulder N, Fadlelmola FM, Souiai O.
Database (Oxford) 2024
An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings
Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T..
medRxiv [Preprint] 2024.01.19.24301519
2023 |
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Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus
Van Borm S, Dellicour S, Martin DP, Lemey P, Agianniotaki EI, Chondrokouki ED, Vidanovic D, Vaskovic N, Petroviċ T, Laziċ S, Koleci X, Vodica A, Djadjovski I, Krstevski K, Vandenbussche F, Haegeman A, De Clercq K, Mathijs E.
J Virol 97(11)
Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance
Francisco NM, van Wyk S, Moir M, San JE, Sebastião CS, Tegally H, Xavier J, Maharaj A, Neto Z, Afonso P, Jandondo D, Paixão J, Miranda J, David K, Inglês L, Pereira A, Paulo A, Carralero RR, Freitas HR, Mufinda F, Lutucuta S, Ghafari M, Giovanetti M, Giandhari J, Pillay S, Naidoo Y, Singh L, Tshiabuila D, Martin DP, Chabuka L, Choga W, Wanjohi D, Mwangi S, Pillay Y, Kebede Y, Shumba E, Ondoa P, Baxter C, Wilkinson E, Tessema SK, Katzourakis A, Lessells R, de Oliveira T, Morais J.
Influenza Other Respir Viruses 17(9):e13198
Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem.
Claverie S, Hoareau M, Chéhida SB, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P.
Virus Evol 9(2):vead043
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein
Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu'a M, Burns JM, Koonin EV, Varsani A, Krupovic M.
Virus Evol 9(1):vead035
Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection
Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S.
Int J Infect Dis 138:91-96
Grand challenges in bioinformatics education and training
Işık EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, Suravajhala P, Singh H, Morgan SL, Zahroh H, Ling M, Satagopam VP, McGrath A, Nakai K, Tan TW, Gao G, Mulder N, Schönbach C, Zheng Y, De Las Rivas J, Khan AM.
Nat Biotechnol 41(8):1171-1174
Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans
Monnakgotla NR, Mahungu AC, Heckmann JM, Botha G, Mulder NJ, Wu G, Rampersaud E, Myers J, Van Blitterswijk M, Rademakers R, Taylor JP, Wuu J, Benatar M, Nel M.
Neurol Genet 9(4):e200077
Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem
Dyke SOM, Connor K, Nembaware V, Munung NS, Reinold K, Kerry G, Mbiyavanga M, Zass L, Moldes M, Das S, Davis JM, De Argila JR, Spalding JD, Evans AC, Mulder N, Karamchandani J.
Neuroinformatics 21(1):89-100
Assessing HLA imputation accuracy in a West African population
Nanjala R, Mbiyavanga M, Hashim S, de Villiers S, Mulder N.
bioRxiv [Preprint] 18(9):e0291437
Developing Clinical Phenotype Data Collection Standards for Research in Africa
Zass L, Johnston K, Benkahla A, Chaouch M, Kumuthini J, Radouani F, Mwita LA, Alsayed N, Allie T, Sathan D, Masamu U, Seuneu Tchamga MS, Tamuhla T, Samtal C, Nembaware V, Gill Z, Ahmed S, Hamdi Y, Fadlelmola F, Tiffin N, Mulder N.
Glob Health Epidemiol Genom 2023:6693323
MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
Potgieter MG, Nel AJM, Fortuin S, Garnett S, Wendoh JM, Tabb DL, Mulder NJ, Blackburn JM.
PLoS Comput Biol 19(6):e1011163
Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations
Sengupta D, Botha G, Meintjes A, Mbiyavanga M; AWI-Gen Study; H3Africa Consortium; Hazelhurst S, Mulder N, Ramsay M, Choudhury A.
Cell Genom 3(6):100332
Rationale, Design, and the Baseline Characteristics of the RHDGen (The Genetics of Rheumatic Heart Disease) Network Study
Machipisa T, Chishala C, Shaboodien G, Zühlke LJ, Muhamed B, Pandie S, de Vries J, Laing N, Joachim A, Daniels R, Ntsekhe M, Hugo-Hamman CT, Gitura B, Ogendo S, Lwabi P, Okello E, Damasceno A, Novela C, Mocumbi AO, Madeira G, Musuku J, Mtaja A, ElSayed A, Alhassan HHM, Bode-Thomas F, Yilgwan C, Amusa G, Nkereuwem E, Mulder N, Ramesar R, Lesosky M, Cordell HJ, Chong M, Keavney B, Paré G, Engel ME; RHDGen Network Consortium.
Circ Genom Precis Med 16(1):e003641
A genome-wide association study identifies distinct variants associated with pulmonary function among European and African ancestries from the UK Biobank
Sinkala M, Elsheikh SSM, Mbiyavanga M, Cullinan J, Mulder NJ.
Commun Biol 6(1):49
Can we design the next generation of digital health communication programs by leveraging the power of artificial intelligence to segment target audiences, bolster impact and deliver differentiated services? A machine learning analysis of survey data from rural India
Bashingwa JJH, Mohan D, Chamberlain S, Scott K, Ummer O, Godfrey A, Mulder N, Moodley D, LeFevre AE.
BMJ Open 13(3):e063354
2022 |
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Polygenic risk scores for CARDINAL study
Adebamowo CA, Adeyemo A, Ashaye A, Akpa OM, Chikowore T, Choudhury A, Fakim YJ, Fatumo S, Hanchard N, Hauser M, Mitchell B, Mulder N, Ofori-Acquah SF, Owolabi M, Ramsay M, Tayo B, VasanthKumar AB, Zhang Y, Adebamowo SN.
Nat Genet 54(5):527-530
Global priorities for large-scale biomarker-based prospective cohorts
Collins R, Balaconis MK, Brunak S, Chen Z, De Silva M, Gaziano JM, Ginsburg GS, Jha P, Kuri P, Metspalu A, Mulder N, Risch N.
Cell Genom 2(6):100141
Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression
Delgado-Diaz DJ, Jesaveluk B, Hayward JA, Tyssen D, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, Allali I, Dabee S, Barnabas S, Gamieldien H, Blackburn JM, Mulder N, Smith SB, Edwards VL, Burgener AD, Bekker LG, Ravel J, Passmore JS, Masson L, Hearps AC, Tachedjian G.
Microbiome 10(1):141
Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem
Dyke SOM, Connor K, Nembaware V, Munung NS, Reinold K, Kerry G, Mbiyavanga M, Zass L, Moldes M, Das S, Davis JM, De Argila JR, Spalding JD, Evans AC, Mulder N, Karamchandani J.
Neuroinformatics 21(1):89-100
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation
Mazandu GK, Hotchkiss J, Nembaware V, Wonkam A, Mulder N.
Database (Oxford) 2022:baac014
Revealing the Mutational Spectrum in Southern Africans With Amyotrophic Lateral Sclerosis
Nel M, Mahungu AC, Monnakgotla N, Botha GR, Mulder NJ, Wu G, Rampersaud E, van Blitterswijk M, Wuu J, Cooley A, Myers J, Rademakers R, Taylor JP, Benatar M, Heckmann JM.
Neurol Genet 8(1):e654
The impact of a direct to beneficiary mobile communication program on reproductive and child health outcomes: a randomised controlled trial in India
LeFevre AE, Shah N, Scott K, Chamberlain S, Ummer O, Bashingwa JJH, Chakraborty A, Godfrey A, Dutt P, Ved R, Mohan D; Kilkari Impact Evaluation Team.
BMJ Glob Health 6(Suppl 5):e008838
Rationale, Design, and the Baseline Characteristics of the RHDGen (The Genetics of Rheumatic Heart Disease) Network Study
Machipisa T, Chishala C, Shaboodien G, Zühlke LJ, Muhamed B, Pandie S, de Vries J, Laing N, Joachim A, Daniels R, Ntsekhe M, Hugo-Hamman CT, Gitura B, Ogendo S, Lwabi P, Okello E, Damasceno A, Novela C, Mocumbi AO, Madeira G, Musuku J, Mtaja A, ElSayed A, Alhassan HHM, Bode-Thomas F, Yilgwan C, Amusa G, Nkereuwem E, Mulder N, Ramesar R, Lesosky M, Cordell HJ, Chong M, Keavney B, Paré G, Engel ME; RHDGen Network Consortium.
Circ Genom Precis Med 16(1):e003641
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana R, Moyo S, Amoako DG, Tegally H, Martin DP, .
Nature 603(7902):679-686
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Martin DP, Baxter C, Lambisia AW.
Science 378(6615):eabq5358
Conserved recombination patterns across coronavirus subgenera
de Klerk A, Swanepoel P, Lourens R, Zondo M, Abodunran I, Lytras S, MacLean OA, Robertson D, Kosakovsky Pond SL, Zehr JD, Kumar V, Stanhope MJ, Harkins G, Murrell B, Martin DP.
Virus Evol 8(2):veac054
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy
Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK.
mBio 13(3):e0026922
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Makatini Z, Moyo S, Amoako DG, Baxter C, Althaus CL, Anyaneji UJ, Kekana D, Viana R, Giandhari J, Lessells RJ, Maponga T, Maruapula D, Choga W, Matshaba M, Mbulawa MB, Msomi N; NGS-SA consortium; Naidoo Y, Pillay S, Sanko TJ, San JE, Scott L, Singh L, Magini NA, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht FK, Venter M, Chiloane G, McIntyre C, O'Toole A, Ruis C, Peacock TP, Roemer C, Kosakovsky Pond SL, Williamson C, Pybus OG, Bhiman JN, Glass A, Martin DP, Jackson B, Rambaut A, Laguda-Akingba O, Gaseitsiwe S, von Gottberg A, de Oliveira T.
Nat Med 28(9):1785-1790
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
Scheepers C, Everatt J, Amoako DG, Tegally H, Wibmer CK, Mnguni A, Ismail A, Mahlangu B, Lambson BE, Martin DP, Wilkinson E, San JE, Giandhari J, Manamela N, Ntuli N, Kgagudi P, Cele S, Richardson SI, Pillay S, Mohale T, Ramphal U, Naidoo Y, Khumalo ZT, Kwatra G, Gray G, Bekker LG, Madhi SA, Baillie V, Van Voorhis WC, Treurnicht FK, Venter M, Mlisana K, Wolter N, Sigal A, Williamson C, Hsiao NY, Msomi N, Maponga T, Preiser W, Makatini Z, Lessells R, Moore PL, de Oliveira T, von Gottberg A, Bhiman JN.
Nat Commun 13(1):1976
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Lucaci AG, Zehr JD, Shank SD, Bouvier D, Mei H, Nekrutenko A, Martin DP, Kosakovsky Pond SL.
bioRxiv [Preprint] 2022.01.15.476448
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Lucaci AG, Zehr JD, Shank SD, Bouvier D, Mei H, Nekrutenko A, Martin DP, Kosakovsky Pond SL..
bioRxiv [Preprint] 2022.01.15.476448
Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study
Sheward DJ, Kim C, Ehling RA, Pankow A, Castro Dopico X, Dyrdak R, Martin DP, Reddy ST, Dillner J, Karlsson Hedestam GB, Albert J, Murrell B.
Lancet Infect Dis 22(6):813-820
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Wertheim JO, Wang JC, Leelawong M, Martin DP, Havens JL, Chowdhury MA, Pekar JE, Amin H, Arroyo A, Awandare GA, Chow HY, Gonzalez E, Luoma E, Morang'a CM, Nekrutenko A, Shank SD, Silver S, Quashie PK, Rakeman JL, Ruiz V, Torian LV, Vasylyeva TI, Kosakovsky Pond SL, Hughes S.
Nat Commun 13(1):3645
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic
Roshdy WH, Khalifa MK, San JE, Tegally H, Wilkinson E, Showky S, Martin DP, Moir M, Naguib A, Elguindy N, Gomaa MR, Fahim M, Abu Elsood H, Mohsen A, Galal R, Hassany M, Lessells RJ, Al-Karmalawy AA, El-Shesheny R, Kandeil AM, Ali MA, de Oliveira T.
Viruses 14(9):1878
Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein
Zehr JD, Pond SLK, Martin DP, Ceres K, Whittaker GR, Millet JK, Goodman LB, Stanhope MJ.
Viruses 14(5):853
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA; Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL.
Mol Biol Evol 39(4):msac061
2021 |
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Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependenciesSinkala M, Nkhoma P, Mulder N, Martin DP. |
IHP-PING-generating integrated human protein-protein interaction networks on-the-flyMazandu GK, Hooper C, Opap K, Makinde F, Nembaware V, Thomford NE, Chimusa ER, Wonkam A, Mulder NJ. |
African Global Representation in Biomedical SciencesMulder N, Zass L, Hamdi Y, Othman H, Panji S, Allali I, Fakim YJ. |
Hypothalamic-pituitary-adrenal axis suppression in asthma: A glucocorticoid receptor polymorphism may protectAkurugu WA, Van Heerden CJ, Mulder N, Zöllner EW. |
Ten simple rules for organizing a bioinformatics training course in low- and middle-income countriesMoore B, Carvajal-López P, Chauke PA, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N. |
H3ABioNet genomic medicine and microbiome data portals hackathon proceedingsFadlelmola FM, Ghedira K, Hamdi Y, Hanachi M, Radouani F, Allali I, Kiran A, Zass L, Alsayed N, Fassatoui M, Samtal C, Ahmed S, Da Rocha J, Chaqsare S, Sallam RM, Chaouch M, Farahat M, Ssekagiri A, Parker Z, Adil M, Turkson M, Benchaalia A, Benkahla A, Panji S, Kassim S, Souiai O, Mulder N. |
Examining the reach and exposure of a mobile phone-based training programme for frontline health workers (ASHAs) in 13 states across IndiaBashingwa JJH, Shah N, Mohan D, Scott K, Chamberlain S, Mulder N, Rahul S, Arora S, Chakraborty A, Ummer O, Ved R, LeFevre AE; Kilkari Impact Evaluation team. |
Assessing exposure to Kilkari: a big data analysis of a large maternal mobile messaging service across 13 states in IndiaBashingwa JJH, Mohan D, Chamberlain S, Arora S, Mendiratta J, Rahul S, Chauhan V, Scott K, Shah N, Ummer O, Ved R, Mulder N, LeFevre AE; Kilkari Impact Evaluation Team. |
Reviewing and assessing existing meta-analysis models and toolsMakinde FL, Tchamga MSS, Jafali J, Fatumo S, Chimusa ER, Mulder N, Mazandu GK. |
Author Correction: High-depth African genomes inform human migration and healthChoudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA; TrypanoGEN Research Group, Rotimi C, Ramsay M; H3Africa Consortium, Adeyemo AA, Lombard Z, Hanchard NA. |
Human OMICs and Computational Biology Research in Africa: Current Challenges and ProspectsHamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. |
SMS feedback system as a quality assurance mechanism: experience from a household survey in rural IndiaShah N, Ummer O, Scott K, Bashingwa JJH, Penugonda N, Chakraborty A, Sahore A, Mohan D, LeFevre AE; Kilkari Impact Evaluation Team. |
Data Management Plans in the genomics research revolution of Africa: Challenges and recommendationsFadlelmola FM, Zass L, Chaouch M, Samtal C, Ras V, Kumuthini J, Panji S, Mulder N. |
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in AfricaRas V, Botha G, Aron S, Lennard K, Allali I, Claassen-Weitz S, Mwaikono KS, Kennedy D, Holmes JR, Rendon G, Panji S, Fields CJ, Mulder N. |
Ensuring best practice in genomics education and evaluation: reporting item standards for education and its evaluation in genomics (RISE2 Genomics)Nisselle A, Janinski M, Martyn M, McClaren B, Kaunein N; Reporting Item Standards for Education and its Evaluation in Genomics Expert Group, Barlow-Stewart K, Belcher A, Bernat JA, Best S, Bishop M, Carroll JC, Cornel M, Dissanayake VHW, Dodds A, Dunlop K, Garg G, Gear R, Graves D, Knight K, Korf B, Kumar D, Laurino M, Ma A, Maguire J, Mallett A, McCarthy M, McEwen A, Mulder N, Patel C, Quinlan C, Reed K, Riggs ER, Sinnerbrink I, Slavotinek A, Suppiah V, Terrill B, Tobias ES, Tonkin E, Trumble S, Wessels TM, Metcalfe S, Jordan H, Gaff C. |
Does exposure to health information through mobile phones increase immunisation knowledge, completeness and timeliness in rural India?Chakraborty A, Mohan D, Scott K, Sahore A, Shah N, Kumar N, Ummer O, Bashingwa JJH, Chamberlain S, Dutt P, Godfrey A, LeFevre AE; Kilkari Impact Evaluation Team. |
2020 |
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2019 |
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A broad survey of DNA sequence data simulation toolsAlosaimi S, Bandiang A, van Biljon N, Awany D, Thami PK, Tchamga MSS, Kiran A, Messaoud O, Hassan RIM, Mugo J, Ahmed A, Bope CD, Allali I, Mazandu GK, Mulder NJ, Chimusa ER. |
Advancing the international data science workforce through shared training and educationVan Horn J, Abe S, Ambite JL, Attwood TK, Beard N, Bellis L, Bhattrai A, Bui A, Burns G, Fierro L, Gordon J, Grethe J, Kamdar J, Lei X, Lerman K, McGrath A, Mulder N, O'Driscoll C, Stewart C, Tyagi S. |
A framework for tiered informed consent for health genomic research in AfricaNembaware V, Johnston K, Diallo AA, Kotze MJ, Matimba A, Moodley K, Tangwa GB, Torrorey-Sawe R, Tiffin N. |
Another night at the museum: searching for traces of plant viruses using the virion-associated nucleic acid metagenomics approachJulian C, Filloux D, Rieux A, Lefeuvre P, Lett J-M, Becker N, Gagnevin L, Trinder-Smith TH., Hartnady P, Martin DP, Roumagnac P. |
Bacterial pan-genomicsIranzadeh A, Mulder NJ. |
Building infrastructure for African human genomic data managementParker Z, Maslamoney S, Meintjes A, Botha G, Panji S, Hazelhurst S, Mulder N. |
Data centre profile: the provincial health data centre of the Western Cape Province, South AfricaBoulle A, Heekes A, Tiffin N, Smith M, Mutemaringa T, Zinyakatira N, Phelanyane F, Pienaar C, Bud-diga K, Coetzee E, van Rooyen R, Dyers R, Fredericks N, Loff A, Shand L, Moodley M, de Vega I, Vallabhjee K. |
Description of the diversity and structure of mastrevirus communities at the scale of an agrosystem in La Réunion based on a metagenomic approachClaverie S, Scussel S, Hoareau MM, Hascoat J, Lebreton G, Grondin M, Filloux D, Roumagnac P, Martin DP, Lett J-M, Lefeuvre P. |
Emergence of southern rice black-streaked dwarf virus in the centuries-old Chinese Yuanyang agrosystem of rice landracesAlonso P, Gladieux P, Moubset O, Shih P-J, Mournet P, Frouin J, Blondin L, Ferdinand R, Fernandez E, Julian C, Filloux D, Adreit H, Fournier E, Ducasse A, Grosbois V, Morel J-B, Huang H, Jin B, He X, Martin DP, Verniere C, Roumagnac P. |
Ethical and practical issues to consider in the governance of genomic and human research data and data sharing in South Africa: a meeting reportStaunton C, Adams R, Dove ES, Harriman N, Horn L, Labuschaigne M, Mulder N, Olckers A, Pope A, Ramsay M, Swanepoel C, Ni Loideain N, De Vries J. |
Evidence for both intermittent and persistent compartmentalization of HIV-1 in the female genital tractMabvakure BM, Lambson BE, Ramdayal K, Masson L, Kitchin D, Allam M, Karim SA, Williamson C, Passmore JA, Martin DP, Scheepers C, Moore PL, Harkins GW, Morris L. |
Evolution and ecology of plant virusesLefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A. |
Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analysesMurahwa AT, Nindo F, Onywera H, Meiring TL, Martin DP, Williamson A-L. |
Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approachClaverie S, Ouattara A, Hoareau M, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. |
FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP dataGeza E, Mulder NJ, Chimusa ER, Mazandu GK. |
GenGraph: a python module for the simple generation and manipulation of genome graphsAmbler JM, Mulaudzi S, Mulder N. |
Global geographical distribution of capulavirusesGalzi S, Filloux D, Richet C, Julian C, Ferdinand R, Davoodi Z, Bejerman N, Kumari SG, Chatzivassiliou EK, Fiallo-Olivé E, Navas-Castillo J, Susi H, Laine A-L, Varsani A, Harkins GW, Martin DP, Roumagnac P. |
Host and microbiome genome-wide association studies: current state and challengesAwany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER. |
How to use relevant data for maximal benefit with minimal risk: digital health data governance to protect vulnerable populations in low income and middle-income countriesTiffin N, George A, LeFevre AE. |
Lenses and levels: the why, what and how of measuring health system drivers of women's, children's and adolescents' health with a governance focusGeorge A, LeFevre AE, Jacobs T, Kinney M, Buse K, Chopra M, Daelmans B, Haakenstad A, Huicho L, Khosla R, Rasanathan K, Sanders D, Singh NS, Tiffin N, Ved R, Zaidi SA, Schneider H. |
Leveraging crowdsourcing to accelerate global health solutionsDavis S, Button-Simons K, Bensellak T, Ahsen EM, Checkley L, Foster GJ, Su X, Moussa A, Mapiye D, Khoo SK, Nosten F, Anderson TJC, Vendrely K, Bletz J, Yu T, Panji S, Ghouila A, Mulder N, Norman T, Kern S, Meyer P, Stolovitzky G, Ferdig MT, Siwo GH. |
Metabolic gene alterations impact the clinical aggressiveness and drug responses of 32 human cancersSinkala M, Mulder N, Martin DP. |
Multi-stage association analysis of glioblastoma gene expressions with texture and spatial patternsElsheikh SSM, Bakas S, Mulder NJ, Chimusa ER, Davatzikos C, Crimi A. |
Nanopore-based detection and characterization of yam virusesFilloux D, Fernandez E, Loire E, Claude L, Galzi S, Candresse T, Winter S, Jeeva ML, Makeshkumar T, Martin DP, Roumagnac P. |
Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminivirusesLett J-M, Scussel S, Campos P, Filloux D, Roumagnac P, Harkins GW, Martin DP, Roumagnac P, Lefeuvre P, Rieux A, Becker N. |
Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New ZealandRichet C, Kraberger S, Filloux D, Bernardo P, Harkins GW, Martin DP, Roumagnac P, Varsani A. |
Partner HIV serostatus impacts viral load, genital HIV shedding and immune activation in HIV-infected individualsJaumdally SZ, Liebenberg LJP, Gumbi PP, Little F, Jaspan HB, Gamieldien H, Tiemessen CT, Coetzee D, Martin DP, Williamson C, Williamson AL, Passmore JS. |
Pervasive tertiary structure in the dengue virus RNA genomeDethoff EA, Boerneke MA, Gokhale NS, Muhire BM, Martin DP, Sacco MT, McFadden MJ, Weinstein JB, Messer WB, Horner SM, Weeks KM. |
Potential risks and solutions for sharing genome summary data from African populationsTiffin N. |
Proposed guideline for minimum information stroke research and clinical data reportingKumuthini J, Zass L, Chaouch M, Thompson M, Olowoyo P, Mbiyavanga M, Moyinoluwalogo F, Wells G, Nembaware V, Mulder NJ, Owolabi M, H3ABioNet Consortium’s Data and Standard Working Group as members of the H3Africa Consortium. |
Proposed minimum information guideline for kidney disease-research and clinical data reporting: a cross-sectional studyKumuthini J, van Woerden C, Mallett A, Zass L, Chaouch M, Thompson M, Johnston K, Mbiyavanga M, Baichoo S, Mungloo-Dilmohamud Z, Patel C, Mulder N. |
Ten simple rules for organizing a webinar seriesFadlelmola FM, Panji S, Ahmed AE, Ghouila A, Akurugu WA, Entfellner J-BD, Souiai O, Mulder N, H3ABioNet Research working group as members of the H3Africa Consortium. |
The African Genomic Medicine Training Initiative (AGMT): show-casing a community and framework driven genomic medicine training for nurses in AfricaMulder N, Nembaware VP, The African Genomic Medicine Training Initiative. |
The diagnosis of tuberculous meningitis in adults and adolescents: protocol for a systematic review and individual patient data meta-analysis to inform a multivariable prediction modelBoyles T, Stadelman A, Ellis J, Cresswell F, Lutje V, Wasserman S, Tiffin N, Wilkinson R. |
The effects of add-on corticosteroids on renal outcomes in patients with biopsy proven HIV associated nephropathy: a single centre study from South AfricaWearne N, Swanepoel CR, Duffield MS, Davidson BJ, Manning K, Tiffin N, Boulle A, Rayner BL, Naidu P, Okpechi IG. |
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics researchKumuthini J, Zass L, Panji S, Salifu SP, Kayondo JK, Nembaware V, Mbiyavanga M, Olabode A, Kishk A, Wells G, Mulder NJ as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium. |
The hearing impairment ontology: a tool for unifying hearing impairment knowledge to enhance collaborative researchHotchkiss J, Manyisa N, Adadey SM, Oluwole OG, Wonkam E, Mnika K, Yalcouye A, Nembaware V, Haendel M, Vasilevsky N, Mulder NJ, Jupp S, Wonkam A, Mazandu GK. |
The Westward journey of alfalfa leaf curl virusDavoodi Z, Bejerman N, Richet C, Filloux D, Kumari SG, Chatzivassiliou EK, Galzi S, Julian C, Samarfard S, Trucco V, Giolitti F, Fiallo-Olivé E, Navas-Castillo J, Asaad N, Moukahel AR, Hijazi J, Mghandef S, Heydarnejad J, Massumi H, Varsani A, Dietzgen RG, Harkins GW, Martin DP, Roumagnac P. |
Use of big data and machine learning methods in the monitoring and evaluation of digital health programs in India: an exploratory protocolsMohan D, Bashingwa JJH, Dane P, Chamberlain S, Tiffin N, Lefevre A. |
Using whole genome sequencing in an African subphenotype of myasthenia gravis to generate a pathogenetic hypothesisNel M, Mulder N, Europa TA, Heckmann JM. |
Vaginal microbiota varies by geographical location in South African womenLennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, Botha G, Mkhize NN, Bekker L, Lewis DA, Gray G, Mulder N, Passmore JS, Jaspan HB. |
[Preprint] crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyadsBrown BP, Wendoh J, Chopera D, Havyarimana E, Jaumdally S, Nyangahu DD, Gray CM, Martin DP, Varsani A, Jaspan HB. |
[Preprint] Development and implementation of the Sickle Cell Disease OntologyMulder N, Wonkam A, Sickle Cell Disease Ontology Working Group. |
[Preprint] MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasetsPotgieter T, Nel AJ, Tabb DL, Fortuin S, Garnett S, Blackburn J, Mulder N. |
2019 |
|---|
Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structuresGolden M, Murrell B, Martin D, Pybus OG, Hein J. |
Genome-wide association study of brain connectivity changes for Alzheimer's diseaseElsheikh SSM, Chimusa ER, Mulder NJ, Crimi A. |
Symptom evolution following the emergence of maize streak virusMonjane AL, Dellicour S, Hartnady P, Oyeniran KA, Owor BE, Bezeidenhout M, Linderme D, Syed RA, Donaldson L, Murray S, Rybicki EP, Kvarnheden A, Yazdkhasti E, Lefeuvre P, Froissart R, Roumagnac P, Shepherd DN, Harkins GW, Suchard MA, Lemey P, Varsani A, Martin DP. |
[Preprint] BiGen: integrative clinical and brain-imaging genetics analysis using structural equation modelElsheikh SSM, Chimusa ER, Crimi A, Mulder NJ. |
Machine learning and network analyses reveal disease subtypes of pancreatic cancer and their molecular characteristicsSinkala M, Mulder N, Martin D. |
2019 |
|---|
A broad survey of DNA sequence data simulation toolsAlosaimi S, Bandiang A, van Biljon N, Awany D, Thami PK, Tchamga MSS, Kiran A, Messaoud O, Hassan RIM, Mugo J, Ahmed A, Bope CD, Allali I, Mazandu GK, Mulder NJ, Chimusa ER. |
Advancing the international data science workforce through shared training and educationVan Horn J, Abe S, Ambite JL, Attwood TK, Beard N, Bellis L, Bhattrai A, Bui A, Burns G, Fierro L, Gordon J, Grethe J, Kamdar J, Lei X, Lerman K, McGrath A, Mulder N, O'Driscoll C, Stewart C, Tyagi S. |
A framework for tiered informed consent for health genomic research in AfricaNembaware V, Johnston K, Diallo AA, Kotze MJ, Matimba A, Moodley K, Tangwa GB, Torrorey-Sawe R, Tiffin N. |
Another night at the museum: searching for traces of plant viruses using the virion-associated nucleic acid metagenomics approachJulian C, Filloux D, Rieux A, Lefeuvre P, Lett J-M, Becker N, Gagnevin L, Trinder-Smith TH., Hartnady P, Martin DP, Roumagnac P. |
Bacterial pan-genomicsIranzadeh A, Mulder NJ. |
Building infrastructure for African human genomic data managementParker Z, Maslamoney S, Meintjes A, Botha G, Panji S, Hazelhurst S, Mulder N. |
Data centre profile: the provincial health data centre of the Western Cape Province, South AfricaBoulle A, Heekes A, Tiffin N, Smith M, Mutemaringa T, Zinyakatira N, Phelanyane F, Pienaar C, Bud-diga K, Coetzee E, van Rooyen R, Dyers R, Fredericks N, Loff A, Shand L, Moodley M, de Vega I, Vallabhjee K. |
Description of the diversity and structure of mastrevirus communities at the scale of an agrosystem in La Réunion based on a metagenomic approachClaverie S, Scussel S, Hoareau MM, Hascoat J, Lebreton G, Grondin M, Filloux D, Roumagnac P, Martin DP, Lett J-M, Lefeuvre P. |
Emergence of southern rice black-streaked dwarf virus in the centuries-old Chinese Yuanyang agrosystem of rice landracesAlonso P, Gladieux P, Moubset O, Shih P-J, Mournet P, Frouin J, Blondin L, Ferdinand R, Fernandez E, Julian C, Filloux D, Adreit H, Fournier E, Ducasse A, Grosbois V, Morel J-B, Huang H, Jin B, He X, Martin DP, Verniere C, Roumagnac P. |
Ethical and practical issues to consider in the governance of genomic and human research data and data sharing in South Africa: a meeting reportStaunton C, Adams R, Dove ES, Harriman N, Horn L, Labuschaigne M, Mulder N, Olckers A, Pope A, Ramsay M, Swanepoel C, Ni Loideain N, De Vries J. |
Evidence for both intermittent and persistent compartmentalization of HIV-1 in the female genital tractMabvakure BM, Lambson BE, Ramdayal K, Masson L, Kitchin D, Allam M, Karim SA, Williamson C, Passmore JA, Martin DP, Scheepers C, Moore PL, Harkins GW, Morris L. |
Evolution and ecology of plant virusesLefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A. |
Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analysesMurahwa AT, Nindo F, Onywera H, Meiring TL, Martin DP, Williamson A-L. |
Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approachClaverie S, Ouattara A, Hoareau M, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. |
FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP dataGeza E, Mulder NJ, Chimusa ER, Mazandu GK. |
GenGraph: a python module for the simple generation and manipulation of genome graphsAmbler JM, Mulaudzi S, Mulder N. |
Global geographical distribution of capulavirusesGalzi S, Filloux D, Richet C, Julian C, Ferdinand R, Davoodi Z, Bejerman N, Kumari SG, Chatzivassiliou EK, Fiallo-Olivé E, Navas-Castillo J, Susi H, Laine A-L, Varsani A, Harkins GW, Martin DP, Roumagnac P. |
Host and microbiome genome-wide association studies: current state and challengesAwany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER. |
How to use relevant data for maximal benefit with minimal risk: digital health data governance to protect vulnerable populations in low income and middle-income countriesTiffin N, George A, LeFevre AE. |
Lenses and levels: the why, what and how of measuring health system drivers of women's, children's and adolescents' health with a governance focusGeorge A, LeFevre AE, Jacobs T, Kinney M, Buse K, Chopra M, Daelmans B, Haakenstad A, Huicho L, Khosla R, Rasanathan K, Sanders D, Singh NS, Tiffin N, Ved R, Zaidi SA, Schneider H. |
Leveraging crowdsourcing to accelerate global health solutionsDavis S, Button-Simons K, Bensellak T, Ahsen EM, Checkley L, Foster GJ, Su X, Moussa A, Mapiye D, Khoo SK, Nosten F, Anderson TJC, Vendrely K, Bletz J, Yu T, Panji S, Ghouila A, Mulder N, Norman T, Kern S, Meyer P, Stolovitzky G, Ferdig MT, Siwo GH. |
Metabolic gene alterations impact the clinical aggressiveness and drug responses of 32 human cancersSinkala M, Mulder N, Martin DP. |
Multi-stage association analysis of glioblastoma gene expressions with texture and spatial patternsElsheikh SSM, Bakas S, Mulder NJ, Chimusa ER, Davatzikos C, Crimi A. |
Nanopore-based detection and characterization of yam virusesFilloux D, Fernandez E, Loire E, Claude L, Galzi S, Candresse T, Winter S, Jeeva ML, Makeshkumar T, Martin DP, Roumagnac P. |
Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminivirusesLett J-M, Scussel S, Campos P, Filloux D, Roumagnac P, Harkins GW, Martin DP, Roumagnac P, Lefeuvre P, Rieux A, Becker N. |
Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New ZealandRichet C, Kraberger S, Filloux D, Bernardo P, Harkins GW, Martin DP, Roumagnac P, Varsani A. |
Partner HIV serostatus impacts viral load, genital HIV shedding and immune activation in HIV-infected individualsJaumdally SZ, Liebenberg LJP, Gumbi PP, Little F, Jaspan HB, Gamieldien H, Tiemessen CT, Coetzee D, Martin DP, Williamson C, Williamson AL, Passmore JS. |
Pervasive tertiary structure in the dengue virus RNA genomeDethoff EA, Boerneke MA, Gokhale NS, Muhire BM, Martin DP, Sacco MT, McFadden MJ, Weinstein JB, Messer WB, Horner SM, Weeks KM. |
Potential risks and solutions for sharing genome summary data from African populationsTiffin N. |
Proposed guideline for minimum information stroke research and clinical data reportingKumuthini J, Zass L, Chaouch M, Thompson M, Olowoyo P, Mbiyavanga M, Moyinoluwalogo F, Wells G, Nembaware V, Mulder NJ, Owolabi M, H3ABioNet Consortium’s Data and Standard Working Group as members of the H3Africa Consortium. |
Proposed minimum information guideline for kidney disease-research and clinical data reporting: a cross-sectional studyKumuthini J, van Woerden C, Mallett A, Zass L, Chaouch M, Thompson M, Johnston K, Mbiyavanga M, Baichoo S, Mungloo-Dilmohamud Z, Patel C, Mulder N. |
Ten simple rules for organizing a webinar seriesFadlelmola FM, Panji S, Ahmed AE, Ghouila A, Akurugu WA, Entfellner J-BD, Souiai O, Mulder N, H3ABioNet Research working group as members of the H3Africa Consortium. |
The African Genomic Medicine Training Initiative (AGMT): show-casing a community and framework driven genomic medicine training for nurses in AfricaMulder N, Nembaware VP, The African Genomic Medicine Training Initiative. |
The diagnosis of tuberculous meningitis in adults and adolescents: protocol for a systematic review and individual patient data meta-analysis to inform a multivariable prediction modelBoyles T, Stadelman A, Ellis J, Cresswell F, Lutje V, Wasserman S, Tiffin N, Wilkinson R. |
The effects of add-on corticosteroids on renal outcomes in patients with biopsy proven HIV associated nephropathy: a single centre study from South AfricaWearne N, Swanepoel CR, Duffield MS, Davidson BJ, Manning K, Tiffin N, Boulle A, Rayner BL, Naidu P, Okpechi IG. |
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics researchKumuthini J, Zass L, Panji S, Salifu SP, Kayondo JK, Nembaware V, Mbiyavanga M, Olabode A, Kishk A, Wells G, Mulder NJ as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium. |
The hearing impairment ontology: a tool for unifying hearing impairment knowledge to enhance collaborative researchHotchkiss J, Manyisa N, Adadey SM, Oluwole OG, Wonkam E, Mnika K, Yalcouye A, Nembaware V, Haendel M, Vasilevsky N, Mulder NJ, Jupp S, Wonkam A, Mazandu GK. |
The Westward journey of alfalfa leaf curl virusDavoodi Z, Bejerman N, Richet C, Filloux D, Kumari SG, Chatzivassiliou EK, Galzi S, Julian C, Samarfard S, Trucco V, Giolitti F, Fiallo-Olivé E, Navas-Castillo J, Asaad N, Moukahel AR, Hijazi J, Mghandef S, Heydarnejad J, Massumi H, Varsani A, Dietzgen RG, Harkins GW, Martin DP, Roumagnac P. |
Use of big data and machine learning methods in the monitoring and evaluation of digital health programs in India: an exploratory protocolsMohan D, Bashingwa JJH, Dane P, Chamberlain S, Tiffin N, Lefevre A. |
Using whole genome sequencing in an African subphenotype of myasthenia gravis to generate a pathogenetic hypothesisNel M, Mulder N, Europa TA, Heckmann JM. |
Vaginal microbiota varies by geographical location in South African womenLennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, Botha G, Mkhize NN, Bekker L, Lewis DA, Gray G, Mulder N, Passmore JS, Jaspan HB. |
[Preprint] crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyadsBrown BP, Wendoh J, Chopera D, Havyarimana E, Jaumdally S, Nyangahu DD, Gray CM, Martin DP, Varsani A, Jaspan HB. |
[Preprint] Development and implementation of the Sickle Cell Disease OntologyMulder N, Wonkam A, Sickle Cell Disease Ontology Working Group. |
[Preprint] MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasetsPotgieter T, Nel AJ, Tabb DL, Fortuin S, Garnett S, Blackburn J, Mulder N. |
2018 |
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A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association studyHamda CB, Sangeda R, Mwita L, Meintjes A, Nkya S, Panji S, Mulder N, Guizani-Tabbane L, Benkahla A, Makani J, Ghedira K; H3ABioNet Consortium. |
A comprehensive survey of models for dissecting local ancestry deconvolution in human genomeGeza E, Mugo J, Mulder N, Wonkam A, Chimusa ER, Mazandu GK. |
Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellitesBriddon RW, Martin DP, Roumagnac P, Navas-Castillo J, Fiallo-Olivé E, Moriones E, Lett J-M, Zerbini FM, Varsani A. |
ANIMA: Association network integration for multiscale analysisDeffur A, Wilkinson RJ, Mayosi BM, Mulder N. |
A systems-level analysis of drug-target-disease associations for drug repositioningRutherford KD, Mazandu GK, Mulder NJ. |
C-reactive protein and procalcitonin to discriminate between tuberculosis, Pneumocystis jirovecii pneumonia, and bacterial pneumonia in HIV-infected inpatients meeting WHO criteria for seriously ill: a prospective cohort studyMendelson F, Griesel R, Tiffin N, Rangaka M, Boulle A, Mendelson M, Maartens G. |
Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunityNyangahu DD, Lennard KS, Brown BP, Darby MG, Wendoh JM, Havyarimana E, Smith P, Butcher J, Stintzi A, Mulder NJ, Horsnell W, Jaspan HB. |
Environmental and social factors impacting on epidemic and endemic tuberculosis: a modelling analysisIssarow CM, Mulder N, Wood R. |
Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infantsWood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL, Jaspan HB. |
From spatial metagenomics to molecular characterization of plant viruses: a geminivirus case study. In: Malmstrom CM (eds) Advances in Virus Research volume 101, pages 55-83 [Book]Claverie S, Bernardo P, Kraberger S, Hartnady P, Lefeuvre P, Lett JM, Galzi S, Filloux D, Harkins GW, Varsani A, Martin DP, Roumagnac P. |
H3Africa: current perspectivesMulder N, Abimiku A, Adebamowo SN, De Vries J, Matimba A, Olowoyo P, Ramsay M, Skelton M, Stein D, on behalf of the members of the H3Africa Consortium. |
Hackathons as a means of accelerating scientific discoveries and knowledge transferGhouila A, Siwo GH, Entfellner JD, Panji S, Button-Simons KA, Davis SZ, Fadlelmola FM, DREAM of Malaria Hackathon Participants, Ferdig MT, Mulder NJ. |
HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohortClaassen-Weitz S, Gardner-Lubbe S, Nicol P, Botha G, Mounaud S, Shankar J, Nierman WC, Mulder N, Budree S, Zar HJ, Nicol MP, Kaba M. |
Improved treatment outcomes with bedaquiline when substituted for second-line injectable agents in multidrug resistant tuberculosis: a retrospective cohort studyZhao Y, Fox T, Manning K, Stewart A, Tiffin N, Khomo N, Leslie J, Boulle A, Mudaly V, Kock Y, Meintjes G, Wasserman S. |
Increase in taxonomic assignment efficiency of viral reads in metagenomic studiesFrançois S, Filloux D, Frayssinet M, Roumagnac P, Martin DP, Ogliastro M, Froissart R. |
Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypesSinkala M, Mulder N, Martin DP. |
Microbial composition predicts genital tract inflammation and persistent bacterial vaginosis in South African adolescent femalesLennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, Botha G, Mkhize NN, Bekker L-G, Lewis DA, Gray G, Mulder N, Passmore J-AS, Jaspan HB. |
Molecular characterization of faba bean necrotic yellows viruses in TunisiaSimona Kraberger S, Kumari SG, Najar A, Stainton D, Martin DP, Varsani A. |
Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhone delta region of FranceGallet R, Kraberger S, Filloux D, Galzi S, Fontes H, Martin DP, Varsani A, Roumagnac P. |
New isolates of sweet potato feathery mottle virus and sweet potato virus C: biological and molecular properties, and recombination analysis based on complete genomesMaina S, Barbetti MJ, Martin DP, Edwards OR, Jones RAC. |
Notes on recombination and reassortment in multipartite/segmented virusesVarsani A, Lefeuvre P, Roumagnac P, Martin D. |
Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experienceAhmed AE, Mpangase PT, Panji S, Baichoo S, Botha G, Fadlelmola FM, Hazelhurst S, Van Heusden P, Jongeneel CV, Joubert F, Mainzer LS, Meintjes A, Armstrong D, Crusoe MR, O'Connor BD, Souilmi Y, Alghali M, Aron S, Bendou H, De Beste E, Mbiyavanga M, Souiai O, Yi L, Zermeno J, Mulder N. |
Passion fruit chlorotic mottle virus: molecular characterization of a new divergent geminivirus in BrazilFontenele RS, Abreu RA, Lamas NS, Alves-Freitas DMT, Vidal AH, Poppiel RR, Melo FL, Lacorte C, Martin DP, Campos MA, A Varsani, Ribeiro SG. |
Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptationMarcel Tongo, Tulio de Oliveira, Martin DP. |
Recombinant goose circoviruses circulating in domesticated and wild geese in PolandStenzel T, Dziewulska D, Muhire BM, Hartnady P, Kraberger S, Martin DP, A Varsani. |
Relating connectivity changes in brain networks to genetic information in Alzheimer patientsElsheikh S, Chimusa ER, Mulder N, Crimi A. |
Self-enrolment antenatal health promotion data as an adjunct to maternal clinical information systems in the Western Cape Province of South AfricaHeekes A, Tiffin N, Dane P, Mutemaringa T, Smith M, Zinyakatira N, Barron P, Seebregts C, Boulle A. |
The development and application of bioinformatics core competencies to improve bioinformatics training and educationMulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L. |
Tiered informed consent: respecting autonomy, agency and individuality in AfricaTiffin N. |
Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineagesTongo M, Harkins GW, Dorfman JR, Billings E, Tovanabutra S, de Oliveira T, Martin DP. |
World management of geminivirusesRojas MR, Macedo MA, Maliano MR, Soto-Aguilar M, Souza JO, Briddon RW, Kenyon L, Rivera Bustamante RF, Zerbini FM, Adkins S, Legg JP, Kvarnheden A, Wintermantel WM, Sudarshana MR, Peterschmitt M, Lapidot M, Martin DP, Moriones E, Inoue-Nagata AK, Gilbertson RL. |
[Accepted] The application of nasopharyngeal aspirates to evaluate changes in airway secretions during influenza virus infection in paediatric casesZekeng E-G, Xia D, Armstrong S, Mazandu GK, Moyo NA, Dia N, French N, Cunliffe N, Niang MN, Sunny S, Bingle CD, Carroll M, Digard P, Laws T, Mulder NJ, Stewart JP and Hiscox JA. |
[Preprint] Change on the fly: using machine learning in the monitoring and evaluation of digital health programs to improve evidence generation and implementation in real timeMohan D, Bashingwa JJH, Dane P, Chamberlain S, Mulder N, Tiffin N, Lefevere A. |
2017 |
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Accessing Biospecimens from the H3Africa ConsortiumBeiswanger CM, Abimiku A, Carstens N, Christoffels A, de Vries J, Duncanson A, du Plessis M, Giovanni M, Littler K, Mulder N, Troyer J, Wideroff L, H3Africa Data and Biospecimen Sharing Organizing Committee. |
A genomic and protein-protein interaction analyses of nonsyndromic hearing impairment in Cameroon using targeted genomic enrichment and massively parallel sequencingLebeko K, Manyisa N, Chimusa ER, Mulder N, Dandara C, Wonkam A. |
A multi-scenario genome-wide medical population genetics simulation frameworkMugo JW, Geza E, Defo J, Elsheikh SSM, Mazandu GK, Mulder NJ, Chimusa ER. |
Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics networkJongeneel CV, Achinike-Oduaran O, Adebiyi E, Adebiyi M, Adeyemi S, Akanle B, Aron S, Ashano E, Bendou H, Botha G, Chimusa E, Choudhury A, Donthu R, Drnevich J, Falola O, Fields CJ, Hazelhurst S, Hendry L, Isewon I, Khetani RS, Kumuthini J, Kimuda MP, Magosi L, Mainzer LS, Maslamoney S, Mbiyavanga M, Meintjes A, Mugutso D, Mpangase P, Munthali R, Nembaware V, Ndhlovu A, Odia T, Okafor A, Oladipo O, Panji S, Pillay V, Rendon G, Sengupta D, Mulder N. |
Capulavirus and Grablovirus: two new genera in the family GeminiviridaeVarsani A, Roumagnac P, Fuchs M, Navas-Castillo J, Moriones E, Idris A, Briddon RW, Rivera-Bustamante R, Murilo Zerbini F, Martin DP. |
Chinks in the armor of the HIV-1 Envelope glycan shield: Implications for immune escape from anti-glycan broadly neutralizing antibodiesMoyo T, Ferreira RC, Davids R, Sonday Z, Moore PL, Travers SA, Wood NT, Dorfman JR. |
Comparative analysis of common regions found in babuviruses and alphasatellite moleculesStainton D, Martin DP, Collings DA, Varsani A. |
Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina FasoPalanga E, Martin DP, Galzi S, Zabré J, Bouda Z, Neya JB, Sawadogo M, Traore O, Peterschmitt M, Roumagnac P, Filloux D. |
Cooperation between strain-specific and broadly neutralizing responses limited viral escape and prolonged the exposure of the broadly neutralizing epitopeAnthony C, York T, Bekker V, Matten D, Selhorst P, Ferreria RC, Garrett NJ, Karim SSA, Morris L, Wood NT, Moore PL, Williamson C. |
Delineation of the HPV11E6 and HPV18E6 Pathways in Initiating Cellular TransformationMwapagha LM, Tiffin N, Parker MI. |
Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experienceGurwitz KT, Aron S, Panji S, Maslamoney S, Fernandes PL, Judge DP, Ghouila A, Domelevo Entfellner J-B, Guerfali FZ, Saunders C, Mansour Alzohairy A, Salifu SP, Ahmed R, Cloete, R, Kayondo J, Ssemwanga D, Mulder N. |
Detecting and analyzing genetic recombination using RDP4. In: Keith J. (eds) Bioinformatics. Methods in Molecular Biology volume 1525, pages 433-460 [Book]Martin DP, Murrell B, Khoosal A, Muhire B. |
Development of bioinformatics infrastructure for genomics researchMulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, Akanle B, Alibi M, Armstrong DL, Aron S, Ashano E, Baichoo S, Benkahla A, Brown DK, Chimusa ER, Fadlelmola FM, Falola D, Fatumo S, Ghedira K, Ghouila A, Hazelhurst S, Isewon I, Jung S, Kassim SK, Kayondo JK, Mbiyavanga M, Meintjes A, Mohammed S, Mosaku A, Moussa A, Muhammd M, Mungloo-Dilmohamud Z, Nashiru O, Odia T, Okafor A, Oladipo O, Osamor V, Oyelade J, Sadki K, Salifu SP, Soyemi J, Panji S, Radouani F, Souiai O, Tastan Bishop O. |
Development to enable precision medicine in AfricaMulder N. |
First report of Maize yellow mosaic virus infecting maize in Burkina FasoPalanga E, Longué RDS, Koala M, Néya JB, Traoré O, Martin DP, Peterschmitt M, Filloux D, Roumagnac P. |
Four simple recommendations to encourage best practices in research softwareJimenez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpi JL, Gladman S, Goble C, Gonzalez Ferreiro M, Gonzalez-Beltran A, Griffin PC, Gruning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskosek B, Lopez Gomez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodova Varekova R, Talvik H-A, Todorov I, Treloar A, Tyagi S, Van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. |
Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discoveryMazandu GK, Chimusa ER, Mulder NJ. |
Genetic diversity and phylogenetic analysis of the ORF5 gene of PRRSV from central ChinaZhang L, Feng Y, Martin DP, Chen J, Ma S, Xia P, Zhang G. |
Genome sequences of a capulavirus infecting Plantago lanceolata in the Åland archipelago of FinlandSusi H, Laine AL, Filloux D, Kraberger S, Farkas K, Bernardo P, Frilander MJ, Martin DP, Varsani A, Roumagnac P. |
Genomic research data generation, analysis and sharing – challenges in the African settingMulder N, Adebamowo CA, Adebamowo SN, Adebayo O, Adeleye O, Alibi M, Baichoo S, Benkahla A, Fadlelmola FM, Ghazal H, Ghedira K, Matimba A, Moussa A, Mungloo-Dilmohamud Z, Owolabi MO, Radouani F, Rotimi CN, Stein DJ, Souiai O. |
Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scaleBernardo P, Charles-Dominique T, Barakat M, Ortet P, Fernandez E, Filloux D, Hartnady P, Rebelo TA, Cousins SR, Mesleard F, Cohez D, Yavercovski N, Varsani A, Harkins GW, Peterschmitt M, Malmstrom CM, Martin DP, Roumagnac P. |
H3ABioNet: developing sustainable bioinformatics capacity in AfricaAron S, Gurwitz K, Panji S, Mulder N, H3ABioNet Education and Training working group as members of the H3Africa Consortium. |
Hoë voorkomskoers van bakteriële vaginose en Chlamydia in ’n lae-inkomste, hoë-bevolkingsdigtheid gemeenskap in Kaapstad[High rates of bacterial vaginosis and chlamydia in a low-income, high-population-density community in Cape Town]Lennard KS, Dabee S, Barnabas SL, Havyarimana E, Jaumdally SZ, Botha G, Mkhize NN, Bekker L-G, Gray G, Mulder N, Passmore J-A, Jaspan HB. |
ICTV virus taxonomy profile: geminiviridaeZerbini FM, Briddon RW, Idris A, Martin DP, Moriones E, Navas-Castillo J, Rivera-Bustamante R, Roumagnac P, Varsani A, ICTV Report Consortium. |
Identification of a nanovirus-alphasatellite complex in Sophora alopecuroidesHeydarnejad J, Kamali M, Massumi H, Kvarnheden A, Male MF, Kraberger S, Stainton D, Martin DP, Varsani A. |
Impact of effective contact rate and post treatment immune status on population tuberculosis infection and disease using a mathematical modelIssarow CM, Mulder N, Wood R. |
Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data setsMazandu GK, Chimusa ER, Rutherford K, Zekeng E-G, Gebremariam ZZ, Onifade MY, Mulder NJ |
Molecular characterization of faba bean necrotic yellows viruses in TunisiaKraberger S, Kumari SG, Najar A, Stainton D, Martin DP, Varsani A. |
Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islandsKraberger S, Saumtally S, Pande D, Khoodoo MHR, Dhayan S, Dookun-Saumtally A, Shepherd DN, Hartnady P, Atkinson R, Lakay FM, Hanson B, Redhi D, Monjane AL, Windram OP, Walters M, Oluwafemi S, Michel-Lett J, Lefeuvre P, Martin DP, Varsani A. |
Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhône delta region of FranceGallet R, Kraberger S, Filloux D, Galzi S, Fontes H, Martin DP, Varsani A, Roumagnac P. |
Novel mastreviruses identified in Australian wild riceKraberger S, Geering ADW, Walters M, Martin DP, Varsani A. |
Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and RéunionBoukari W, Alcalá-Briseño RI, Kraberger S, Fernandez E, Filloux D, Daugrois JH, Comstock JC, Lett JM, Martin DP , Varsani A, Roumagnac P, Polston JE, Rott PC. |
Recent advances in predicting gene-disease associationsOpap K, Mulder N. |
Sickle cell disease: tipping the balance of genomic research to catalyse discoveries in AfricaMakani J, Ofori-Acquah SF, Tluway F, Mulder N, Wonkam A. |
Ten simple rules for forming a scientific professional societyGaeta BA, De Las Rivas J, Horton P, Meysman P, Mulder N, Romano P, Welch L. |
The influence of HIV on the evolution of Mycobacterium tuberculosisKoch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ. |
The role of Kenya in the trans-African spread of maize streak virus strain APande D, Madzokere E, Hartnady P, Kraberger S, Hadfield J, Rosario K, Jäschke A, Monjane AL, Owor BE, Dida MM, Shepherd DN, Martin DP, Varsani A, Harkins GW. |
Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomovirusesZaidi SS, Martin DP, Amin I, Farooq M, Mansoor S. |
Where do HIV-infected adolescents go after transfer? - Tracking transition/transfer of HIV-infected adolescents using linkage of cohort data to a health information system platformDavies MA, Tsondai P, Tiffin N, Eley B, Rabie H, Euvrard J, Orrell C, Prozesky H, Wood R, Cogill D, Haas AD, Sohn AH, Boulle A. |
Whole-genome sequencing for an enhanced understanding of genetic variation among South AfricansChoudhury A, Ramsay M, Hazelhurst S, Aron S, Bardien S, Botha G, Chimusa ER, Christoffels A, Gamieldien J, Sefid-Dashti MJ, Joubert F, Meintjes A, Mulder N, Ramesar R, Rees J, Scholtz K, Sengupta D, Soodyall H, Venter P, Warnich L, Pepper MS. |
[Preprint] A global perspective on bioinformatics training needsBrazas MD, Brooksbank C, Jimenez RC, Blackford S, Palagi PM, De Las Rivas J, Ouellette BFF, Kumuthini J, Korpelainen E, Lewitter F, Van Gelder CWG, Mulder N, Corpas M, Schneider MV, Tan TW, Clements D, Davies A, Attwood TK. |
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