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CBIO Publications: 2014 - present (by year, alphabetical order)

2019

Advancing the international data science workforce through shared training and education

Van 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.
F1000Research 8, 251 [version 1]

Another night at the museum: searching for traces of plant viruses using the virion-associated nucleic acid metagenomics approach

Julian C, Filloux D, Rieux A, Lefeuvre P, Lett J-M, Becker N, Gagnevin L, Trinder-Smith TH., Hartnady P, Martin DP, Roumagnac P.
In: Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois: INRA, Résumé, Page 80. Rencontres de Virologie Végétale (RVV 2019) 17, Aussois, France.

Description of the diversity and structure of mastrevirus communities at the scale of an agrosystem in La Réunion based on a metagenomic approach

Claverie S, Scussel S, Hoareau MM, Hascoat J, Lebreton G, Grondin M, Filloux D, Roumagnac P, Martin DP, Lett J-M, Lefeuvre P.
In: Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois: INRA, Résumé, Page 48. Rencontres de Virologie Végétale (RVV 2019) 17, Aussois, France.

Ethical and practical issues to consider in the governance of genomic and human research data and data sharing in South Africa: a meeting report

Staunton 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.
JAAS Open Res 2:15 [version 1; peer review: awaiting peer review]

Evidence for both intermittent and persistent compartmentalization of HIV-1 in the female genital tract

Mabvakure 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.
J Virol JVI.00311-19 [ePub ahead of print]

Evolution and ecology of plant viruses

Lefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A.
Nat Rev Microbiol [ePub ahead of print]

Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

Murahwa AT, Nindo F, Onywera H, Meiring TL, Martin DP, Williamson A-L.
BMC Genomics 20, 1, 368

Global geographical distribution of capulaviruses

Galzi 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.
In: Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois: INRA, Résumé, Page 101. Rencontres de Virologie Végétale (RVV 2019) 17, Aussois, France.

Host and microbiome genome-wide association studies: current state and challenges

Awany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER.
Front Genet 9, 637

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 countries

Tiffin N, George A, LeFevre AE.
BMJ Glob Health 4, e001395

Lenses and levels: the why, what and how of measuring health system drivers of women's, children's and adolescents' health with a governance focus

George 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.
BMJ Glob Health 4 (Suppl 4), e001316

Leveraging crowdsourcing to accelerate global health solutions

Davis 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.
Nat Biotechnol [ePub ahead of print]

Multi-stage association analysis of glioblastoma gene expressions with texture and spatial patterns

Elsheikh SSM, Bakas S, Mulder NJ, Chimusa ER, Davatzikos C, Crimi A.
In: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Lecture Notes in Computer Science, Volume 11383, Pages 239-250, Crimi A, Bakas S, Kuijf H, Keyvan F, Reyes M, Van Walsum T (Ed.), Springer, Cham, Switzerland.

Nanopore-based detection and characterization of yam viruses

Filloux D, Fernandez E, Loire E, Claude L, Galzi S, Candresse T, Winter S, Jeeva ML, Makeshkumar T, Martin DP, Roumagnac P.
Sci Rep 8, 1, 17879

Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminiviruses

Lett J-M, Scussel S, Campos P, Filloux D, Roumagnac P, Harkins GW, Martin DP, Roumagnac P, Lefeuvre P, Rieux A, Becker N.
In: Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois: INRA, Résumé, Page 52. Rencontres de Virologie Végétale (RVV 2019) 17, Aussois, France.

Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand

Richet C, Kraberger S, Filloux D, Bernardo P, Harkins GW, Martin DP, Roumagnac P, Varsani A.
Arch Virol 164, 1, 237-242

Partner HIV serostatus impacts viral load, genital HIV shedding and immune activation in HIV-infected individuals

Jaumdally SZ, Liebenberg LJP, Gumbi PP, Little F, Jaspan HB, Gamieldien H, Tiemessen CT, Coetzee D, Martin DP, Williamson C, Williamson AL, Passmore JS.
J Acquir Immune Defic Syndr [ePub ahead of print]

Pervasive tertiary structure in the dengue virus RNA genome

Dethoff EA, Boerneke MA, Gokhale NS, Muhire BM, Martin DP, Sacco MT, McFadden MJ, Weinstein JB, Messer WB, Horner SM, Weeks KM.
Proc Natl Acad Sci USA 115, 45, 11513-11518

Proposed guideline for minimum information stroke research and clinical data reporting

Kumuthini 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.
Data Science Journal 18, 1, 26

Ten simple rules for organizing a webinar series

Fadlelmola 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.
PLoS Comput Biol 15, 4, e1006671

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 model

Boyles T, Stadelman A, Ellis J, Cresswell F, Lutje V, Wasserman S, Tiffin N, Wilkinson R.
Wellcome Open Res 4, 19 [version 1; peer review: 1 approved, 1 approved with reservations]

The effects of add-on corticosteroids on renal outcomes in patients with biopsy proven HIV associated nephropathy: a single centre study from South Africa

Wearne N, Swanepoel CR, Duffield MS, Davidson BJ, Manning K, Tiffin N, Boulle A, Rayner BL, Naidu P, Okpechi IG.
BMC Nephrol 20, 1, 44

The Westward journey of alfalfa leaf curl virus

Davoodi 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.
Viruses 10, 10, E542

Use of Big Data and Machine Learning Methods in the Monitoring and Evaluation of Digital Health Programs in India: An Exploratory Protocols

Mohan D, Bashingwa JJH, Dane P, Chamberlain S, Tiffin N, Lefevre A.
JMIR Res Protoc 8, 5, e11456

Using whole genome sequencing in an African subphenotype of myasthenia gravis to generate a pathogenetic hypothesis

Nel M, Mulder N, Europa TA, Heckmann JM.
Front Genet 10, 136

Vaginal microbiota varies by geographical location in South African women

Lennard 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.
South African Journal for Science and Technology

[Preprint] crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads

Brown BP, Wendoh J, Chopera D, Havyarimana E, Jaumdally S, Nyangahu DD, Gray CM, Martin DP, Varsani A, Jaspan HB.
BioRxiv

[Preprint] Development and implementation of the Sickle Cell Disease Ontology

Mulder N, Wonkam A, Sickle Cell Disease Ontology Working Group.
Preprints with The Lancet

[Preprint] Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures

Golden MT, Murrell B, Martin D, Hein J.
BioRxiv

[Preprint] MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets

Potgieter T, Nel AJ, Tabb DL, Fortuin S, Garnett S, Blackburn J, Mulder N.
BioRxiv

 

2018

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

Hamda CB, Sangeda R, Mwita L, Meintjes A, Nkya S, Panji S, Mulder N, Guizani-Tabbane L, Benkahla A, Makani J, Ghedira K; H3ABioNet Consortium.
PLoS One 6, 13, 7

A comprehensive survey of models for dissecting local ancestry deconvolution in human genome

Geza E, Mugo J, Mulder N, Wonkam A, Chimusa ER, Mazandu GK.
Brief. Bioinform. bby044

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

Briddon RW, Martin DP, Roumagnac P, Navas-Castillo J, Fiallo-Olivé E, Moriones E, Lett J-M, Zerbini FM, Varsani A.
Arch. Virol. 4, 1, vey015

ANIMA: Association network integration for multiscale analysis

Deffur A, Wilkinson RJ, Mayosi BM, Mulder N.
Wellcome Open Res. 3, 27 [version 2; referees: 1 approved, 1 approved with reservations]

A systems-level analysis of drug-target-disease associations for drug repositioning

Rutherford KD, Mazandu GK, Mulder NJ.
Brief. Funct. Genomics 17, 34–41

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 study

Mendelson F, Griesel R, Tiffin N, Rangaka M, Boulle A, Mendelson M, Maartens G.
BMC Infect Dis 18, 1, 399

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity

Nyangahu DD, Lennard KS, Brown BP, Darby MG, Wendoh JM, Havyarimana E, Smith P, Butcher J, Stintzi A, Mulder NJ, Horsnell W, Jaspan HB.
Microbiome 6, 124

Environmental and social factors impacting on epidemic and endemic tuberculosis: a modelling analysis

Issarow CM, Mulder N, Wood R.
R. Soc. Open Sci. 5, 170726

Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants

Wood 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.
Clin. Infect. Dis. [ePub ahead of print]

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.
Elsevier Inc.

H3Africa: current perspectives

Mulder 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.
Pharmgenomics. Pers. Med. 11, 59-66

Hackathons as a means of accelerating scientific discoveries and knowledge transfer

Ghouila A, Siwo GH, Entfellner JD, Panji S, Button-Simons KA, Davis SZ, Fadlelmola FM, DREAM of Malaria Hackathon Participants, Ferdig MT, Mulder NJ.
Genome Res. 28, 759-765

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort

Claassen-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.
Sci. Rep. 86, e00410-17

Improved treatment outcomes with bedaquiline when substituted for second-line injectable agents in multidrug resistant tuberculosis: a retrospective cohort study

Zhao Y, Fox T, Manning K, Stewart A, Tiffin N, Khomo N, Leslie J, Boulle A, Mudaly V, Kock Y, Meintjes G, Wasserman S.
Clin Infect Dis [Epub ahead of print]

Increase in taxonomic assignment efficiency of viral reads in metagenomic studies

François S, Filloux D, Frayssinet M, Roumagnac P, Martin DP, Ogliastro M, Froissart R.
Virus Res. 244, 230-234

Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes

Sinkala M, Mulder N, Martin DP.
Oncotarget. 9:29123-2913986, e00410-17

Microbial composition predicts genital tract inflammation and persistent bacterial vaginosis in South African adolescent females

Lennard 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.
Infect. Immun. 86, e00410-17

Molecular characterization of faba bean necrotic yellows viruses in Tunisia

Simona Kraberger S, Kumari SG, Najar A, Stainton D, Martin DP, Varsani A.
Arch. Virol. 163, 3, 687–694

Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhone delta region of France

Gallet R, Kraberger S, Filloux D, Galzi S, Fontes H, Martin DP, Varsani A, Roumagnac P.
Arch. Virol. 163, 3, 695-700

New isolates of sweet potato feathery mottle virus and sweet potato virus C: biological and molecular properties, and recombination analysis based on complete genomes

Maina S, Barbetti MJ, Martin DP, Edwards OR, Jones RAC.
Plant Dis 102, 10, 1899-1914

Notes on recombination and reassortment in multipartite/segmented viruses

Varsani A, Lefeuvre P, Roumagnac P, Martin D.
Curr Opin Virol 33:156-166

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

Ahmed 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.
AAS Open Res. 1:9 [version 1; referees: 3 approved with reservations]

Passion fruit chlorotic mottle virus: molecular characterization of a new divergent geminivirus in Brazil

Fontenele RS, Abreu RA, Lamas NS, Alves-Freitas DMT, Vidal AH, Poppiel RR, Melo FL, Lacorte C, Martin DP, Campos MA, A Varsani, Ribeiro SG.
Viruses 10, 4, 169

Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation

Marcel Tongo, Tulio de Oliveira, Martin DP.
Virus Evol. 4, 1, vey015

Recombinant goose circoviruses circulating in domesticated and wild geese in Poland

Stenzel T, Dziewulska D, Muhire BM, Hartnady P, Kraberger S, Martin DP, A Varsani.
Viruses 10, 3, 107

Relating connectivity changes in brain networks to genetic information in Alzheimer patients

Elsheikh S, Chimusa ER, Mulder N, Crimi A.
In: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Pages 1390-1393.

Self-enrolment antenatal health promotion data as an adjunct to maternal clinical information systems in the Western Cape Province of South Africa

Heekes A, Tiffin N, Dane P, Mutemaringa T, Smith M, Zinyakatira N, Barron P, Seebregts C, Boulle A.
BMJ Glob Health 3 (Suppl 2), e000565

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L.
PLoS Comput. Biol. 14, e1005772

Tiered informed consent: respecting autonomy, agency and individuality in Africa

Tiffin N.
BMJ Glob Health 3, 6, e001249

Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages

Tongo M, Harkins GW, Dorfman JR, Billings E, Tovanabutra S, de Oliveira T, Martin DP.
Virus Evol. 4, 1

World management of geminiviruses

Rojas 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.
Annu Rev Phytopathol 25, 56, 637-677

[Accepted] The application of nasopharyngeal aspirates to evaluate changes in airway secretions during influenza virus infection in paediatric cases

Zekeng 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.
J. Proteome Res.

[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 time

Mohan D, Bashingwa JJH, Dane P, Chamberlain S, Mulder N, Tiffin N, Lefevere A.
JMIR Preprints

[Preprint] Genome-wide association study of brain connectivity changes for Alzheimer's disease

Elsheikh SSM, Chimusa ER, Mulder N, Crimi A.
BioRxiv

 

2017

Accessing Biospecimens from the H3Africa Consortium

Beiswanger 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.
Biopreserv. Biobank. 15, 2, 95-98

A genomic and protein-protein interaction analyses of nonsyndromic hearing impairment in Cameroon using targeted genomic enrichment and massively parallel sequencing

Lebeko K, Manyisa N, Chimusa ER, Mulder N, Dandara C, Wonkam A.
Omics J. Integr. Biol. 21, 90–99

A multi-scenario genome-wide medical population genetics simulation framework

Mugo JW, Geza E, Defo J, Elsheikh SSM, Mazandu GK, Mulder NJ, Chimusa ER.
Bioinformatics 33, 2995–3002

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

Jongeneel 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.
PLoS Comput. Biol. 13, e1005419

Capulavirus and Grablovirus: two new genera in the family Geminiviridae

Varsani A, Roumagnac P, Fuchs M, Navas-Castillo J, Moriones E, Idris A, Briddon RW, Rivera-Bustamante R, Murilo Zerbini F, Martin DP.
Arch. Virol. 162, 6, 1819-1831

Chinks in the armor of the HIV-1 Envelope glycan shield: Implications for immune escape from anti-glycan broadly neutralizing antibodies

Moyo T, Ferreira RC, Davids R, Sonday Z, Moore PL, Travers SA, Wood NT, Dorfman JR.
Virology 501, 12-24

Comparative analysis of common regions found in babuviruses and alphasatellite molecules

Stainton D, Martin DP, Collings DA, Varsani A.
Arch. Evol. 162, 3, 849-855

Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso

Palanga E, Martin DP, Galzi S, Zabré J, Bouda Z, Neya JB, Sawadogo M, Traore O, Peterschmitt M, Roumagnac P, Filloux D.
Arch. Virol. 162, 7, 2149-2152

Cooperation between strain-specific and broadly neutralizing responses limited viral escape and prolonged the exposure of the broadly neutralizing epitope

Anthony C, York T, Bekker V, Matten D, Selhorst P, Ferreria RC, Garrett NJ, Karim SSA, Morris L, Wood NT, Moore PL, Williamson C.
J. Virol. 91, 18

Delineation of the HPV11E6 and HPV18E6 Pathways in Initiating Cellular Transformation

Mwapagha LM, Tiffin N, Parker MI.
Front Oncol 7, 258

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

Gurwitz 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.
PLoS Comput. Biol. 13, e1005715

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.
Humana Press, New York, NY

Development of bioinformatics infrastructure for genomics research

Mulder 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.
Glob. Heart 12, 91–98

Development to enable precision medicine in Africa

Mulder N.
Per. Med. 14, 6, 467-470

First report of Maize yellow mosaic virus infecting maize in Burkina Faso

Palanga E, Longué RDS, Koala M, Néya JB, Traoré O, Martin DP, Peterschmitt M, Filloux D, Roumagnac P.
New Disease Reports 35, 26

Four simple recommendations to encourage best practices in research software

Jimenez 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.
F1000Research 6, 876

Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery

Mazandu GK, Chimusa ER, Mulder NJ.
Brief. Bioinform. 18, 886–901

Genetic diversity and phylogenetic analysis of the ORF5 gene of PRRSV from central China

Zhang L, Feng Y, Martin DP, Chen J, Ma S, Xia P, Zhang G.
Res. Vet. Sci. 115, 226-234

Genome sequences of a capulavirus infecting Plantago lanceolata in the Åland archipelago of Finland

Susi H, Laine AL, Filloux D, Kraberger S, Farkas K, Bernardo P, Frilander MJ, Martin DP, Varsani A, Roumagnac P.
Arch. Virol. 162, 7, 2041-2045

Genomic research data generation, analysis and sharing – challenges in the African setting

Mulder 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.
Data Science Journal 16, 49

Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Bernardo 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.
ISME J. 12, 1, 173-184

H3ABioNet: developing sustainable bioinformatics capacity in Africa

Aron S, Gurwitz K, Panji S, Mulder N, H3ABioNet Education and Training working group as members of the H3Africa Consortium.
EMBnet.journal 23, e886

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.
Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie 36, 1, a1495. [published in Afrikaans]

ICTV virus taxonomy profile: geminiviridae

Zerbini FM, Briddon RW, Idris A, Martin DP, Moriones E, Navas-Castillo J, Rivera-Bustamante R, Roumagnac P, Varsani A, ICTV Report Consortium.
J Gen Virol. 98, 2, 131-133

Identification of a nanovirus-alphasatellite complex in Sophora alopecuroides

Heydarnejad J, Kamali M, Massumi H, Kvarnheden A, Male MF, Kraberger S, Stainton D, Martin DP, Varsani A.
Virus Res. 2, 235, 24-32

Impact of effective contact rate and post treatment immune status on population tuberculosis infection and disease using a mathematical model

Issarow CM, Mulder N, Wood R.
F1000Research 6, 1817

Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets

Mazandu GK, Chimusa ER, Rutherford K, Zekeng E-G, Gebremariam ZZ, Onifade MY, Mulder NJ
Brief. Bioinform. [ePub ahead of print]

Molecular characterization of faba bean necrotic yellows viruses in Tunisia

Kraberger S, Kumari SG, Najar A, Stainton D, Martin DP, Varsani A.
Arch. Virol. 163, 3, 687-694

Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Kraberger 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.
Virus Res. 238, 171-178

Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhône delta region of France

Gallet R, Kraberger S, Filloux D, Galzi S, Fontes H, Martin DP, Varsani A, Roumagnac P.
Arch. Virol. 163, 3, 695-700

Novel mastreviruses identified in Australian wild rice

Kraberger S, Geering ADW, Walters M, Martin DP, Varsani A.
Virus Res. 238, 193-197

Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion

Boukari 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.
Virol. J. 14, 1, 146

Recent advances in predicting gene-disease associations

Opap K, Mulder N.
F1000Research 6, 578

Sickle cell disease: tipping the balance of genomic research to catalyse discoveries in Africa

Makani J, Ofori-Acquah SF, Tluway F, Mulder N, Wonkam A.
Lancet Lond. Engl. 389, 2355–2358

Ten simple rules for forming a scientific professional society

Gaeta BA, De Las Rivas J, Horton P, Meysman P, Mulder N, Romano P, Welch L.
PLoS Comput. Biol. 13, e1005226

The influence of HIV on the evolution of Mycobacterium tuberculosis

Koch 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.
Mol. Biol. Evol. 34, 1654–1668

The role of Kenya in the trans-African spread of maize streak virus strain A

Pande 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.
Virus Res. 232, 69-76

Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomoviruses

Zaidi SS, Martin DP, Amin I, Farooq M, Mansoor S.
Mol. Plant Pathol. 18, 7, 901-911

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 platform

Davies 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.
J Int AIDS Soc 20(Suppl 3), 21668

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

Choudhury 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.
Nat. Commun. 8, 2062

[Preprint] A global perspective on bioinformatics training needs

Brazas 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.
BioRxiv

 

2016
  1. Chimusa ER, Mbiyavanga M, Mazandu GK, Mulder NJ, "ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations", Bioinformatics, 2016 Feb 15;32(4):549-56. doi: 0.1093/bioinformatics/btv619. Epub 2015 Oct 27. PMID: 26508762
  2. Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ, "A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool", Bioinformatics, 2016 Feb 1;32(3):477-9. doi: 10.1093/bioinformatics/btv590. Epub 2015 Oct 17.PMID: 26476781
  3. Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N; H3ABioNet Consortium, "H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa", Genome Res, 2016 Feb;26(2):271-7. doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.PMID: 26627985
  4. Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop Ö, Tiffin N, "The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt", PLoS Comput Biol, 2016 Feb 4;12(2):e1004395. doi: 10.1371/journal.pcbi.1004395. eCollection 2016 Feb.PMID: 26845152
  5. Camilla T. Weyer, John D. Grewar, Phillippa Burger, Esthea Rossouw, Carina Lourens, Christopher Joone, Misha le Grange, Peter Coetzee, Estelle H. Venter, Darren P. Martin, N. James MacLachlan, and Alan J. Guthrie, Ahead of Print-"African Horse Sickness Caused by Genome Reassortment and Reversion to Virulence of Live, Attenuated Vaccine Viruses, South Africa", 2004–2014-Volume 22, Number 12—December 2016-Emerging Infectious Disease Journal-CDC
  6. Batsirai Mabvakure, Darren P. Martin, Simona Kraberger, Leendert Cloete, Sharon van Brunschote, Andrew D.W. Geering, John E. Thomas, Kaveh Bananej, Jean-Michel Lett, Pierre Lefeuvre, Arvind Varsani, Gordon W. Harkins, "Ongoing geographical spread of Tomato yellow leaf curl virus", Virology 498, 257-264
  7. Essowè Palanga, Denis Filloux, Darren P. Martin, Emmanuel Fernandez, Daniel Gargani, Romain Ferdinand, Jean Zabré, Zakaria Bouda, James Bouma Neya, Mahamadou Sawadogo, Oumar Traore, Michel Peterschmitt, Philippe Roumagnac, "Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso", PloS ONE 11 (10), e0165188
  8. Syed Shan‐E‐Ali Zaidi, Darren P Martin, Imran Amin, Muhammad Farooq, Shahid Mansoor, "Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomoviruses", Molecular Plant Pathology
  9. Alexandre De Bruyn, Mireille Harimalala, Innocent Zinga, Batsirai M Mabvakure, Murielle Hoareau, Virginie Ravigné, Matthew Walters, Bernard Reynaud, Arvind Varsani, Gordon W Harkins, Darren P Martin, Jean-Michel Lett, Pierre Lefeuvre, "Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar", BMC Evolutionary Biology 16 (1), 182
  10. Marta Giovanetti, Nuno Rodrigues Faria, Marcio Roberto Teixeira Nunes, Janaina Mota de Vasconcelos, José Lourenço, Sueli Guerreiro Rodrigues, Joao Lidio Vianez, Sandro Patroca da Silva, Poliana Silva Lemos, Fernando Neto Tavares, Darren Patrick Martin, Mateus Santana do Rosário, Isadora Cristina Siqueira, Massimo Ciccozzi, Oliver G Pybus, Tulio de Oliveira, Luiz Carlos Alcantara, "Zika virus complete genome from Salvador, Bahia, Brazil", Infection, Genetics and Evolution 41, 142-145
  11. Pauline Bernardo, Brejnev Muhire, Sarah François, Maëlle Deshoux, Penelope Hartnady, Kata Farkas, Simona Kraberger, Denis Filloux, Emmanuel Fernandez, Serge Galzi, Romain Ferdinand, Martine Granier, Armelle Marais, Pablo Monge Blasco, Thierry Candresse, Fernando Escriu, Arvind Varsani, Gordon W Harkins, Darren P Martin, Philippe Roumagnac, "Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa", Virology 493, 142-153
  12. Anisha Dayaram, Mark L Galatowitsch, Gerardo R Argüello-Astorga, Katherine van Bysterveldt, Simona Kraberger, Daisy Stainton, Jon S Harding, Philippe Roumagnac, Darren P Martin, Pierre Lefeuvre, Arvind Varsani, "Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem", Infection, Genetics and Evolution 39, 304-316
  13. Daisy Stainton, Darren P Martin, David A Collings, John E Thomas, Arvind Varsani, "Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus", Archives of Virology 161 (4), 1019-1026
  14. Marcel Tongo, Jeffrey R Dorfman, Darren P Martin, "High Degree of HIV-1 Group M (HIV-1M) Genetic Diversity within Circulating Recombinant Forms: Insight into the Early Events of HIV-1M Evolution", Journal of Virology 90 (5), 2221-2229
  15. Ruth L Amata, Emmanuel Fernandez, Denis Filloux, Darren P Martin, Philippe Rott, Philippe Roumagnac, "Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method", Plant Disease 100 (2), 260-268, 2016
  16. Rafaël Molina, Dominique Didelot, Joël Huat, Stéphane Dupuy, Jérôme Mathey, Anne Puissant, A Puissant, "Apport des images THRS pour la catégorisation des agro-systèmes complexes à Mayotte", Géomatique Expert, 30-37
  17. Mireille Aurélie Harimalala, Alexandre De Bruyn, Frédéric Chiroleu, Murielle Hoareau, Innocent Zinga, Sahondramalala Ranomenjanahary, Virginie Ravigné, Bernard Reynaud, Arvind Varsani, Gordon William Harkins, Darren Patrick Martin, Pierre Lefeuvre, Jean-Michel Lett, "Cassava mosaic disease in Madagascar: complex epidemiology and evolutionary dynamics of cassava mosaic geminiviruses", INRA
  18. Sarah François, Denis Filloux, Philippe Roumagnac, D Bigot, Philippe Gayral, Darren Patrick Martin, Rémi Froissart, Mylène Ogliastro, "Discovery of parvovirus-related sequences in an unexpected broad range of animals", Scientific Reports 6
  19. Issarow CM, Wood R, Mulder N (2016) "Seminal Mycobacterium Tuberculosis in vivo Transmission Studies: Reanalysis Using Probabilistic Modelling" Mycobact Dis 6:217. doi:10.4172/2161-1068.1000217

 

2015
  1. Chacha M. Issarow, Nicola Mulder, Robin Wood, "Modelling the risk of airborne infectious disease using exhaled air", Journal of Theoretical Biology 372 (2015) 100-106. http://dx.doi.org/10.1016/j.jtbi.2015.02.010
  2. Darren P. Martin, Ben Murrell, Michael Golden, Arjun Khoosal, and Brejnev Muhire, "RDP4: Detection and analysis of recombination patterns in virus genomes", Virus Evolution, (2015), 1(1): vev003. doi: 10.1093/ve/vev003.
  3. Simona Kraberger, Safaa G. Kumari , Abdelmagid A. Hamed , Bruno Gronenborn, John E. Thomas, Murray Sharman, Gordon W. Harkins, Brejnev M. Muhire, Darren P. Martin, Arvind Varsani, "Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains", Infection, Genetics and Evolution 29 (2015) 203–215. http://dx.doi.org/10.1016/j.meegid.2014.11.024
  4. Filloux D, Murrell S, Koohapitagtam M, Golden M, Julian C, Galzi S, Uzest M, Rodier-Goud M, D'Hont A, Vernerey MS, Wilkin P, Peterschmitt M, Winter S, Murrell B, Martin DP, Roumagnac P, "The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed", Virus Evolution 1(1), vev002, 2015

 

2014
  1. De Vries J, Tindana P, Littler K, Ramsay M, Rotimi C, Abayomi A, Mulder N, Mayosi BM. "Negotiating Fairness in International Genomics Research in Africa: the example of the H3Africa Consortium", Trends in Genetics, accepted.
  2. Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BFF, Pawlik A, Blomberg N. "A Quick Guide for Building a Successful Bioinformatics Community", PLOS Computational Biology, accepted.
  3. Mazandu GK and Mulder NJ. "Information Content-based Gene Ontology Functional Similarity Measures: Which one to use for a given biological data type?", PLOS ONE, 9(12): e113859, DOI: 10.1371/journal.pone.0113859.
  4. Mulder NJ, Akinola RO, Mazandu GK, Rapanoel H. "Using biological networks to improve our understanding of infectious diseases", Computational and Structural Biotechnology Journal 11 (2014) 1–10. DOI: 10.1016/j.csbj.2014.08.006
  5. Rotimi C and Mulder N, "Data acquisition and data/knowledge sharing in global genomic studies", Applied & Translational Genomics, DOI: 10.1016/j.atg.2014.09.002
  6. Mazandu GK and Mulder N. "The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines", Frontiers in Genetics - Bioinformatics and Computational Biology, 5(264) doi: 10.3389/fgene.2014.00264.
  7. Tastan Bishop O, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton HG, "Bioinformatics Education -Perspectives and Challenges out of Africa", Briefings in Bioinformatics, July doi:10.1093/bib/bbu022.
  8. The H3Africa Consortium. "Enabling African Scientists to Engage Fully in the Genomic Revolution", Science, 344(6190): 1346-1348.
  9. Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Sefid Dashti MJ, Mulder N, Tiffin N and Ramsay M, "Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance", BMC Genomics 15:437, doi: 10.1186/1471-2164-15-437.
  10. Salazar GA, Meintjes A, Mazandu G, Rapanoel H, Akinola RO and Mulder N, "A Web-based Protein Interaction Network Visualizer", BMC Bioinformatics, 15 :129  doi:10.1186/1471-2105-15-129. 
  11. International Glossina Genome Initiative, "Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis", Science, 344(6182):380-6. doi: 10.1126/science.1249656.
  12. Salazar GA, Meintjes A, Mulder N, "PPI layouts: BioJS components for the display of Protein-Protein Interactions", F1000Research 2014, 3:50.
  13. Hotchkiss J, Mulder NJ, "Comparative analysis of microbial pathogen genomes to study unique gene families. Bioinformatics and Data Analysis in Microbiology", Tastan Bishop O, Joubert F (Eds). Horizon Scientific Press. Chapter 5, ISBN: 978-1-908230-73-7.