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Publications: Prof. Nicola Mulder (ordered by publication date)


Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies

Sinkala M, Nkhoma P, Mulder N, Martin DP.
Commun Biol 4, 1, 9

Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches

Alosaimi S, van Biljon N, Awany D, Thami PK, Defo J, Mugo JW, Bope CD, Mazandu GK, Mulder NJ, Chimusa ER.
Brief Bioinform bbaa366

Microbial function and genital inflammation in young South African women at high risk of HIV infection

Alisoltani A, Manhanzva MT, Potgieter M, Balle C, Bell L, Ross E, Iranzadeh A, du Plessis M, Radzey N, McDonald Z, Calder B, Allali I, Mulder N, Dabee S, Barnabas S, Gamieldien H, Godzik A, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JS, Masson L.
Microbiome 8, 1, 165

High-depth African genomes inform human migration and health

Choudhury 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.
Nature 586, 7831, 741-748

IHP-PING-generating integrated human protein-protein interaction networks on-the-fly

Mazandu GK, Hooper C, Opap K, Makinde F, Nembaware V, Thomford NE, Chimusa ER, Wonkam A, Mulder NJ.
Brief Bioinform [Epub ahead of print]

Editorial: The Genetic and Environmental Basis for Diseases in Understudied Populations

Mulder N, Lombard Z, Owolabi MO, Ofori-Acquah SF.
Front Genet 11, 559956

A genomics network established to respond rapidly to public health threats in South Africa

Msomi N, Mlisana K, de Oliveira T; Network for Genomic Surveillance in South Africa writing group.
Lancet Microbe 1, 6, e229-e230

The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications

Nembaware V, Mazandu GK, Hotchkiss J, Safari Serufuri JM, Kent J, Kengne AP, Anie K, Munung NS, Bukini D, Bitoungui VJN, Munube D, Chirwa U, Chunda-Liyoka C, Jonathan A, Flor-Park MV, Esoh KK, Jonas M, Mnika K, Oosterwyk C, Masamu U, Morrice J, Uwineza A, Nguweneza A, Banda K, Nyanor I, Adjei DN, Siebu NE, Nkanyemka M, Kuona P, Tayo BO, Campbell A, Oron AP, Nnodu OE, Painstil V, Makani J, Mulder N, Wonkam A.
OMICS 24, 10, 559-567

Hypothalamic-pituitary-adrenal axis suppression in asthma: A glucocorticoid receptor polymorphism may protect

Akurugu WA, Van Heerden CJ, Mulder N, Zöllner EW.
Pediatr Allergy Immunol [ePub ahead of print]

Genetic modifiers of long-term survival in sickle cell anemia

Wonkam A, Chimusa ER, Mnika K, Pule GD, Ngo Bitoungui VJ, Mulder N, Shriner D, Rotimi CN, Adeyemo A.
Clin Transl Med 10, 4, e152

Does having a mobile phone matter? Linking phone access among women to health in India: An exploratory analysis of the National Family Health Survey

Mohan D, Bashingwa JJH, Tiffin N, Dhar D, Mulder N, George A, LeFevre AE.
PLoS One 15, 7, e0236078

A review of clinical pharmacogenetics Studies in African populations

Radouani F, Zass L, Hamdi Y, Rocha JD, Sallam R, Abdelhak S, Ahmed S, Azzouzi M, Benamri I, Benkahla A, Bouhaouala-Zahar B, Chaouch M, Jmel H, Kefi R, Ksouri A, Kumuthini J, Masilela P, Masimirembwa C, Othman H, Panji S, Romdhane L, Samtal C, Sibira R, Ghedira K, Fadlelmola F, Kassim SK, Mulder N.
Per Med 17, 2, 155-170

[Preprint] BiGen: integrative clinical and brain-imaging genetics analysis using structural equation model

Elsheikh SSM, Chimusa ER, Crimi A, Mulder NJ.


Makani J, Sangeda RZ, Nnodu O, Nembaware V, Osei-Akoto A, Paintsil V, Balandya E, Kent J, Luzzatto L, Ofori-Acquah S, Olopade OI, Pallangyo K, Minja IK, Jonas M, Mazandu GK, Mulder N, Ohene-Frempong K, Wonkam A.
Lancet Haematol 7, 2, e98-e99

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

Elsheikh SSM, Chimusa ER, Mulder NJ, Crimi A.
Sci Rep 10, 1, 1433

Machine learning and network analyses reveal disease subtypes of pancreatic cancer and their molecular characteristics

Sinkala M, Mulder N, Martin D.
Sci Rep 10, 1, 1212

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research

Kumuthini 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.
BMC Bioinformatics 20, 1, 741

A broad survey of DNA sequence data simulation tools

Alosaimi 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.
Brief Funct Genomics [ePub ahead of print]

The African Genomic Medicine Training Initiative (AGMT): show-casing a community and framework driven genomic medicine training for nurses in Africa

Mulder N, Nembaware VP, The African Genomic Medicine Training Initiative.
Front Genet [Provisionally accepted]

Proposed minimum information guideline for kidney disease-research and clinical data reporting: a cross-sectional study

Kumuthini 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.
BMJ Open 9, 11, e029539

The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation

Sickle Cell Disease Ontology Working Group.
Database (Oxford) 2019:baz118

The hearing impairment ontology: a tool for unifying hearing impairment knowledge to enhance collaborative research

Hotchkiss 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.
Genes 10, 12, pii: E960

Metabolic gene alterations impact the clinical aggressiveness and drug responses of 32 human cancers

Sinkala M, Mulder N, Martin DP.
Commun Biol 2, 14

GenGraph: a python module for the simple generation and manipulation of genome graphs

Ambler JM, Mulaudzi S, Mulder N.
BMC Bioinformatics 20, 1, 519

FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data

Geza E, Mulder NJ, Chimusa ER, Crimi A.
Brief Bioinform/em> bbz117

[Preprint] Relating global and local connectome changes to dementia and targeted gene expression in Alzheimer’s disease

Elsheikh SSM, Chimusa ER, Mulder NJ, .

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]

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

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] 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.

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

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

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

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

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

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.

Bacterial pan-genomics

Iranzadeh A, Mulder NJ.
In: Microbial Genomics in Sustainable Agroecosystems, Pages 21-38, Tripathi V, Kumar P, Tripathi P, Kishore A (Ed.), Springer, Singapore.

Building infrastructure for African human genomic data management

Parker Z, Maslamoney S, Meintjes A, Botha G, Panji S, Hazelhurst S, Mulder N.
Data Science Journal 18, 47

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]

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



Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Baichoo S, Souilmi Y, Panji S, Botha S, Meintjes A, Hazelhurst S, Bendou H, De Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O’Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Van Heusden P, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N.
BMC Bioinformatics 19, 457

Strategies and opportunities for promoting bioinformatics in Zimbabwe

Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H.
PLoS Comput Biol 14, 11, e1006480

[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

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

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

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

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

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.

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

ANIMA: Association network integration for multiscale analysis

Deffur A, Wilkinson RJ, Mayosi BM, Mulder N.
Wellcome Open Res 3, 27 [Version 3]

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

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

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 67, 8, 1237–1246

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

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]

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

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

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

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 8, 1, 5078



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, a1484 [English version]

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]

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

Development to enable precision medicine in Africa

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

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

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

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

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 [Version 1]

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

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

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

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

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

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

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 389, 2355–2358

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

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]

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

Recent advances in predicting gene-disease associations

Opap K, Mulder N.
F1000Research 6, 578

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

[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.

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



[White paper] Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem

Attwood TK, Leskosek BL, Dimec J, Morgan S, Mulder N, Van Gelder CWG, Palagi PM.

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

Supplementary Material: Expressions of different semantic similarity measures in the context of biomedical sciences and WordNet

Seminal Mycobacterium tuberculosis in vivo transmission studies: reanalysis using probabilistic modelling

Issarow CM, Wood R, Mulder N.
Mycobact Dis 6, 217

A federated ecosystem for sharing genomic, clinical data

The Global Alliance for Genomics and Health. Page A, Baker D, Bobrow M, Burn J, Boycott K, Chanock S, Dove E, Durbin R, Fiume M, Flicek P, Glazer D, Goodhand P, Haussler D, Kato K, Keenan S, Liao R, Lloyd D, Knoppers BM, Mulder N, Navarro A, North K, Philippakis A, Rahman N, Rehm H, Sawyers C, Thorogood A, Altshuler D, Hudson TJ.
Science 352, 6291, 1278-1280

Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for sickle cell disease

Mulder N, Nembaware V, Adekile A, Anie KA, Inusa B, Brown B, Campbell A, Chinenere F, Chunda-Liyoka C, Derebail VK, Geard A, Ghedira K, Hamilton CM, Hanchard NA, Haendel M, Huggins W, Ibrahim M, Jupp S, Kamga KK, Knight-Madden J, Lopez-Sall P, Mbiyavanga M, Munube D, Nirenberg D, Nnodu O, Ofori-Acquah SF, Ohene-Frempong K, Opap KB, Panji S, Park M, Pule G, Royal C, Sangeda R, Tayo B, Treadwell M, Tshilolo L, Wonkam A.
Appl Transl Genomics 9, 23–29

Applying, evaluating and refining bioinformatics core competencies (an update from the curriculum task force of ISCB’s education committee)

Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T.
PLoS Comput Biol 12, e1004943

Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence

Peters JS, Calder B, Gonnelli G, Degroeve S, Rajaonarifara E, Mulder N, Soares NC, Martens L, Blackburn JM.
Front Microbiol 7, 813

Proteogenomic analysis of Mycobacterium smegmatis using high resolution mass spectrometry

Potgieter MG, Nakedi KC, Ambler JM, Nel AJM, Garnett S, Soares NC, Mulder N, Blackburn JM.
Front Microbiol 7, 427

A quantitative approach to analyzing genome reductive evolution using protein-protein interaction networks: a case study of Mycobacterium leprae

Akinola RO, Mazandu GK, Mulder NJ.
Front Genet 7, 39

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

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 O, Tiffin N, Ulenga N.
Genome Res 26, 271–277

The development of computational biology in South Africa: successes achieved and lessons learnt

Mulder NJ, Christoffels A, De Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop O, Tiffin N.
PLoS Comput Biol 12, e1004395

Real-time investigation of tuberculosis transmission: developing the Respiratory Aerosol Sampling Chamber (RASC)

Wood R, Morrow C, Barry CE 3rd, Bryden WA, Call CJ, Hickey AJ, Rodes CE, Scriba TJ, Blackburn J, Issarow C, Mulder N, Woodward J, Moosa A, Singh V, Mizrahi V, Warner DF.
PloS One 11, e0146658




Biotechnology innovators to convene in Cape Town, South Africa: pharmacogenetics and precision medicine conference (April 7-9, 2016)

Dandara C, Mpye K, Agenbag G, Skelton M, Zaahl M, Masimirembwa C, Mulder N, Warnich L, Pepper M.
Omics: J Integr Biol 19, 731–732

H3ABioNet Computational Metagenomics Workshop in Mauritius: training to analyse microbial diversity for Africa

Baichoo S, Botha G, Jaufeerally Fakim Y, Mungloo-Dilmohamud Z, Lundin D, Mulder N, Promponas VJ, Ouzounis CA.
Stand Genomic Sci 10, 115

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool

Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.
Bioinformatics 32, 477–479

ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations

Chimusa ER, Mbiyavanga M, Mazandu GK, Mulder NJ.
Bioinformatics 32, 549–556

Modelling the risk of airborne infectious disease using exhaled air

Issarow CM, Mulder N, Wood R.
J Theor Biol 372, 100–106

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training

Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, Van Gelder CWG.
PLoS Comput Biol 11, e1004143 [correction published in PLoS Comput. Biol. 11, e1004281]

A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations

Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, Ramesar R.
PLoS Genet 11, e1005052

A quick guide for building a successful bioinformatics community

Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BFF, Pawlik A, Blomberg N.
PLoS Comput Biol 11, e1003972

The H3Africa policy framework: negotiating fairness in genomics

De Vries J, Tindana P, Littler K, Ramsay M, Rotimi C, Abayomi A, Mulder N, Mayosi BM.
Trends Genet 31, 117–119




Data acquisition and data/knowledge sharing in global genomic studies

Rotimi C, Mulder N.
Appl Transl Genomics 3, 109–110

Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?

Mazandu GK, Mulder NJ.
PloS One 9, e113859

The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines

Mazandu GK, Mulder NJ.
Front Genet 5, 264

Using biological networks to improve our understanding of infectious diseases

Mulder NJ, Akinola RO, Mazandu GK, Rapanoel H.
Comput Struct Biotechnol J 11, 1–10

Bioinformatics education--perspectives and challenges out of Africa

Tastan Bishop O, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton H-G.
Brief Bioinform 16, 355–364

Enabling the genomic revolution in Africa

The H3Africa Consortium.
Science 344, 1346–1348

Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Jalali Sefid Dashti M, Mulder N, Tiffin N, Ramsay M.
BMC Genomics 15, 437

A web-based protein interaction network visualizer

Salazar GA, Meintjes A, Mazandu GK, Rapanoel HA, Akinola RO, Mulder NJ.
BMC Bioinformatics 15, 129

Genome sequence of the Tsetse fly (Glossina morsitans): vector of African trypanosomiasis

International Glossina Genome Initiative.
Science 344, 6182, 380-6

PPI layouts: BioJS components for the display of Protein-Protein Interactions

Salazar GA, Meintjes A, Mulder N.
F1000Research 3, 50

Comparative analysis of microbial pathogen genomes to study unique gene families

Hotchkiss J, Mulder NJ.
In: Bioinformatics and Data Analysis in Microbiology, Chapter 5, Bishop ÖT, Joubert F (Ed.), Caister Academic Press, Norfolk, UK.
ISBN: 978-1-908230-73-7




Co-infection with Mycobacterium tuberculosis and Human Immunodeficiency Virus: an overview and motivation for systems approaches

Deffur A, Mulder N, Wilkinson R.
Pathog Dis 69, 2, 103

Best Practices in Bioinformatics Training for Life Scientists

Via A, Blatter M-C, Blicher T, Brazas M, Brooksbank C, Budd A, Dreyer J, Fernandes P, Van de Gelder C, Jacob J, Jimenez R, Judge DP, Loveland J, McDowall J, Moran F, Mulder N, Nyroren T, De Las Rivas J, Rother K, Vlahovicek K, Schneider MV and Attwood TK.
Brief Bioinform 14, 5, 528-537

DaGO-Fun: Tool for Gene Ontology-based functional analysis using term information content measures

Mazandu GK, Mulder NJ.
BMC Bioinformatics 14, 284

Determining Ancestry Proportions in Complex Admixture Scenarios in South Africa using a novel Proxy Ancestry Selection Method

Chimusa ER, Daya M, Möller M, Ramesar R, Henn BM, Van Helden PD, Mulder NJ, Hoal EG.
PLoS One 8, 9, e73971

Genome-wide association study of ancestry-specific TB risk in the South African Coloured population

Chimusa ER, Zaitlen N, Daya M, Möller M, Mulder NJ, Price AL, Hoal EG.
Hum Mol Genet 23, 3, 796-809

Information content-based Gene Ontology semantic similarity approaches: Toward a unified framework theory

Mazandu GK, Mulder NJ
Biomed Res Int

Using host-pathogen functional interactions for filtering potential drug targets in Mycobacterium tuberculosis

Mulder NJ, Mazandu GK, Rapanoel HA.
Mycobact Dis 3, 126

A Systems Level Comparison of Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium smegmatis based on Functional Interaction Network Analysis

Akinola RO, Mazandu GK, Mulder NJ.
J Bacteriol Parasitol 4, 4, 173

Latent Tuberculosis: Models, Computational efforts and the Pathogen's regulatory mechanisms during dormancy

Magombedze G, Dowdy D, Mulder NJ.
Front Bioeng Biotechnol 1, 4

Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host

Rapanoel HA, Mazandu GK, Mulder NJ.
PloS One 8, 7, e67472

iAnn: An Informatics Platform for Scientific Event Sharing

Jimenez RC, Albar JP, Bhak J, Blatter M-C, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Van Driel M, Dunn MJ, Fernandes PL, Van Gelder CWG, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider MV, Schneider R, Via A, Villaveces JM, Yu P, Attwood TK, Corpas M.
Bioinformatics 29, 15, 1919-1921

Accumulation of splice variants and transcripts in response to PI3K inhibition in T cells

Riedel A, Mofolo B, Avota E, Schneider-Schaulies S, Meintjes A, Mulder N, Kneitz S.
PLoS One 8, 2, e50695

Understanding TB latency using computational and dynamic modelling procedures

Magombedze G, Mulder N.
Infect Genet Evol 13, 267–283

Identification of All Exact and Approximate Inverted Repeats in Regular and Weighted Sequences

Barton C, Iliopoulos CS, Mulder N, Watson B.
In: Engineering Applications of Neural Networks. Communications in Computer and Information Science, Volume 384, Pages 11-19, Iliadis L, Papadopoulos H, Jayne C (Ed.), Springer, Berlin, Heidelberg.
ISBN: 978-3-642-41016-1

Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation

Duarte J, Serufuri J-M, Mulder N, Blackburn J.
In: Bioinformatics of Human Proteomics, Translational bioinformatics, Volume 3, Pages 39-74, Wang X (Ed.), Springer, Dordrecht.
ISBN: 978-94-007-5811-7



MyDas, an Extensible Java DAS Server

Salazar GA, Garca LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.
PLoS One 7, 9, e44180

Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction

Mazandu GK, Mulder NJ.
Infect Genet Evol 12, 5, 922-932.

Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins

Mazandu GK, Mulder NJ.
Int J Mol Sci 13, 7283-7302

A Topology-based Metric for Measuring Term Similarity in the Gene Ontology (GO)

Mazandu GK, Mulder NJ.
Adv Bioinformatics 2012, 975783

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S-Y, Mulder N, Hunter S.
Database 2012, bar068

A mathematical representation of the development of Mycobacterium tuberculosis active, latent and dormant stages

Magombedze G, Mulder N.
J Theor Biol 292, 44-59

Enhancing drug target identification in Mycobacterium tuberculosis

Mazandu GK, Mulder NJ.
In: Tuberculosis: Risk Factors, Drug Resistance and Treatment, Walker SE, Martin DF (Ed.). Nova Science Publishers, Inc, New York.
ISBN: 978-1-62081-991-3

Mathematical modelling of infection and treatment of Mycobacterium tuberculosis latency

Magombedze G, Dube N Mulder N.
In: A Treatise of Biological Models, Chapter 2, Nyabadza F, Kgosimore M, Lungu EM (Ed.) Nova Science Publishers, Inc, New York.
ISBN: 978-1-62257-398-1

Protein Family Databases

Mulder NJ.
In: eLS. John Wiley & Sons, Ltd, Chichester.



Generation and analysis of large-scale data driven Mycobacterium tuberculosis functional networks for drug target identification

Mazandu GK, Mulder NJ.
Adv Bioinformatics 2011, 801478

InterPro in 2011: new developments in the family and domain prediction database

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, De Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF,
Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong S-Y.
Nucleic Acids Res 40, 1, D306-312

myKaryoView: A Light-Weight Client for Visualization of Genomic Data

Jimenez RC, Salazar GA, Gel B, Bevan P, Dopazo J, Mulder N, Corpas M.
PLoS One 6, 10, e26345

Dasty3, a WEB Framework for DAS

Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N,Martin M, Garcia A, Hermjakob H.
Bioinformatics 27, 2616-2617

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

Geistlinger L, Csaba G, Küffner R, Mulder N, Zimmer R.
Bioinformatics 27, i366-i373

Bamako 2009 conference on the bioinformatics of infectious diseases

Corpas M, Doumbia S, Gascuel O, Mulder N.
Infect Genet Evol 11, 4, 695-697

Contribution of Microarray Data to the Advancement of Knowledge on the Mycobacterium tuberculosis Interactome: use of the random Partial Least Squares approach

Mazandu GK, Oppap K, Mulder N.
Infect Genet Evol 11, 181-189

DAS Writeback: A Collaborative Annotation System

Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.
BMC Bioinformatics 12, 143

Scoring Protein Relationships in Functional Interaction Networks Predicted from Sequence Data

Mazandu GK, Mulder NJ.
PLoS One 6, 4, e18607

Investigating the effect of paralogs on microarray gene-set analysis

Faure AJ, Seoighe C, Mulder N.
BMC Bioinformatics 12, 29

Analysis of Duplicate Gene Families in Microbial Genomes and Application to the Study of the Role of Gene Duplication in M. tuberculosis Evolution

Vuppu V and Mulder N.
In: Gene Duplication, Chapter 10, Pages 173-196, Friedberg F (Ed.), InTech Open Access Publisher.
ISBN: 978-953-307-387-3



Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity

Kanapin AA, Mulder N, Kuznetsov VA.
BMC Genomics 11, S4

Protein Domain Architectures

Mulder NJ.
In: Data Mining Techniques for the Life Sciences, Methods in Molecular Biology, Volume 609, Pages 83-95, Carugo O, Eisenhaber F (Ed.), Humana Press, New York.
ISBN: 978-1-60327-241-4



Comparative analysis of microbial genomes to study unique and expanded gene families in Mycobacterium tuberculosis

Mulder N, Rabiu H, JamiesonG, Vuppu V.
Infect Genet Evol 9, 3, 314-321

InterPro: the integrative protein signature database

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res 37, 1, D211-215.



Building a biological space based on protein sequence similarities and biological ontologies

Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Comb Chem High Throughput Screen, special issue "Forefront in chemogenomics" 11, 8, 653-60.

The InterPro Database and Tools for Protein Domain Analysis

Mulder NJ , Apweiler R.
In: Current Protocols in Bioinformatics, Chapter 2, Unit 2.7, John Wiley & Sons.

In silico Characterization of Proteins: UniProt, InterPro and Integr8

Mulder NJ, Kersey P, Pruess M, Apweiler R.
Mol Biotechnol 38, 165-177

Resources for functional annotation

Bridge AJ, Veuthey A-L, Mulder NJ.
In: Modern genome annotation, Chapter 4.1, Frishman D, Valencia A (Ed.), SpringerWien publishers, New York.
ISBN: 978-3-211-75122-0



The Gene Ontology project in 2008

The Gene Ontology Consortium.
Nucleic Acids Res 36, D440-444

The minimum information required for reporting a molecular interaction experiment (MIMIx)

Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin A-C, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas JDL, Prieto C, Perreau VM, Hogue C, Mewes H-W, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
Nat Biotechnol 25, 8, 894-898

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing Y, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin Y-C, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, OOta S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J.-i, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T. for the Rice Annotation Project.
Genome Res 17, 175-183

New developments in the InterPro database

Mulder NJ, R Apweiler, TK Attwood, A Bairoch, A Bateman, D Binns, P Bork, V Buillard, L Cerutti, R Copley, E Courcelle, U Das, L Daugherty, M Dibley, R Finn, W Fleischmann, J Gough, D Haft, N Hulo, S Hunter, D Kahn, A Kanapin, A Kejariwal, A Labarga, PS Langendijk, D Lonsdale, R Lopez, I Letunic, M Madera, J Maslen, C McAnulla, J McDowall, J Mistry, A Mitchell, AN Nikolskaya, S Orchard, C Orengo, R Petryszak, JD Selengut, CJA Sigrist, PD Thomas, F Valentin, D WIlson, CH Wu, C Yeats.
Nucleic Acids Res 35, D224-228

Database searching using domains

Mulder NJ , Apweiler R.
In: Bioinformatics in Proteomics, Babnigg G, Giometti CS (Ed.), Humana Press Inc, USA.
ISBN: 1588295656

InterPro and InterProScan – tools for protein sequence classification and comparison

Mulder NJ , Apweiler R.
In: Comparative Genomics Volume 2, Methods Molecular Biology Volume 396, Pages 59-70.
ISBN: 978-1-59745-515-2

Protein Family Databases

Mulder NJ .
In: Encyclopedia of Life Sciences, John Wiley & Sons Ltd, Chichester.



InterPro as a new tool for complete genome analysis: An example of comparative analysis

Mulder NJ, Fleischmann W, Kanapin A, Apweiler R.
Biophysics 51, 587-591 [English version]

InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study [Translated title]

Mulder NJ, Fleischmann W, Kanapin A, Apweiler R.
Biofizika 51, 656-660 [Original Russian version]

The Gene Ontology (GO) project in 2006

Gene Ontology Consortium.
Nucleic Acids Res 34, D322-D326

Function prediction with protein signatures and InterPro

Mulder NJ.
In: In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins, Chapter 3, Mulder NJ, Apweiler R (Ed.), Nova Science Publishers.

Genomics and the genome era

Mulder NJ , Apweiler R.
In: In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins, Chapter 3, Mulder NJ, Apweiler R (Ed.), Nova Science Publishers.

In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins

Mulder NJ , Apweiler R (Ed.).
Nova Science Publishers
ISBN: 1-59454-995-8



The Transcriptional Landscape of the Mammalian Genome

The FANTOM Consortium, Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest ARR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, De Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, et al..
Science 309, 1559-1563

InterProScan: protein domains identifier

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
Nucleic Acids Res 33, W116-W120

InterPro, progress and status in 2005

Mulder N, R Apweiler, TK Attwood, A Bairoch, A Bateman, D Binns, P Bradley, P Bork, P Bucher, L Cerutti, R Copley, E Courcelle, U Das, R Durbin, W Fleischmann, J Gough, D Haft, N Harte, N Hulo, D Kahn, A Kanapin, M Krestyaninova, D Lonsdale, R Lopez, I Letunic, M Madera, J Maslen, J McDowall, A Mitchell, AN Nikolskaya, S Orchard, M Pagni, CP Ponting, E Quevillon, J Selengut, CJA Sigrist, V Silventoinen, DJ Studholme, R Vaughan, CH Wu.
Nucleic Acids Res 33, D201-D205

Bioinformatics tools for large-scale functional classification of proteins – the InterPro database

Mulder NJ, TK Attwood, A Bairoch, R Apweiler, A Bateman, WC Barker, D Binns, P Bradley, U Das, W Fleischmann, N Harte, N Hulo, A Kanapin, M Krestyaninova, PS Langendijk-Genevaux, V Le Saux, D Lonsdale, R Lopez, J Maslen, J McDowall, A Mitchell, DA Natale, AN Nikolskaya, S Orchard, E Quevillon, CJA Sigrist, DJ Studholme, CH Wu.
In: Trends in Bioinformatics Research, Chapter III, Pages 59-94, Yan PV (Ed.), Nova Science Publishers Inc.
ISBN: 1-59454-739-4

In Silico Characterization of Proteins InterPro and Proteome Analysis

Mulder NJ, Pruess M, Apweiler R.
In: The Proteomics Protocols Handbook, Chapter 54, Pages 619-628, Walker JM (Ed.), Humana Press Inc, New Jersey, USA.


Mulder NJ , Apweiler R.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Chapter 83, Pages 2435-2439, Jorde LB, Little PFR, Dunn MJ, Subramaniam S (Ed.), John Wiley and Sons Ltd, Chichester.



Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, et al.
PLoS Biol 2, 6, E162

Classification of proteins into families

Mulder NJ, Apweiler R.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Chapter 78, Pages 2351-2358, Jorde LB, Little PFR, Dunn MJ, Subramaniam S (Ed.), John Wiley and Sons ltd, Chichester.

Tutorial: Getting the most out protein family classification resources

Mulder NJ , Apweiler R.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Chapter 93, Pages 2492-2499, Jorde LB, Little PFR, Dunn MJ, Subramaniam S (Ed.), John Wiley and Sons Ltd, Chichester.

InterPro - prediction of protein families, domains and functional sites

Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bordoli L, Bucher P, Courcelle E, Das U, Durbin R, Flegel V, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Maslen J, McDowall J, Mulder N, Nikolskaya AN, Orchard S, Quevillon E, Servant F, Sigrist CJA, Silventoinen V, Studholme DJ, Wu CH.
In: Focus on Genome Research, Chapter 5, Pages 161-194, Williams CR (Ed.), Nova Science Publishers Inc, New York.

InterPro and Proteome Analysis – in silico analysis of proteins and proteomes

Mulder NJ, Pruess M, Apweiler R.
In: Methods in Proteome and Protein Analysis, Chapter 21, Pages 307-318 Kamp RM, Calvete JJ, Choli-Papadopoulou T (Ed.), Springer Publishing House, Germany.

Survey of sequence databases: derived databases

Pruess M, Mulder N, Apweiler R.
In: Database Annotation in Molecular Biology: Principles and Practice, Chapter 3, Pages 45-62, Lesk AM (Ed.), Wiley & Sons Ltd, London.



The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL and InterPro

Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.
Genome Res 13, 4, 662-72

The European Bioinformatics Institute's data resources

Brooksbank C, Camon E, Harris MA, Magrane M, Jesus Martin M, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr O, Cameron G.
Nucleic Acids Res 31, 43-50

The InterPro Database, 2003 brings increased coverage and new features

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJA, Vaughan R, Zdobnov EM.
Nucleic Acids Res 31, 315-318

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes

Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Nucleic Acids Res 31, 414-417

The InterPro Database and tools for protein domain analysis

Mulder NJ, Apweiler R.
In: Current Protocols in Bioinformatics, Unit 2.7, Pages 2.7.1-2.7.19, Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD, Stormo GD (Ed.), John Wiley & Sons Inc, London.



Applications of InterPro in protein annotation and genome analysis

Biswas M, O´Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Brief Bioinform 3, 3, 285-95

InterPro: An integrated documentation resource for protein families, domains and functional sites

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJA.
Brief Bioinform 3, 3, 225-35

Interactive InterPro-based comparisons of proteins in whole genomes

Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics 18, 2, 374-5

Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis

Apweiler R, Biswas M, Fleischmann W, Kriventseva EV, Mulder N.
In: Gene Regulation and Metabolism: Post-Genomic Computational Approaches, Chapter 2, Pages 19-47, Collado-Vides J, Hofestadt R (Ed.), MIT Press, USA.



Tools and resources for identifying protein families, domains and motifs

Mulder NJ, Apweiler R.
Genome Biol 3, 1, reviews2001.1-2001.8

Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species

Carlton JM-R, Muller R, Yowell CA, Fluegge MR, Sturrock KA, Vargas-Serrato E, Galinski MR, Barnwell JW, Mulder N, Kanapin A, Cawley S, Hide WA, Dame JB.
Mol Biochem Parasitol 118, 2, 201-210

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium.
Nature 409, 860-921

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes

Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic Acids Res 29, 1, 44-48

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.
Nucleic Acids Res 29, 1, 37-40



InterPro – an integrated documentation resource for protein families, domains and functional sites

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MDR, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJA, Zdobnov EM.
Bioinformatics 16, 12, 1145-1150

Proteome analysis: application of InterPro and CluSTr for the functional classification of proteins in whole genomes

Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Oinn T, Phan I, Zdobnov E.
In: Proceedings of the German Conference on Bioinformatics (GCB’00), Pages 149-157, Bornberg-Bauer E, Rost U, Stoye J, Vingron M (Ed.), LogosVerlag, Berlin, Germany.



The Mycobacterium tuberculosis mysB gene product is a functional equivalent of the Escherichia coli sigma factor, KatF

Mulder NJ, Powles RE, Zappe H, Steyn LM.
Gene 240, 2, 361-70

Characterization of a Mycobacterium tuberculosis homologue of the Streptomyces coelicolor whiB gene

Mulder NJ, Zappe H, Steyn LM.
Tuber Lung Dis 79, 5, 299-308



Identification and characterisation of transcriptional regulatory proteins from Mycobacterium tuberculosis

Disseration for PhD degree
University of Cape Town



Improvement of the colonisation of plants by bacteria by introduction of the Erwinia pectate lyase gene

Dissertation for BSc Hons degree
University of Cape Town