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Publications: Prof. Nicola Mulder

2018

ANIMA: Association network integration for multiscale analysis

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

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]

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. [ePub ahead of print]

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

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

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: 1 approved with reservations]

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

[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.

 

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

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

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

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

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

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

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]

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]

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

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

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

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

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

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

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

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.
Zenodo. [white paper]

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

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

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

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

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

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

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

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

 

 

2015

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

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

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

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

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

Modelling the risk of airborne infectious disease using exhaled air

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

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

 

Earlier Work
2014 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.
2014 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.
2014 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.
2014 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
2014 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
2014 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.
2014 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.
2014 The H3Africa Consortium. Enabling African Scientists to Engage Fully in the Genomic Revolution. Science, 344(6190): 1346-1348.
2014 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.
2014 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.
2014 Salazar GA, Meintjes A, Mulder N. PPI layouts: BioJS components for the display of Protein-Protein Interactions. F1000Research 2014, 3:50.
2014 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.
2013 Duarte J, Serufuri J-M, Mulder N, Blackburn J. Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation, In: Bioinformatics of Human Proteomics Translational Bioinformatics Springer Science+Business Media Dordrecht, 3:39-74.
2013 Barton C, Iliopoulos CS, Mulder N, Watson B. Identification of all exact and approximate inverted repeats in regular and weighted sequences. Communications in Computer and Information Science. Volume 384: 11-19.
2013 Mulder NJ, Mazandu GK, Rapanoel HA et al Using Host-Pathogen functional interactions for filtering potential drug targets in Mycobacterium tuberculosis. Mycobacterial Diseases. 3: 126, doi: 10.4172/2161-1068.1000126.
2013 Chimusa ER, Zaitlen N, Daya M, Möller M, Mulder NJ, Price AL, Hoal EG. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Human Molecular Genetics, 23(3):796-809. doi: 10.1093/hmg/ddt462.
2013 Mazandu GK, Mulder NJ. DaGO-Fun: Tool for Gene Ontology-based functional analysis using term information content measures. BMC Bioinformatics 14:284. DOI: 10.1186/10.1186/1471-2105-14-284.
2013 Akinola RO, Mazandu GK, Mulder NJ. A Systems Level Comparison of Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium smegmatis based on Functional Interaction Network Analysis. Journal of Bacteriology and Parasitology. 4(4):173, doi: 10.4172/2155-9597.1000173.
2013 Magombedze G, Dowdy D, Mulder NJ. Latent Tuberculosis: Models, Computational efforts and the Pathogen's regulatory mechanisms during dormancy. Frontiers Bioeng. Biotechnol., 1:4 doi: 10.3389/fbioe.2013.00004.
2013 Mazandu GK, Mulder NJ. Information content-based Gene Ontology semantic similarity approaches: Toward a unified framework theory. BioMed Research International. vol. 2013, Article ID 292063, 11 pages, 2013. doi:10.1155/2013/292063.
2013 Chimusa ER, Daya M, Möller M, Ramesar R, Henn BM, Van Helden PD, Mulder NJ, Hoal EG. Determining Ancestry Proportions in Complex Admixture Scenarios in South Africa using a novel Proxy Ancestry Selection Method. PLOS ONE, 8(9): e73971. doi:10.1371/journal.pone.0073971.
2013 Deffur A, Mulder N, Wilkinson R. Co-infection with Mycobacterium tuberculosis and Human Immunodeficiency Virus: an overview and motivation for systems approaches. Pathogens and Disease, doi: 10.1111/2049-632X.12060.
2013 Rapanoel HA, Mazandu GK, Mulder NJ. Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PloSOne, 8(7): e67472. doi:10.1371/journal.pone.0067472
2013 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. iAnn: An Informatics Platform for Scientific Event Sharing, Bioinformatics, 29(15):1919-1921.
2013 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. Best Practices in Bioinformatics Training for Life Scientists, Briefings in Bioinformatics, 14 (5): 528-537. doi: 10.1093/bib/bbt043
2013 Riedel A, Mofolo B, Avota E, Schneider-Schaulies S, Meintjes A, Mulder N and Kneitz S. Accumulation of splice variants and transcripts in response to PI3K inhibition in T cells. PLOS ONE, 2013;8(2):e50695. doi: 10.1371/journal.pone.0050695.
2013 Mulder NJ. Protein Family Databases, In: eLS. John Wiley & Sons, Ltd: Chichester.DOI: 10.1002/9780470015902.a0003058.pub3.
2013 Magombedze G, Mulder N. Understanding TB latency using computational and dynamic modelling procedures. Infection, Genetics and Evolution. 13: 267–283 DOI: 10.1016/j.meegid.2012.09.017.
2012 Salazar GA, Garca LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H. MyDas, an Extensible Java DAS Server. PLOS ONE 7(9): e44180. doi:10.1371/journal.pone.0044180
2012 Magombedze G, Dube N Mulder N. Mathematical modelling of infection and treatment of Mycobacterium tuberculosis latency. In: A Treatise of Biological Models, Chapter 2, Nyabadza F, Kgosimore M, Lungu EM (Eds.) Nova Science Publishers, Inc, New York. ISBN: 978-1-62257-398-1.
2012 Mazandu GK, Mulder NJ. Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins. International Journal of Molecular Sciences. 13:7283-7302, doi:10.3390/ijms13067283
2012 Mazandu GK, Mulder NJ. Enhancing drug target identification in Mycobacterium tuberculosis. In: Tuberculosis: Risk Factors, Drug Resistance and Treatment, Walker SE and Martin DF (Eds). Nova Science Publishers, Inc, New York. ISBN: 978-1-62081-991-3.
2012 Mazandu GK, Mulder NJ. A Topology-based Metric for Measuring Term Similarity in the Gene Ontology (GO). Advances in Bioinformatics. Volume 2012, Article ID 975783, doi:10.1155/2012/975783.
2012 Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S-Y, Mulder N and Hunter S. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database, Vol. 2012, doi:10.1093/database/bar068.
2012 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 and Yong S-Y. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40(1):D306-312
2012 Mazandu GK, Mulder NJ. Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction. Infection, Genetics and Evolution. 12(5):922-932.
2011 Jimenez RC, Salazar GA, Gel B, Bevan P, Dopazo J, Mulder N, Corpas M. myKaryoView: A Light-Weight Client for Visualization of Genomic Data. PLoS ONE. 6(10):e26345.
2011 Magombedze G, Mulder N. A mathematical representation of the development of Mycobacterium tuberculosis active, latent and dormant stages. Journal of Theoretical Biology 292: 44-59 (Jan 2012).
2011 Mazandu GK, Mulder NJ. Generation and analysis of large-scale data driven Mycobacterium tuberculosis functional networks for drug target identification. Advances in Bioinformatics. 2011:801478.
2011 Vuppu V and Mulder N. Analysis of Duplicate Gene Families in Microbial Genomes and Application to the Study of the Role of Gene Duplication in M. tuberculosis Evolution. In: Gene Duplication / Book 1", Friedberg F (Ed), InTech Open Access Publisher. Chapter 10, pg 173-196 ISBN 978-953-307-387-3.
2011 Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N,Martin M, Garcia A and Hermjakob H. Dasty3, a WEB Framework for DAS. Bioinformatics 27:2616-2617.
2011 Geistlinger L, Csaba G, Küffner R, Mulder N and Zimmer R. From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics 27:i366-i373, doi:10.1093/bioinformatics/btr228.
2011 Mazandu GK, Mulder NJ. Scoring Protein Relationships in Functional Interaction Networks Predicted from Sequence Data. PLoS One 6:4 e18607.
2011 Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E. DAS Writeback: A Collaborative Annotation System. BMC Bioinformatics 12:143.
2011 Faure AJ, Seoighe C, Mulder N. Investigating the effect of paralogs on microarray gene-set analysis. BMC Bioinformatics 12:29.
2011 Mazandu GK, Oppap K, Mulder N. Contribution of Microarray Data to the Advancement ofKnowledge on the Mycobacterium tuberculosis Interactome: use of the random Partial Least Squares approach. Infection, Genetics and Evolution 11:181-189.
2011 Corpas M, Doumbia S, Gascuel O, Mulder N. Bamako 2009 conference on the bioinformatics of infectious diseases. Infect Genet Evol. 11(4):695-697.
2010 Mulder NJ. Protein Domain Architectures. Methods in Molecular Biology 609:83-95. In: Data Mining Techniques for the Life Sciences, Carugo O and Eisenhaber F (Eds.), Humana Press, New York, ISBN: 978-1-60327-240-7
2010 Kanapin AA, Mulder N, Kuznetsov VA. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. BMC Genomics 11:S4.
2009 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 and Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Research 37(1):D211-215.
2009 Mulder N, Rabiu H, JamiesonG and Vuppu V. Comparative analysis of microbial genomes to study unique and expanded gene families in Mycobacterium tuberculosis. Infection, Genetics and Evolution 9(3):314-321.
2008 Bridge AJ, Veuthey A-L and Mulder NJ. Resources for functional annotation. In: Modern genome annotation, Frishman D and Valencia A (Eds.), SpringerWien publishers, New York, Chapter 4.1, ISBN: 978-3-211-75122-0.
2008 Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R. Building a biological space based on protein sequence similarities and biological ontologies. Combinatorial Chemistry and High Throughput Screening special issue "Forefront in chemogenomics" 11(8), 653-60.
2008 The Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Research 36, D440-444.
2008 Mulder NJ and Apweiler R. The InterPro Database and Tools for Protein Domain Analysis. In: Current Protocols in Bioinformatics. Chapter 2, Unit 2.7. John Wiley & Sons.
2008 Mulder NJ, Kersey P, Pruess M and Apweiler R. In silico Characterization of Proteins: UniProt, InterPro and Integr8. Molecular Biotechnology 38, 165-177.
2007 Mulder NJ.Protein Family Databases. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester.
2007 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 and Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology 25(8), 894-898.
2007 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 and Sasaki T. for the Rice Annotation Project. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research 17, 175-183.
2007 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.  New developments in the InterPro database. Nucleic Acids Research 35, D224-228.
2007 Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Research 34, D322-D326.
2007 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. The Transcriptional Landscape of the Mammalian Genome. Science 309, 1559-1563.
2006 Mulder NJ and Apweiler R. Database searching using domains. In: Bioinformatics in Proteomics. Babnigg G and Giometti CS (Eds.). Humana Press Inc. USA. ISBN: 1588295656.
2006 Mulder NJ and Apweiler R. InterPro and InterProScan – tools for protein sequence classification and comparison. Methods Molecular Biology 396, 59-70 (Comparative Genomics vol.2).
2006 Mulder NJ and Apweiler R. Genomics and the genome era. In: In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder NJ and Apweiler R (Ed.). Nova Science Publishers. Chapter 1.
2006 Mulder NJ Function prediction with protein signatures and InterPro. In: In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder NJ and Apweiler R (Ed.). Nova Science Publishers. Chapter 3.
2006 Mulder NJ and Apweiler R (Ed.) In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Nova Science Publishers ISBN: 1-59454-995-8.
2005 Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Research 34, D322-D326.
2005 Mulder NJ, Fleischmann W, Kanapin A and Apweiler R. InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study. Biofizika 51, 656-660.
2005 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. Bioinformatics tools for large-scale functional classification of proteins – the InterPro database In: Trends in Bioinformatics Research. Yan, PV (Ed.). Nova Science Publishers Inc., Chapter III, pp. 59-94, ISBN: 1-59454-739-4.
2005 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. The Transcriptional Landscape of the Mammalian Genome. Science 309, 1559-1563.
2005 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R and Lopez R. InterProScan: protein domains identifier. Nucleic Acids Research 33, W116-20.
2005 Mulder NJ and Apweiler R. Classification of proteins into families In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Jorde LB, Little PFR, Dunn MJ and Subramaniam S (Eds.). John Wiley and Sons ltd, Chichester, Chapter 78, pp. 2351-2358.
2005 Mulder NJ and Apweiler R. InterPro In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Jorde LB, Little PFR, Dunn MJ and Subramaniam S (Eds.). John Wiley and Sons ltd, Chichester, Chapter 83, pp. 2435-2439.
2005 Mulder NJ and Apweiler R. Tutorial: Getting the most out protein family classification resources In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Jorde LB, Little PFR, Dunn MJ and Subramaniam S (Eds.). John Wiley and Sons ltd, Chichester, Chapter 93, pp. 2492-2499.
2004 Mulder NJ, Pruess M and Apweiler R. In silico analysis of proteins and proteomes - InterPro and Proteome Analysis In: The Proteomics Protocols Handbook. Walker JM (Ed.). Humana Press Inc, New Jersey, U.S.A. Chapter 54, pp. 619-628.
2004 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.Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology 2(6), E162.
2004 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. InterPro -prediction of protein families, domains and functional sites In: Focus on Genome Research. Williams CR (Ed.). Nova Science Publishers Inc., New York, Chapter 5, pp. 161-194.
2004 Pruess M, Mulder N and Apweiler R. Survey of sequence databases: derived databases. In: Database Annotation in Molecular Biology: Principles and Practice. Lesk, A. M. (Ed.). Wiley & Sons Ltd., London, Chapter 3, pp. 45-62.
2003 Mulder NJ, Pruess M and Apweiler R. InterPro and Proteome Analysis –in silico analysis of proteins and proteomes In: Methods in Proteome and Protein Analysis. Kamp RM, Calvete JJ, Choli-Papadopoulou T (Eds.). Springer Publishing House, Germany, Chapter 21, pp. 307-318.
2003 Mulder NJ, and Apweiler R. The InterPro Database and tools for protein domain analysis In: Current Protocols in Bioinformatics. Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD and Stormo GD (Eds.). John Wiley & Sons Inc., London, Unit 2.7, pp. 2.7.1-2.7.19.
2003 Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL and InterPro. Genome Research 13(4), 662-72.
2003 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. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research 31, 315-318.
2003 Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F and Apweiler R. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Research 31, 414-417.
2002 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 and Cameron G. The European Bioinformatics Institute's data resources. Nucleic Acids Research 31, 43-50.
2002 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 and Apweiler R. Applications of InterPro in protein annotation and genome analysis. Briefings in Bioinformatics 3(3), 285-95.
2002 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 and Sigrist CJA. InterPro – An integrated documentation resource for protein families, domains and functional sites. Briefings in Bioinformatics 3(3), 225-35.
2002 Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F and Zdobnov E. Interactive InterPro-based comparisons of proteins in whole genomes. Bioinformatics 18(2), 374-5.
2001 Apweiler R, Biswas M, Fleischmann W, Kriventseva EV and Mulder N. Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis. In: Gene Regulation and Metabolism: Post-Genomic Computational Approaches. Collado-Vides J. and Hofestadt R (Eds.). MIT Press, USA, Chapter 2, pp. 19-47.
2001 Mulder NJ and Apweiler R. Tools and resources for identifying protein families, domains and motifs. Genome Biology 3(1), reviews2001.1-2001.8
2001 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 and Dame JB. Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species. Molecular and Biochemical Parasitology 118(2), 201-210.
2001 International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature 409, 860-921.
2001 Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I and Zdobnov E. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.Nucleic Acids Research 29(1), 44-48.
2000 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 and Zdobnov EM. InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16(12), 1145-1150.
2000 Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Oinn T, Phan I and Zdobnov E. Proteome analysis: application of InterPro and CluSTr for the functional classification of proteins in whole genomes. In: Proceedings of the German Conference on Bioinformatics (GCB’00), Bornberg-Bauer E., Rost U., Stoye J., Vingron M. (Eds.). LogosVerlag, Berlin, Germany, pp. 149-157.
1999 Mulder NJ, Zappe H and Steyn LM. Characterization of a Mycobacterium tuberculosis homologue of the Streptomyces coelicolor whiB gene. Tubercle and Lung Disease 79(5), 299-308.
1999 Mulder NJ, Powles RE, Zappe H and Steyn LM. The Mycobacterium tuberculosis mysB gene product is a functional equivalent of the Escherichia coli sigma factor, KatF. Gene 240(2), 361-70.