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MULDER Nicky

Position: Professor, Group Head
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Phone: +27 21 406 6058


Publications

2015            Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop O, Tiffin N. The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. PLOS Computational Biology. Accepted

 

2015           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, and the H3ABioNet Consortium. H3ABioNet, a Sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa. Genome Research. Accepted Nov 2015

 

 2015           Baichoo S, Botha G, Jaufeerally Fakim Y, Mungloo-Dilmohamud Z, Lundin D, Mulder N, Promponas VJ, Ouzounis CA. H3ABioNet Computational Metagenomics Workshop in Mauritius: training to analyse microbial diversity for Africa. Standards in Genomic Sciences. Accepted Nov 2015

 

 2015           Dandara C, Mpye K, Agenbag G, Skelton M, Zaahl M, Masimirembwa C, Mulder N, Warnich L, Pepper M. Biotechnology Innovators To Convene in Cape Town, South Africa: Pharmacogenetics and Precision Medicine Conference (April 7–9, 2016). Letter to the Editor, OMICS A Journal of Integrative Biology, 19(12) DOI: 10.1089/omi.2015.0160, PMID: 26575827

 

 2015           Chimusa ER, Mbiyavanga M, Mazandu GK, Mulder NJ. ancGWAS: a Post Genome-wide Association Study Method for Interaction, Pathway, and Ancestry Analysis in Homogeneous and Admixed Populations. Bioinformatics, doi: 10.1093/bioinformatics/btv619, PMID: 26508762

 

 2015           Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder, NJ A-DaGO-Fun: an adaptable gene ontology semantic similarity-based functional analysis tool. Bioinformatics, doi: 10.1093/bioinformatics/btv590, PMID: 26476781

 

 2015           Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, Ramesar R. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations. PLoS Genet. 2015 Mar 26;11(3):e1005052. doi: 10.1371/journal.pgen.1005052.

 

 2015           Attwood, T.K., Bongcam-Rudloff, E., Brazas, M.D., Corpas, M., Gaudet, P., Lewitter, F., Mulder, N., Palagi, P.M., Schneider, M.V., van Gelder, C.W.G. and the GOBLET Consortium. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLOS Computational Biology. 11(4): e1004143. DOI: 10.1371/journal.pcbi.1004143

 

 2015           Issarow CM, Mulder N, Wood R. Modelling the risk of airborne infectious disease using exhaled air. J. Theoretical Biol. 372(2015)100–106. http://dx.doi.org/10.1016/j.jtbi.2015.02.010.

 

 2015           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, 11(2):e1003972. doi: 10.1371/journal.pcbi.1003972.

 

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            International Glossina Genome Initiative. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science, 344(6182):380-6. doi: 10.1126/science.1249656. 

 

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            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. 

 

2007            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.

 

 2006            Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Research 34, D322-D326.

 

 2006            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, N. Mulder 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, 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. InterPro, progress and status in 2005. Nucleic Acids Research. 33, D201-205

 

 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.  

 

 2005            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.

 

 

 

2004            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.

 

 

 

2003            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.

 

 

 

2002            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, 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 and Zdobnov EM. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29(1), 37-40.

 

 

 

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.

 

 

 

 

 

 



 

 

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