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Items: 48

1.

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. 2019 Dec 30;20(1):741. doi: 10.1186/s12859-019-3322-3.

2.

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. 2019 Dec 23. pii: elz033. doi: 10.1093/bfgp/elz033. [Epub ahead of print]

PMID:
31867604
3.

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 (Basel). 2019 Nov 21;10(12). pii: E960. doi: 10.3390/genes10120960.

4.

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.

Brainlesion. 2019;11383:239-250. doi: 10.1007/978-3-030-11723-8_24. Epub 2019 Jan 26.

5.

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

Geza E, Mugo J, Mulder NJ, Wonkam A, Chimusa ER, Mazandu GK.

Brief Bioinform. 2019 Sep 27;20(5):1709-1724. doi: 10.1093/bib/bby044.

PMID:
30010715
6.

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

Rutherford KD, Mazandu GK, Mulder NJ.

Brief Funct Genomics. 2018 Jan 1;17(1):34-41. doi: 10.1093/bfgp/elx015.

PMID:
28968683
7.

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. 2017 Oct 1;33(19):2995-3002. doi: 10.1093/bioinformatics/btx369.

8.

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 EG, Gebremariam ZZ, Onifade MY, Mulder NJ.

Brief Bioinform. 2018 Nov 27;19(6):1141-1152. doi: 10.1093/bib/bbx052.

PMID:
28520909
9.

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 Ö; H3ABioNet Consortium, as members of the H3Africa Consortium.

Glob Heart. 2017 Jun;12(2):91-98. doi: 10.1016/j.gheart.2017.01.005. Epub 2017 Mar 13. Review.

10.

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

Mazandu GK, Chimusa ER, Mulder NJ.

Brief Bioinform. 2017 Sep 1;18(5):886-901. doi: 10.1093/bib/bbw067.

PMID:
27473066
11.

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. 2016 Mar 29;7:39. doi: 10.3389/fgene.2016.00039. eCollection 2016.

12.

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 Ö, Tiffin N.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004395. doi: 10.1371/journal.pcbi.1004395. eCollection 2016 Feb.

13.

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 Ö, Tiffin N, Ulenga N; H3ABioNet Consortium.

Genome Res. 2016 Feb;26(2):271-7. doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.

14.

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. 2016 Feb 15;32(4):549-56. doi: 10.1093/bioinformatics/btv619. Epub 2015 Oct 27.

15.

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

Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.

Bioinformatics. 2016 Feb 1;32(3):477-9. doi: 10.1093/bioinformatics/btv590. Epub 2015 Oct 17.

16.

A quick guide for building a successful bioinformatics community.

Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N.

PLoS Comput Biol. 2015 Feb 5;11(2):e1003972. doi: 10.1371/journal.pcbi.1003972. eCollection 2015 Feb.

17.

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

Mazandu GK, Mulder NJ.

PLoS One. 2014 Dec 4;9(12):e113859. doi: 10.1371/journal.pone.0113859. eCollection 2014.

18.

Using biological networks to improve our understanding of infectious diseases.

Mulder NJ, Akinola RO, Mazandu GK, Rapanoel H.

Comput Struct Biotechnol J. 2014 Aug 27;11(18):1-10. doi: 10.1016/j.csbj.2014.08.006. eCollection 2014 Aug. Review.

19.

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

Mazandu GK, Mulder NJ.

Front Genet. 2014 Aug 6;5:264. doi: 10.3389/fgene.2014.00264. eCollection 2014.

20.

Bioinformatics education--perspectives and challenges out of Africa.

Tastan Bishop Ö, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton HG; H3ABioNet Consortium; H3Africa Consortium.

Brief Bioinform. 2015 Mar;16(2):355-64. doi: 10.1093/bib/bbu022. Epub 2014 Jul 2.

21.

A web-based protein interaction network visualizer.

Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ.

BMC Bioinformatics. 2014 May 6;15:129. doi: 10.1186/1471-2105-15-129.

22.

Information content-based gene ontology semantic similarity approaches: toward a unified framework theory.

Mazandu GK, Mulder NJ.

Biomed Res Int. 2013;2013:292063. doi: 10.1155/2013/292063. Epub 2013 Sep 2.

23.

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

Mazandu GK, Mulder NJ.

BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

24.

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. 2013 Sep 16;8(9):e73971. doi: 10.1371/journal.pone.0073971. eCollection 2013.

25.

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

Chimusa ER, Zaitlen N, Daya M, Möller M, van Helden PD, Mulder NJ, Price AL, Hoal EG.

Hum Mol Genet. 2014 Feb 1;23(3):796-809. doi: 10.1093/hmg/ddt462. Epub 2013 Sep 20.

26.

Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host.

Rapanoel HA, Mazandu GK, Mulder NJ.

PLoS One. 2013 Jul 2;8(7):e67472. doi: 10.1371/journal.pone.0067472. Print 2013.

27.

Co-infection with Mycobacterium tuberculosis and human immunodeficiency virus: an overview and motivation for systems approaches.

Deffur A, Mulder NJ, Wilkinson RJ.

Pathog Dis. 2013 Nov;69(2):101-13. doi: 10.1111/2049-632X.12060. Epub 2013 Jul 17. Review.

PMID:
23821533
28.

Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins.

Mazandu GK, Mulder NJ.

Int J Mol Sci. 2012;13(6):7283-302. doi: 10.3390/ijms13067283. Epub 2012 Jun 13.

29.

A topology-based metric for measuring term similarity in the gene ontology.

Mazandu GK, Mulder NJ.

Adv Bioinformatics. 2012;2012:975783. doi: 10.1155/2012/975783. Epub 2012 May 15.

30.

Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification.

Mazandu GK, Mulder NJ.

Adv Bioinformatics. 2011;2011:801478. doi: 10.1155/2011/801478. Epub 2011 Nov 29.

31.

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

Mazandu GK, Mulder NJ.

Infect Genet Evol. 2012 Jul;12(5):922-32. doi: 10.1016/j.meegid.2011.10.027. Epub 2011 Nov 7.

PMID:
22085822
32.

Scoring protein relationships in functional interaction networks predicted from sequence data.

Mazandu GK, Mulder NJ.

PLoS One. 2011 Apr 19;6(4):e18607. doi: 10.1371/journal.pone.0018607.

33.

Contribution of microarray data to the advancement of knowledge on the Mycobacterium tuberculosis interactome: use of the random partial least squares approach.

Mazandu GK, Opap K, Mulder NJ.

Infect Genet Evol. 2011 Jun;11(4):725-33. doi: 10.1016/j.meegid.2011.04.012. Epub 2011 Apr 14.

PMID:
21514402
34.

Investigating the effect of paralogs on microarray gene-set analysis.

Faure AJ, Seoighe C, Mulder NJ.

BMC Bioinformatics. 2011 Jan 24;12:29. doi: 10.1186/1471-2105-12-29.

35.

Contribution of microarray data to the advancement of knowledge on the Mycobacterium tuberculosis interactome: use of the random partial least squares approach.

Mazandu GK, Opap K, Mulder NJ.

Infect Genet Evol. 2011 Jan;11(1):181-9. doi: 10.1016/j.meegid.2010.09.003. Epub 2010 Sep 17.

PMID:
20850566
36.

Protein domain architectures.

Mulder NJ.

Methods Mol Biol. 2010;609:83-95. doi: 10.1007/978-1-60327-241-4_5.

PMID:
20221914
37.

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. 2008 Sep;11(8):653-60. Review.

PMID:
18795884
38.

The InterPro database and tools for protein domain analysis.

Mulder NJ, Apweiler R.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.7. doi: 10.1002/0471250953.bi0207s21.

PMID:
18428686
39.

In silico characterization of proteins: UniProt, InterPro and Integr8.

Mulder NJ, Kersey P, Pruess M, Apweiler R.

Mol Biotechnol. 2008 Feb;38(2):165-77. doi: 10.1007/s12033-007-9003-x. Epub 2007 Oct 4. Review.

PMID:
18219596
40.

New developments in the InterPro database.

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

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

41.

InterPro, progress and status in 2005.

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

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D201-5.

42.

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 CJ, Vaughan R, Zdobnov EM.

Nucleic Acids Res. 2003 Jan 1;31(1):315-8.

43.

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, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ; InterPro Consortium.

Brief Bioinform. 2002 Sep;3(3):225-35.

PMID:
12230031
44.

Tools and resources for identifying protein families, domains and motifs.

Mulder NJ, Apweiler R.

Genome Biol. 2002;3(1):REVIEWS2001. Epub 2001 Dec 19. Review.

45.

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 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; InterPro Consortium.

Bioinformatics. 2000 Dec;16(12):1145-50.

PMID:
11159333
46.

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

Mulder NJ, Zappe H, Steyn LM.

Tuber Lung Dis. 1999;79(5):299-308.

PMID:
10707258
47.

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. 2001 Jan 1;29(1):37-40.

48.

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