Nicola J Mulder

Nicola J Mulder

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Nicola J Mulder

Nicola J Mulder

Publications by authors named "Nicola J Mulder"

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

Brief Bioinform 2018 11;19(6):1141-1152

Department of Integrative Biomedical Sciences and the Head of the Computational Biology Division, UCT.

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http://dx.doi.org/10.1093/bib/bbx052DOI Listing
November 2018

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

Bioinformatics 2017 Oct;33(19):2995-3002

Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa.

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http://dx.doi.org/10.1093/bioinformatics/btx369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870573PMC
October 2017

A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae.

Front Genet 2016 29;7:39. Epub 2016 Mar 29.

Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa.

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http://dx.doi.org/10.3389/fgene.2016.00039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809885PMC
April 2016

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

Bioinformatics 2016 Feb 17;32(3):477-9. Epub 2015 Oct 17.

Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and.

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http://dx.doi.org/10.1093/bioinformatics/btv590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006308PMC
February 2016

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

Bioinformatics 2016 Feb 27;32(4):549-56. Epub 2015 Oct 27.

Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, 7925, Observatory, South Africa and.

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http://dx.doi.org/10.1093/bioinformatics/btv619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939890PMC
February 2016

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.

PLoS Comput Biol 2016 Feb 4;12(2):e1004395. Epub 2016 Feb 4.

South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa.

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http://dx.doi.org/10.1371/journal.pcbi.1004395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742231PMC
February 2016

Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins.

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

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa; E-Mail:

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http://dx.doi.org/10.3390/ijms13067283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397526PMC
August 2015

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

PLoS One 2014 4;9(12):e113859. Epub 2014 Dec 4.

Computational Biology Group, Department of clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113859PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256219PMC
July 2015

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

Front Genet 2014 6;5:264. Epub 2014 Aug 6.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa.

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http://dx.doi.org/10.3389/fgene.2014.00264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123725PMC
August 2014

Using biological networks to improve our understanding of infectious diseases.

Comput Struct Biotechnol J 2014 Aug 27;11(18):1-10. Epub 2014 Aug 27.

Computational Biology Group, Department of Clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.csbj.2014.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212278PMC
August 2014

Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method.

PLoS One 2013 16;8(9):e73971. Epub 2013 Sep 16.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073971PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774743PMC
May 2014

A web-based protein interaction network visualizer.

BMC Bioinformatics 2014 May 6;15:129. Epub 2014 May 6.

Computational Biology Group, IDM, Faculty of Health Sciences, University of Cape Town, Anzio Road, Cape Town, South Africa.

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http://dx.doi.org/10.1186/1471-2105-15-129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029974PMC
May 2014

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

Biomed Res Int 2013 2;2013:292063. Epub 2013 Sep 2.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Medical School, Observatory, Cape Town 7925, South Africa.

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http://dx.doi.org/10.1155/2013/292063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775452PMC
April 2014

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

Hum Mol Genet 2014 Feb 20;23(3):796-809. Epub 2013 Sep 20.

Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1093/hmg/ddt462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888262PMC
February 2014

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

PLoS One 2013 2;8(7):e67472. Epub 2013 Jul 2.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067472PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699628PMC
January 2014

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

Pathog Dis 2013 Nov 17;69(2):101-13. Epub 2013 Jul 17.

Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1111/2049-632X.12060DOI Listing
November 2013

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

BMC Bioinformatics 2013 Sep 25;14:284. Epub 2013 Sep 25.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Observatory, Cape Town, 7925, South Africa.

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http://dx.doi.org/10.1186/1471-2105-14-284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849277PMC
September 2013

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

Adv Bioinformatics 2011 29;2011:801478. Epub 2011 Nov 29.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.

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http://www.hindawi.com/journals/abi/2011/801478/
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http://dx.doi.org/10.1155/2011/801478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235424PMC
August 2012

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

Adv Bioinformatics 2012 15;2012:975783. Epub 2012 May 15.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.

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http://dx.doi.org/10.1155/2012/975783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361142PMC
August 2012

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

Infect Genet Evol 2012 Jul 7;12(5):922-32. Epub 2011 Nov 7.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, 7925 Observatory, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.meegid.2011.10.027DOI Listing
July 2012

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

Infect Genet Evol 2011 Jun 14;11(4):725-33. Epub 2011 Apr 14.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, 7925 Observatory, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.meegid.2011.04.012DOI Listing
June 2011

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

PLoS One 2011 Apr 19;6(4):e18607. Epub 2011 Apr 19.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018607PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079720PMC
April 2011

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

Infect Genet Evol 2011 Jan 17;11(1):181-9. Epub 2010 Sep 17.

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, 7925, Observatory, Cape Town, South Africa.

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https://linkinghub.elsevier.com/retrieve/pii/S15671348100024
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http://dx.doi.org/10.1016/j.meegid.2010.09.003DOI Listing
January 2011

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

BMC Bioinformatics 2011 Jan 24;12:29. Epub 2011 Jan 24.

Computational Biology Group, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa.

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http://link.springer.com/content/pdf/10.1186%2F1471-2105-12-
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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037853PMC
January 2011

Protein domain architectures.

Authors:
Nicola J Mulder

Methods Mol Biol 2010 ;609:83-95

Faculty of Health Sciences, National Bioinformatics Network Node, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1007/978-1-60327-241-4_5DOI Listing
May 2010

The InterPro database and tools for protein domain analysis.

Curr Protoc Bioinformatics 2008 Mar;Chapter 2:Unit 2.7

The EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://doi.wiley.com/10.1002/0471250953.bi0207s21
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http://dx.doi.org/10.1002/0471250953.bi0207s21DOI Listing
March 2008

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

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

The EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC150457PMC
http://dx.doi.org/10.1186/gb-2001-3-1-reviews2001DOI Listing
May 2002