Ian Donaldson's Homepage

I work as an experimental officer in the Bioinformatics Core facility of the Faculty of Life Sciences - University of Manchester, which I joined in October 2006. My current role is to provide bioinformatics support for the faculty, including ChIP-seq, RNA-seq and resequencing analysis. Historically most of my projects came from a SOLiD4 sequencer, now replaced by an Illumina HiSeq 2500. I previously worked with the group of Prof. Andrew Sharrocks providing bioinformatics support (including ChIP-chip, ChIP-seq and other general genomic analyses).

Previous to working in Manchester, I completed a M.Res. in Bioinformatics at the University of Leeds. I then joined the group of Prof. Berthold Gottgens at the Cambridge Institute for Medical Research (CIMR), where I developed methods to identify conserved transcriptional regulatory elements in mammlian genomes.

My research interests include:

  • Analysis of ChIP-chip and ChIP-seq datasets to discover novel transcription factor binding targets and modes of action.
  • Understanding the genomic regulatory code, which deterimines how gene expression is governed, particularly by conserved, non-coding sequences in mammalian genomes.
  • Methods for locating functional transcription factor binding sites and regulatory elements.


Quick Links
[Bioinformatics Tools] [Publications] [Contact Information]


Bioinformatics Tools

I have developed a number of databases and tools that are publicly available.

CoMoDis: Extracts regions of sequence surrounding conserved transcription factor binding sites (TFBSs) of the users choice (seed motifs) within a given distance of a set of coregulated genes. The output can be used for novel motif discovery and the identification of novel regulatory elements.

TFBScluster: Identifies clusters of transcription factor binding sites throughout the human or mouse genomes that are conserved in multiple species.

During my time a the University of Cambridge I developed the HSCL website for the Gottgens group. I adapted a number of existing programs to work via CGI interfaces as well as developing new tools (including CoMoDis and TFBScluster).

RE1db: The original version of this database sought to catalogue the location of RE1 motifs in human, mouse and pufferfish genomes that match a specific IUPAC consensus sequence. Genes are identified that lie close to these motifs. A new and updated site by the Leeds group RE1db MkII utilises a weight matrix (PSSM) to identify RE1 motifs.


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Publications

Amin S, Donaldson IJ, Zannino DA, Hensman J, Rattray M, Losa M, Spitz F, Ladam F, Sagerstr├Âm C, Bobola N. "Hoxa2 selectively enhances meis binding to change a branchial arch ground state". Dev Cell. 2015 Feb 9;32(3):265-77. PubMed PMID: 25640223.

Hewitt SK, Donaldson IJ, Lovell SC, Delneri D. "Sequencing and Characterisation of Rearrangements in Three S. pastorianus Strains Reveals the Presence of Chimeric Genes and Gives Evidence of Breakpoint Reuse". PLoS One. 2014 Mar 18;9(3):e92203. doi: 10.1371/journal.pone.0092203. eCollection 2014. PubMed PMID: 24643015. PubMed Central PMCID: PMC3958482.

Engelmoer DJ, Donaldson I, Rozen DE. "Conservative Sex and the Benefits of Transformation in Streptococcus pneumoniae". PLoS Pathog. 2013 Nov;9(11):e1003758. PubMed PMID: 24244172.

Donaldson IJ, Amin S, Hensman JJ, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward CM, Bobola N. "Genome-wide occupancy links Hoxa2 to Wnt-╬▓-catenin signaling in mouse embryonic development". Nucleic Acids Res. 2012 May;40(9):3990-4001. PubMed PMID: 22223247.

Ji Z, Donaldson IJ, Liu J, Hayes A, Zeef LA, Sharrocks AD. "The Forkhead Transcription Factor FOXK2 Promotes AP-1-Mediated Transcriptional Regulation". Mol Cell Biol. 2012 Jan;32(2):385-98. PubMed PMID: 22083952. Joint first author.

Boros J, O'Donnell A, Donaldson IJ, Kasza A, Zeef L, Sharrocks AD. "Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members". Nucleic Acids Res. 2009 Dec;37(22):7368-80. PubMed PMID: 19789270.

Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. "Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery". Genome Res. 2009 Nov;19(11):1963-73. PubMed PMID: 19687146. Joint first author.

Wood AD, Chen E, Donaldson IJ, Hattangadi S, Burke KA, Dawson MA, Miranda-Saavedra D, Lodish HF, Green AR, Gottgens B. "Id1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signalling". Blood. 2009 Aug 27;114(9):1820-30. PubMed PMID: 19571317.

Wilson NK, Miranda-Saavedra D, Kinston S, Bonadies N, Foster SD, Calero-Nieto F, Dawson MA, Donaldson IJ, Dumon S, Frampton J, Janky R, Sun XH, Teichmann SA, Bannister AJ, Gottgens B. "The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development". Blood. 2009 May 28;113(22):5456-65. PubMed PMID: 19346495.

Landry JR, Bonadies N, Kinston S, Knezevic K, Wilson NK, Oram SH, Janes M,Piltz S, Hammett M, Carter J, Hamilton T, Donaldson IJ, Lacaud G, Frampton J, Follows G, Kouskoff V, Gottgens B. "Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors". Blood. 2009 Jun 4;113(23):5783-92. PubMed PMID: 19171877.

Smith AM, Sanchez MJ, Follows GA, Kinston S, Donaldson IJ, Green AR, Gottgens B. "A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity". Genome Res. 2008 Sep;18(9):1422-32. PubMed PMID: 18687876

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; The Open Regulatory Annotation Consortium. "ORegAnno: an open-access community-driven resource for regulatory annotation". Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. PMID: 18006570

Soneji S, Huang S, Loose M, Donaldson IJ, Patient R, Gottgens B, Enver T, May G. "Inference, validation and dynamic modelling of transcription networks in multipotent hematopoietic cells". Ann N Y Acad Sci. 2007 Jun;1106:30-40. PMID: 17442775

Pimanda JE, Donaldson IJ, de Bruijn MF, Kinston S, Knezevic K, Huckle L, Piltz S, Landry JR, Green AR, Tannahill D, Gottgens B. "The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity". Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):840-5. PMID: 17213321

Castro DS, Skowronska-Krawczyk D, Armant O, Donaldson IJ, Parras C, Hunt C, Critchley JA, Nguyen L, Gossler A, Gottgens B, Matter JM, Guillemot F. "Proneural bHLH and Brn Proteins Coregulate a Neurogenic Program through Cooperative Binding to a Conserved DNA Motif". Dev Cell. 2006 Dec;11(6):831-44. PMID: 17141158

Donaldson IJ, Gottgens B. "CoMoDis: composite motif discovery in mammalian genomes". Nucleic Acids Res. 2007;35(1):e1. PMID: 17130158

Chan WY, Follows GA, Lacaud G, Pimanda JE, Landry JR, Kinston S, Knezevic K, Piltz S, Donaldson IJ, Gambardella L, Sablitzky F, Green AR, Kouskoff V, Gottgens B. "The paralogous haemopoietic regulators Lyl1 and SCL are co-regulated by Ets and GATA factors yet Lyl1 cannot rescue the early SCL-/- phenotype". Blood. 2007 Mar 1;109(5):1908-16. PMID: 17053063

Follows GA, Dhami P, Gottgens B, Bruce AW, Campbell PJ, Dillon SC, Smith AM, Koch C, Donaldson IJ, Scott MA, Dunham I, Janes ME, Vetrie D, Green AR. "Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites". Genome Res. 2006 Oct;16(10):1310-9. PMID: 16963707

Johnson R, Gamblin RJ, Ooi L, Bruce AW, Donaldson IJ, Westhead DR, Wood IC, Jackson RM, Buckley NJ. "Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication". Nucleic Acids Res. 2006;34(14):3862-77. PMID: 16899447

Donaldson IJ, Gottgens B. "TFBScluster web server for the identification of mammalian composite regulatory elements". Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W524-8. PMID: 16845063

Donaldson IJ, Gottgens B. "Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence". Genome Biol. 2006;7(6):R52. PMID: 16808854

Pimanda JE, Chan WY, Donaldson IJ, Bowen M, Green AR, Gottgens B. "Endoglin expression in the endothelium is regulated by Fli-1, Erg, and Elf-1 acting on the promoter and a -8-kb enhancer". Blood. 2006 Jun 15;107(12):4737-45. PMID: 16484587

Wheeler E, Miller EN, Peacock CS, Donaldson IJ, Shaw MA, Jamieson SE, Blackwell JM, Cordell HJ. "Genome-wide scan for loci influencing quantitative immune response traits in the Belem family study: comparison of methods and summary of results". Ann Hum Genet. 2006 Jan;70(Pt 1):78-97. PMID: 16441259

Landry JR, Kinston S, Knezevic K, Donaldson IJ, Green AR, Gottgens B. "Fli1, Elf1, and Ets1 regulate the proximal promoter of the LMO2 gene in endothelial cells". Blood. 2005 Oct 15;106(8):2680-7. PMID: 15994290

Donaldson IJ, Chapman M, Gottgens B. "TFBScluster: a resource for the characterization of transcriptional regulatory networks". Bioinformatics. 2005 Jul 1;21(13):3058-9. PMID: 15855248

Lawson CA, Donaldson IJ, Bowman SJ, Shefta J, Morgan AW, Gough A, Isaacs JD, Griffiths B, Emery P, Pease CT, Boylston AW. "Analysis of the insertion/deletion related polymorphism within T cell antigen receptor beta variable genes in primary Sjogren's syndrome". Ann Rheum Dis. 2005 Mar;64(3):468-70. PMID: 15708895

Donaldson IJ, Chapman M, Kinston S, Landry JR, Knezevic K, Piltz S, Buckley N, Green AR, Gottgens B. "Genome-wide identification of cis-regulatory sequences controlling blood and endothelial development". Hum Mol Genet. 2005 Mar 1;14(5):595-601. PMID: 15649946

Bruce AW, Donaldson IJ, Wood IC, Yerbury SA, Sadowski MI, Chapman M, Gottgens B, Buckley NJ. "Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes". Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10458-63. PMID: 15240883. Joint first author.

Chapman MA, Donaldson IJ, Gilbert J, Grafham D, Rogers J, Green AR, Gottgens B. "Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci". Genome Res. 2004 Feb;14(2):313-8. PMID: 14718377

Pre-bioinformatics

Donaldson IJ, Shefta J, Hill AV, Boylston AW. "Malaria is not responsible for the selection of TCR beta-subunit variable gene haplotypes in The Gambia". Immunogenetics. 2002 Feb;53(10-11):894-9. PMID: 11862389

Donaldson IJ, Shefta J, Lawson CA, Bushnell JR, Morgan AW, Isaacs JD, Carpenter D, Shaw MA, Rooth I, Quinnell RJ, Zumla AM, Ollier WR, Chintu CZ, Muyinda GP, Hill AS, Boylston AW. "Unique TCR beta-subunit variable gene haplotypes in Africans". Immunogenetics. 2002 Feb;53(10-11):884-93. PMID: 11862388

Shaw MA, Donaldson IJ, Collins A, Peacock CS, Lins-Lainson Z, Shaw JJ, Ramos F, Silveira F, Blackwell JM. "Association and linkage of leprosy phenotypes with HLA class II and tumour necrosis factor genes". Genes Immun. 2001 Jun;2(4):196-204. PMID: 11477474


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Contact Information
Ian Donaldson, Ph.D.
Faculty of Life Sciences
University of Manchester
Michael Smith Building
Oxford Road, M13 9PT
Manchester, UK

Email: Ian dot Donaldson at manchester dot ac dot uk

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Last updated 9 December 2013