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About

I specialize in bioinformatics research related to the construction and use of protein interaction maps. I have over 17 years of experience building and using bioinformatics applications and leading both small and large development teams.

The last release of the iRefIndex database of consolidated protein interactions is freely available at irefindex.org.

Ian Donaldson
ian@donaldsonresearch.com

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Past experience

Adaptimmune

Presently, I am working at Adaptimmune as a bioinformatician. This is a UK biotech company working on a novel and promising form of T-cell therapy to treat cancer.

Barts and the London Genome Centre

I moved to London in 2015 and was very grateful to get the chance to get some hands-on experience with next-generation sequence data while working with this great group of people. I worked on a pipeline for processing and analyzing single-cell RNASeq data as well as a number of other data types from DNA sequencing, bisulphite sequencing, and short-read sequencing of miRNAs. Tools used on a day-to-day basis included Bash, Sun Grid Engine and R. Some code can be found here.

University of Oslo

During 2005 to 2013, I ran my own research group at the University of Oslo. This work focused mainly on integration of protein interaction data from multiple primary databases and towards the end, we used these data to investigate their use in identifying drug-targets and genes involved in multi-locus diseases.

The highlight of this work was a series of papers on the iRefIndex database and the production of a series of tools that we used to carry out and share our work. These included an R statistics package and a Cytoscape plugin for visualization of protein interaction data.

Most importantly, this work allowed us to closely examine the use of curation and data exchange standards across multiple databases and quantified just how important these standards are.

Blueprint Initiative

Between 2002 and 2005 I worked at the Samuel Lunenfeld Research Institute as part of the Blueprint Initiative. This project involved over 100 people that worked to build the Biomolecular Interaction Network Database. Here, I continued to work on project management as well as designing new modules for an in-house bioinformatics platform (called SeqHound) that supported the BIND database. After this initiative ended, both database systems were bought and are now operated by Thomson as the BOND database.

MDS Proteomics

I first cut my teeth on project management at MDS Proteomics under the kind tutelage of an IBM consultant on the job while I planned and managed a group of eight developers that worked on an in-house bioinformatics platform.

MDSP grew at an explosive rate but unfortunately imploded before going public. However, we did manage to push out one of the first protein interactomes for yeast. My small contribution to this work was to estimate the interactions that were already known in the literature using a text-mining system I had written during my post-doctoral work (PreBIND).

Postdoctoral work

My post-doctoral work was a departure from my Ph.D. in molecular biology and was largely motivated as a means to escape the cold-room.

PreBIND was my first program. Written in C (including the web-page api) and making use of the NCBI toolkit, this program collected co-occurrences of protein/gene mentions in pubmed abstracts and assessed the likelihood that they contained interaction data using a support vector machine. The study was one of the first to quantify the time savings of computer-assisted curation of biomedical literature.

Ph.D.

This thesis now seems buried in the murky past but involved countless hours in a cold-room, a myriad tooth-picks and way too many agar plates. Mostly forgettable but taught me the importance of never giving up and asking a good question (not necessarily in that order of importance). Writing my thesis raised the question, “Why aren’t all these genetic/physical interactions written down somewhere in a structured-data format that could be easily retreived…?”.

Publications

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Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ.
Navigating the global protein-protein interaction landscape using iRefWeb.
Methods Mol Biol. 2014;1091:315-31. View article.

Antonio Mora, Katerina Michalickova, Ian M. Donaldson.
*A Survey of Protein Interaction Data and Multigenic Inherited Disorders.
BMC Bioinformatics. 2013 11;14:47. View article.

Antonio Mora and Ian M. Donaldson*
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction.
BMC Bioinformatics. 2012 Nov 12;13:294. View article.

Antonio Mora and Ian M. Donaldson.
*iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database.
BMC Bioinformatics. 2011 12:455. View article.

Razick S, Mora A, Michalickova K, Boddie P, Donaldson IM.
*iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.
BMC Bioinformatics. 2011 Oct 5;12(1):388. View article.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O’Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
*PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Nature Methods. 2011 8(7):528-9. View article.

Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson* and Shoshana J. Wodak*
Interaction databases on the same page.
Nature Biotechnology. 2011. 29(5) :391-3. View article.

Ole Audun Werner Haabeth, Kristina Berg Lorvik, Clara Hammarström, Ian M. Donaldson, Guttorm Haraldsen, Bjarne Bogen, and Alexandre Corthay*
Inflammation driven by tumor-specific Th1 cells protects against B-cell cancer Nature Communications. 2011. 2 :240. View article.

Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ.
Literature curation of protein interactions: measuring agreement across major public databases.
Database (Oxford). 2010 Dec 22;2010:baq026. View article.

Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ.
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford). 2010 Oct 12;2010:baq023. View article.

Ian M. Donaldson.
*Protein Interaction Data Resources.
Ralph A. Bradshaw and Edward A. Dennis, editors: Handbook of Cell Signaling 2nd edition, Oxford:Academic Press,2009, pp. 1375-1386.

Kozielski F, Riaz T, Debonis S, Koehler CJ, Kroening M, Panse I, Strozynski M, Donaldson IM, Thiede B.
*Proteome analysis of microtubule-associated proteins and their interacting partners from mammalian brain.
Amino Acids. 2011. 41(2):363-85. View article.

Katarzyna D. Arczewska, Katerina Michalickova, Ian Donaldson, and Hilde Nilsen.
*The Contribution of DNA Base Damage to Human Cancer Is Modulated by the Base Excision Repair Interaction Network. Critical Reviews in Oncogenesis. 2008. 14(4):217-273. View article.

Razick S, Magklaras G, Donaldson IM*
iRefIndex: A consolidated protein interaction database with provenance.
BMC Bioinformatics. 2008. 9(1):405. View article.

Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D’Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, Hogue CW.*
The Biomolecular Interaction Network Database and related tools 2005 update.
Nucleic Acids Res. 2005 Jan 1; 33(Database issue): D418-24. View article.

Donaldson I, Martin J, de Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW.
*PreBIND and Textomy–mining the biomedical literature for protein-protein interactions using a support vector machine.
BMC Bioinformatics. 2003 Mar 27;4(1):11. View article.

Salama J.J., Donaldson I, Hogue C.W.V.*
Automatic Annotation of BIND Molecular Interactions from Three-Dimensional Structures. Biopolymers (Nucleic Acid Sciences). 2002. 61: 111-120. View abstract.

Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sørensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M.
*Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
Nature. 2002 Jan 10;415(6868):180-3. View article.

Berry de Bruijn, Joel Martin, Cheryl Wolting and Ian Donaldson
*Extracting sentences to justify categorization.
Proceedings of the American Society for Information Science and Technology Annual Meeting, ASIST 2001, pp 450-457. View abstract.

Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW.*
BIND—The Biomolecular Interaction Network Database.
Nucleic Acids Res. 2001 Jan 1;29(1):242-5. View article.

Donaldson, I.M. and J.D. Friesen.*
Zinc stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit.
J Biol Chem. 2000 May 5;275(18):13780-8. View article.

Shared Notes

Shared Projects

Editing: see the README for the project [iandonaldson.github.io] (https://github.com/iandonaldson/iandonaldson.github.io)