Publications

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* = corresponding author(s)

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.