Ian Donaldson

Ian Donaldson

Ph.D.

About

43
Publications
4,794
Reads
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6,632
Citations
Introduction
I am an independent researcher living in Oslo. I am looking for a new position while developing a bioinformatics resource and consulting company (http://donadsonresearch.com). I continue to maintain the iRefIndex data resource of protein-protein interactions (http://irefindex.org) that we developed at the University of Oslo.
Additional affiliations
January 2009 - December 2011
University of Oslo
Position
  • Course coordinator and lecturer
Description
  • http://irefindex.org/wiki/index.php?title=Bioinformatics_course
November 2005 - April 2013
University of Oslo
Position
  • Group Leader, Bioinformatics
Description
  • Interests included protein interaction data consolidation and data mining especially with respect to diseases. See http://irefindex.org/wiki/index.php?title=Donaldson_Research for more information.
September 2002 - May 2005
Samuel Lunenfeld Research Institute
Position
  • Manager Bioiformatics Software Development and Researcher
Description
  • http://web.archive.org/web/20050515075109/http://www.blueprint.org/
Education
September 1999 - December 2000
Samuel Lunenfeld Research Institute
Field of study
  • Bioinformatics
September 1992 - June 1999
University of Toronto
Field of study
  • Department of Molecular and Medical Genetics

Publications

Publications (43)
Chapter
iRefWeb is a resource that provides web interface to a large collection of protein–protein interactions aggregated from major primary databases. The underlying data-consolidation process, called iRefIndex, implements a rigorous methodology of identifying redundant protein sequences and integrating disparate data records that reference the same pept...
Article
iRefWeb is a bioinformatics resource that offers access to a large collection of data on protein-protein interactions in over a thousand organisms. This collection is consolidated from 14 major public databases that curate the scientific literature. The collection is enhanced with a range of versatile data filters and search options that categorize...
Article
Full-text available
Background Multigenic diseases are often associated with protein complexes or interactions involved in the same pathway. We wanted to estimate to what extent this is true given a consolidated protein interaction data set. The study stresses data integration and data representation issues. Results We constructed 497 multigenic disease groups from O...
Data
Significance of overlaps between disease groups and binary data was calculated as described in the text. Number of interaction edges for each disease group is listed. Only those disease group overlaps with raw p-values less than 0.0004 are considered statistically significant.
Data
Mapping of OMIM titles to disease groups and Entrez Gene identifiers.
Data
The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 3 and explore disease groups and their overlaps with n-ary data in iRefIndex.
Data
Overlaps between disease groups and regenerated complex data showing best overlaps and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Example regenerated complexes have regular names that can be used to retrieve the binary interactions that make up the regenerated complex. For example: in the name “MI...
Data
The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 1 and explore disease groups and their overlaps.
Data
Overlaps between disease groups and n-ary records showing best overlaps (icrigid) and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Additional information on n-ary records with the best overlap with a disease group can be found at http://wodaklab.org/iRefWeb/interaction/show/xxx where xxx is the icri...
Data
Summary of disease groups in terms of both genes and proteins.
Article
Full-text available
Background Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different source databases, data integration strategies, representation of proteins and complexes, and data reliability assumptions. Here we ex...
Data
Full-text available
Supplementary Tables 1–6.
Data
S2_R_Code_for_paper.txt. R script showing code to generate data and figures for this paper.
Data
Full-text available
This is a plain text file that contains R code to reproduce all R analyses in the paper. See http://www.r-project.org/.
Article
Full-text available
The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment. The iRefR package includes tools for selecting specific subsets of interest from the iRefIndex by criteria such as organism, source database, experimental method...
Article
Full-text available
The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were qu...
Article
The microtubule (MT) cytoskeleton is essential for a variety of cellular processes. MTs are finely regulated by distinct classes of MT-associated proteins (MAPs), which themselves bind to and are regulated by a large number of additional proteins. We have carried out proteome analyses of tubulin-rich and tubulin-depleted MAPs and their interacting...
Article
To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood. A plethora of resources now exist to capture molecular interaction data from the many laboratories generating…
Data
Bioinformatic analysis of genes upregulated in tumoricidal macrophages
Data
Full-text available
Supplementary Figures S1-S9 and Supplementary Tables S1-S2
Data
Genes that are downregulated in tumoricidal macrophages
Article
Full-text available
The immune system can both promote and suppress cancer. Chronic inflammation and proinflammatory cytokines such as interleukin (IL)-1 and IL-6 are considered to be tumour promoting. In contrast, the exact nature of protective antitumour immunity remains obscure. Here, we quantify locally secreted cytokines during primary immune responses against my...
Article
Full-text available
We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number o...
Article
Full-text available
Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact o...
Article
Full-text available
Interaction data for a given protein may be spread across multiple databases. We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping. We present a method to generate a key for a protein interaction record...
Article
Base excision repair (BER) is a major mode of repair of DNA base damage. BER is required for maintenance of genetic stability, which is important in the prevention of cancer. However, direct genetic associations between BER deficiency and human cancer have been difficult to firmly establish, and the first-generation mouse models deficient in indivi...
Article
Full-text available
The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researc...
Article
Full-text available
The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the fo...
Article
Full-text available
The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gen...
Article
Full-text available
The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed...
Article
Software to automate the process of extracting molecular interactions from three-dimensional (3D) structures has been developed that records these as Biomolecular Interaction Network Database (BIND) pairwise interaction records. Full annotation of BIND records is provided through a database processing tool called MMDBind, including detailed atom-at...
Article
Text categorization tools make errors. However, if a justification is provided to explain why a document is assigned to a class, a user can sometimes verify the categorization without reading the entire document. In our work, the text categorization system processes abstracts from biomedical literature and distinguishes between those that report pr...
Article
Full-text available
Atomic absorption spectroscopy demonstrated that highly purified RNA polymerase II from the yeast Saccharomyces cerevisiae binds seven zinc ions. This number agrees with the number of potential zinc-binding sites among the 12 different subunits of the enzyme and with our observation that the ninth largest subunit alone is able to bind two zinc ions...
Article
Proteomics represents a collection of experimental approaches that may be used to investigate biological systems. Such approaches commonly produce vast amounts of data that relate to physical interactions between biomolecules. One challenge in extracting useful information from these data is determining how they relate to current knowledge. The goa...

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