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= Donaldson Research =
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== Research Interests ==
== Research Interests ==

Revision as of 15:29, 27 November 2012

Research Interests

Our primary interests include protein interaction data consolidation, text mining and data mining especially with respect to diseases.

Our recent work on a consolidated protein interaction database can be found at http://irefindex.org/.

Email: ian.oslo@gmail.com


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iRefIndex, iRefWeb, iRefScape, iRefR

iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.

iRefIndex is available via a number of interfaces: in MITAB tab-delimited text (iRefIndex), web-site (iRefWeb), Cytoscape plugin (iRefScape) and an R package (iRefR).

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Magrathea is prototype software demonstrating how animations of molecular pathways can be driven automatically using local context of the participant molecules.


The Biolibrarian Proposal

The Biolibrarian proposal proposes the creation of new positions at university libraries around the world. These people would act as local biocurators that help local university researchers submit data to relevant biological databases.

Vitruvian man.jpg

DiG: Disease Groups

The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome.

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Bioscape is our in-house text-mining system used to locate gene and protein mentions in PubMed abstracts.

Group Members

  • [Ian Donaldson]
  • [Paul Boddie]

Past Group Members

  • Katerina Michalickova
  • Hanna Nemchenko
  • Sabry Razick: Now in Trondheim at NTNU.
  • Antonio Mora

Local Seminar Series

The Computational Life Science seminars

Links to Past Courses

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Bioinformatics for molecular biology

A new, two-week, intensive bioinformatics course that covers various aspects of bioinformatics analyses for molecular biology. Statistics, multiple hypothesis testing, microarray analysis, sequence alignments, working with protein structures, protein interaction networks and more. See the course page for schedule information along with all material used in the course. The course is composed of lectures and practical tutorials.

Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the MBV3070 course. The slides for these lectures are available here at Perl lectures for MBV3070.


ian.oslo at gmail.com