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| Russell S. Hamilton: |
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| Job Title: |
Senior Postdoctoral Research Associate |
| Specialty: |
Bioinformatics / Computational Biology |
| Contact Details: |
Ilan Davis Lab,
Department of Biochemistry,
University of Oxford,
South Parks Road, Oxford, OX1 3QU |
| Email: |
Russell.Hamilton -at- bioch.ox.ac.uk
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| Internet: |
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| Research Interests: |
- Defining and Searching for RNA Motifs - including RNA Localization Signals
- RNA Binding Proteins and Targets
- RNA Secondary Structure Motifs in Human Disease
- Peptide Nucleic Acids (PNA) to investigate in vivo RNA:protein interactions
- Analysis of tracked particles in live cell imaging (ParticleStats and TrackAlign)
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| Software: |
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RNA2DSearch
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[RNA2DSearch Site]
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RNA2DSearch is an open source bioinformatics pipeline for searching for short RNA secondary structures similar to user defined reference structures on a genomic scale.
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Hamilton, R.S. et al (2009) RNA, 15, 200-207. [DOI]
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TrackAlign
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[TrackAlign Site]
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TrackAlign is a suite of tools forthe comparison and evaluation of tracking algorithms. The aim of the project is to determine the most appropriate tracking algorithm and parameters to use for a particular data set
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RNA-Seq
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[RNA-Seq Site]
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Software for the analysis and interpretation of RNA-Seq data from IP pull down experiments. This also includes the generation of SVG images to show the read coverage for individal genes and transcripts.
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| Publications: |
2012
(in press) |
Ball, G., Parton, R.M., Hamilton, R.S. & Davis, I. (2012) A cell biologist's guide to high resolution imaging. Methods in Enzymology - Imaging and Spectroscopic Analysis of Living Cells: Optical and Spectroscopic Techniques
Hamilton, R.S., Ball, G., & Davis, I. (2012) A multidiciplinary approach to mRNA localization. Biophysical approaches to translational control of gene expression
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| 2011 |
Parton, R.M., Hamilton, R.S., Ball, G., Yang, L., Cullen, F., Lu, W., Ohkura, H. & Davis, I. (2011) A PAR-1 dependent orientation gradient of dynamic microtubules establishes cell polarity in the Drosophila oocyte. Journal of Cell Biology, 194, 121-135. [DOI] [Biosights Video]
Hamilton, R.S. & Davis, I. (2011) Identifying putative conserved RNA localization signals. Methods in Molecular Biology - RNA Detection and Visualization. Chapter 27, 447-466 [DOI] [Amazon]
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| 2010 |
Hamilton, R.S., Parton, R.M., Oliveira, R.A., Ball, G., Vendra, G., Nasmyth, K. & Davis, I. (2010) ParticleStats: Open source software for the analysis of intracellular particle motility. Nucl. Acids Res. Web Server Edition [DOI]
Oliveira, R.A., Hamilton, R.S., Pauli, A., Davis, I., Nasmyth, K. (2010) Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei. Nature Cell Biology, 12,185-192. [DOI]
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| 2009 |
Beckett, M.G., Allton, C.R., Davies, C.T.H., Davis, I., Flynn, J.M., Grant, E.J., Hamilton, R.S., Irving, A.C., Kenway, R.D., Ostrowski, R.H., Perry, J.T., Swedlow, J.R., & Trew, A.S. (2009) Building a scientific data grid with DiGS Phil. Trans. R. Soc. A, 367:1897, 2471-2481. [DOI]
Hamilton, R.S., Hartswood, E., Jones, C., Vendra, G., Van De Bor, V., Finnegan, D., & Davis, I. (2009) A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons RNA, 15, 200-207. [DOI]
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| 2008 |
Pickard, B.S., Knight, H.M., Hamilton, R.S., Soares, D.C., Walker, R., Boyd, J.K.F., Machell, J., Maclean, A., McGhee, K.A., Condie, A., Porteous, D.J., Clair, D., Davis, I., Blackwood, D.H.R. & Muir, W.J. (2008) A common variant in the 3'UTR of the GRIK4 glutamate receptor gene affects transcript abundance and protects against bipolar disorder. PNAS, 105, 14940-14945. [DOI] |
| 2007 |
Vendra, G., Hamilton, R.S. & Davis, I (2007) Dynactin suppresses the retrograde movement of apically localized mRNA in Drosophila blastoderm embryos. RNA, 13, 1-8. [DOI]
Hamilton, R.S. & Davis, I. (2007) RNA localization signals: deciphering the message with bioinformatics. Semin Cell Dev Biol. 18(2), 178-185. [DOI] |
| Theses |
Hamilton, R.S. (2006) DAROGAN: Enzyme Function Prediction from Multiple Sequence Alignments. PhD Thesis: University of Edinburgh
Hamilton, R.S. (2000) Dividing Up Large Protein Surfaces. MSc Thesis: University of Aberdeen
Hamilton, R.S. (1999) 3D Structural Studies Of Drug Binding To Dihydrofolate Reductase. BSc Project: University of Leeds
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| Contact: Russell.Hamilton @ bioch.ox.ac.uk |
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