Passionate about chromatin and machine learning
Christopher Clarkson
PhD Student (2017-2020)
School of Biological Sciences
University of Essex
Wivenhoe Park
Colchester CO4 3SQ, UK
I am a PhD student in computational biology. My ambition is to apply my skills in data-science and machine learning to real-world problems. I have a range of projects under my belt (detailed below).
I have BSc in Biomedical Sciences from the National University of Ireland Galway, MSc in Bioinformatics from Imperial College London, and currently working towards PhD in Bioinformatics in Vlad Teif’s Lab in the University of Essex. The title of my PhD is “Changes of nucleosome positioning and 3D chromatin organization in cell transitions”.
Apart from science I like sports- including lacrosse, wall climbing and football. I also act as co-organiser of the “Pint of Science” scientific outreach festival
Click here for my detailed CV in PDF.
Publications:
- Clarkson C.T., Deeks E.A., Samarista R., Mamayusupova H., Zhurkin V.B., Teif V.B. (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Res 47, 11181-11196.
- Wiehle L., Thorn G.J., Raddatz G., Clarkson C.T., Rippe K., Lyko F., Breiling A., Teif V.B. (2019) DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Research 29, 750-761
- Pavlaki I., Docquier F., Chernukhin I., Kita G., Gretton S., Clarkson C.T., Teif V.B., Klenova E. (2018) Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells. Biochim Biophys Acta (BBA) – Gene Regulatory Mechanisms 1861, 718-730
- Teif V.B. and Clarkson C.T. (2019) Nucleosome Positioning. In Encyclopedia of Bioinformatics and Computational Biology (Ed.: S. Ranganathan, M. Gribskov, K. Nakai, and C. Schönbach), vol. 2, pp. 308–317 . Oxford: Academic Press. |Published version | Authors’ manuscript
- Whitton L., Cosgrove D., Clarkson C., Harold D., Kendall K., Richards A., Mantripragada K., Owen M.J., O’Donovan M.C., Walters J., Hartmann A., Konte B., Rujescu D.; WTCCC, Gill M., Corvin A., Rea S., Donohoe G., Morris D.W. (2016). Cognitive analysis of schizophrenia risk genes that function as epigenetic regulators of gene expression. Am J Med Genet B Neuropsychiatr Genet, 171, 1170-1179.
Software:
NRLcalc – Calculation of the nucleosome repeat length for many genomic regions
Paper to Audio – Text to speech conversion tailored specifically for academic papers