ABOUT ME

I'm Rob, a postdoctoral researcher at the Weatherall Institute of Molecular Medicine in Oxford. My main research interest is regulatory sequences in animal genomes - regions of DNA that can control the activity of other genes. I am especially interested the way that cells fold their DNA, and how this can influence the effects of these regulatory sequences. There is growing evidence that this folding may be disregulated in some human diseases, and I think research in this area has the potential for opening new therapeutic avenues.

I'm also a keen programmer, especially in python. I've contributed to a number of open source projects, including doit and pybedtools. I'm currently writing a genome browser in python called EIYBrowse (Extend It Yourself Browser). I've found programming an invaluable skill during my research and I like to spread the knowledge around, so I contribute to and teach for Software Carpentry. I've written a series of Software Carpentry lessons on using python's doit for automating scientific analysis pipelines.

Here's some other stuff I've been enjoying recently:

Listening

Watching

Snapping

Reading

RESEARCH

  • 2017
  • Postdoctoral Scientist

    MRC Weatherall Institute of Molecular Medicine, Oxford (Nov 2016-Current)

  • 2016
  • Postdoctoral Researcher

    Berlin Institute for Medical Systems Biology, Berlin (Aug 2015-Nov 2016)

    • Working on chromatin folding and nuclear organization in Prof. Ana Pombo's laboratory
  • 2015
  • MRC Funded PhD Studentship

    MRC Clinical Sciences Centre, London (Oct 2011-Jul 2015)

    • Implemented and applied Genome Architecture Mapping (GAM) to study chromatin folding in mouse embryonic stem cells
    • Co-supervised by Prof. Ana Pombo (MDC) and Prof. Niall Dillon (CSC)
  • 2011
  • Research Assistant

    Department of Biochemistry, Cambridge University (Oct 2010-Aug 2011)

    • Studied C. crescentus polynucleotide phosphorylase in Prof. Ben Luisi’s group
    • Cloning, expression, protein affinity purification, enzymatic assays and crystallography
  • 2010
  • Cancer Research UK Summer Studentship

    CRUK London Research Institute, London (Holborn) (Jun 2010-Sep 2010)

    • Studied Polycomb group proteins and their interaction with the ncRNA HOTAIR with Dr. Gordon Peters
    • Chromatin Immunoprecipitation, qPCR, lentiviral shRNA knockdowns, qRT-PCR and western blotting
  • Research Assistant

    Department of Biochemistry, Cambridge University (Jan 2010-May 2010)

    • Development of the NMR analysis tool “DANGLE” with Dr. William Broadhurst
    • Programming, data analysis and statistical work to improve the accuracy of the DANGLE algorithm for predicting protein dihedral angles from chemical shift data
  • 2005
  • Work Experience Student

    Wellcome Trust Sanger Centre, Hinxton (Jun 2005-Jun 2005)

    • 1 week placement with an ENCODE project group
    • 1 week placement in the sequencing centre

PUBLICATIONS

 

Examining Topological Domain Influence on Enhancer Function.
Beagrie, R. and Pombo, A. (2016).
Developmental Cell, 39(5), pp.523-524.

BLOG POSTS

Enhancer Journal Club: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

By: Rob Beagrie

I've been thinking a lot about super-enhancers recently and I found this paper1 from Jennifer Mitchell's lab very interesting, especially as whether and how super-enhancers are distinct from "normal" enhancers has been generating a lot of discussion in the enhancer/gene-regulation literature recently2,3 Here's the abstract: Transcriptional …

Enhancer Journal Club: Enhancer runaway and the evolution of diploid gene expression

By: Rob Beagrie

I came across this very interesting theoretical paper about enhancer evolution a couple of months ago1 and thought it was worth a little discussion. The paper comes from Frederic Fyon and others at the CNRS in Montpellier. The original paper can be found at PLOS Genetics, and it's well …

Enhancer Journal Club: Functional annotation of native enhancers with a Cas9-histone demethylase fusion

By: Rob Beagrie

I really enjoyed Eric Mendenhall's 2013 paper in Nature Biotechnology1, where he was able to target LSD1 histone demethylase activity to endogenous enhancers using TALE fusion proteins (read my thoughts on that paper here). So I was very interested to see a similar approach published earlier this year in …

TWEETS

CONTACT

Follow me on twitter.

Email me at rob{at}beagrie.com

Rob Beagrie

MRC Clinical Sciences Centre

Hammersmith Hospital

London

W12 0NN