Richard Norris

Richard Norris
University of Sussex · Brighton and Sussex Medical School

PhD Bioinformatics

About

6
Publications
5,815
Reads
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78
Citations
Introduction
PhD in Molecular Biology & Bioinformatics from the University of Barcelona, developed computational methods to elucidate gene-regulatory networks in pancreatic neuroendocrine tumours. Now working on Therapeutic targeting of refractory relapsed diffuse large B-cell lymphoma through systems biology at Brighton and Sussex Medical School with funding from a UKRI Future Leaders Fellowship.
Additional affiliations
September 2012 - September 2014
Brunel University London
Position
  • Master's Student
May 2005 - December 2007
Wellcome Sanger Institute
Position
  • Research Assistant
Education
April 2017 - October 2021
University of Barcelona
Field of study
  • Biomedicine
September 2012 - September 2014
Brunel University London
Field of study
  • Molecular Medicine
September 2001 - May 2004
University of Manchester Institute of Science and Technology
Field of study
  • Biochemistry

Publications

Publications (6)
Article
Full-text available
The early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells. Here we show that exposure to proinflammatory cytokines reveals a marked plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stim...
Preprint
Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells. We show here that exposure to pro-inflammatory cytokines unmasks a marked plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulu...

Questions

Questions (5)
Question
So far I've tried a couple of different approaches (EdgeR and DiffReps). I've been thinking about trying MAnorm - the original version doesn't allow for replicates but it seems like the latest version does. EdgeR seemed to work quite well but I think I need to tweak the DiffReps parameters a bit as the results using the defaults didn't look right.
But I would welcome any advice as to which tool, or combination of tools gives the best results in terms of minimising biases and identifying changes with real biological significance.
Thanks
Question
I don't mean cell types, I mean individual cells. I've been working on roughly 1000 cells per islet, is this way off or about right? Or does it vary?
Question
I've been performing ChIP-seq experiments using the Abcam antibody for H3K27 acetylation. I use a 1% SDS buffer to sonicate and then dilute the sample down for the IP. I have used different SDS concentrations in the IP but so far 0.4% seems to give the best results (large enough library concentration and strong enrichment), however I've read that most people dilute their samples down to <0.3% SDS or even <0.1% and that SDS can interfere with the action of the antibody.
So is it a problem to use 0.4% SDS in the IP if it seems to be working, or could it be having a negative effect on the assay whilst still giving good results in terms of enrichment?
Thanks!
Question
I've found what looks like a heterozygous mutation in my DNA sequencing. It's more convincing in some reads than others but it definitely looks like the mutation is there. However it only shows up in the forward sequence and the reverse has just the wild type allele. I repeated the sequencing and got the same result. I SNP checked the primers and checked they're unique in the genome - all fine. There is a pseudogene related to the gene I'm investigating but it doesn't seem to have the same sequence in the region that I've sequenced.
I'd be grateful for any suggestions. Thanks.

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Projects

Project (1)
Project
Gene regulatory mechanisms in pancreatic neuroendocrine tumours