Main
Richard J. Acton
Professional Interests:
- Academic Software Development
- Reproducible Computational Analysis
- Ageing Biology
- Epigenetics
Employment
CECAD
Post-Doctoral Researcher & Bioinformatician (Schumacher Lab / Bioinformatics Core)
Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases: Cologne, North Rhine-Westphalia, DE
present - 2020
PI Prof. Dr. Björn Schumacher bjoern.schumacher@uni-koeln.de
interim facility manager (present - 2021-06) Prof. Dr. Andreas Beyer andreas.beyer@uni-koeln.de
facility manager (2021-06 - ) Prof. Dr. Alexander Dilthey Alexander.Dilthey@med.uni-duesseldorf.de
Education
MRC PhD Studentship
Epigenomics of Human Ageing
University of Southampton
2020 - 2016-09
Including examination of changes in tRNA gene methylation with Age and performing EWAS for Bone health outcomes.
Supervisor: Dr. Chris Bell c.bell@qmul.ac.uk
MSc - Bioinformatics and Systems biology (Distinction)
Project: Differential Expression of circRNAs in daf-2 and daf-2/16 mutant C. elegans Neurons.
Birkbeck University of London
2016-07 - 2015-09
Supervisor: Irilenia Nobeli i.nobeli@mail.cryst.bbk.ac.uk
MSci - Biochemistry and Genetics (1st Hons)
Undergraduate Degree
University of Nottingham
2015-07 - 2011-09
Programming & Bioinformatic Skills*
| R | ●●●●● |
| nextflow | ●●○○○ |
| Perl5 | ●●○○○ |
| Bash | ●●○○○ |
| Python | ●○○○○ |
| SQL | ●○○○○ |
| HTML/CSS/javascript | ●○○○○ |
| PHP | ●○○○○ |
| Linux Use | ●●●●○ |
Proficient wit git for source control. Automated unit testing and continuous integration for R packages.
Shiny app development for interactive data exploration and visualisation.
Experience with the R targets pipeline managements tool.
Use of HPC Clusters, Experience with SLURM, PBS/TORQUE schedulers & R HPC backends such as future.batchtools.
Familiar with the use of containerisation technologies such as docker and singularity for reproducible computational environments.
Research Projects During this period:
- 2015 CRISPR based KO and screens of B methylase in the N6-methyladensine RNA modification system in Arabidopsis. (Supervisor: Dr. Rupert Fray rupert.fray@nottingham.ac.uk)
- 2014 BBSRC REP Summer project (See Grants).
- 2013 Interactions of PilZ proteins of the Cyclic-dimeric-3’→5’-Guanosine Mono Phosphate (c-di-GMP) signalling system in Bdellovibrio bacteriovorus. (Supervisor: Prof. Liz Sockett liz.sockett@nottingham.ac.uk)
- 2012 Summer project Identifying possible chlamydial effector protein genes and expressing in Human cell lines (Supervisor: Dr. Alan Huett Alan.Huett@nottingham.ac.uk)
A-levels
Further education
The Sixth Form College Farnborough
2011-07 - 2009-09
| Subject | Grade |
|---|---|
| Biology (A2) | A |
| Chemistry (A2) | A |
| Physics (A2) | A |
| Maths (A2) | B |
| Economics (AS) | A |
| General Studies (A2) | B |
GCSEs
Secondary School
Frensham Heights School
2009-07 - 2005-09
| Subject | Grade |
|---|---|
| Double Science | (A*)A* |
| Maths | A* |
| ICT | A* |
| French | A* |
| Photography | A* |
| Design Tech(RM) | A* |
| Art and Design 3D | A* |
| Geography | A* |
| English | A |
| English Literature | B |
(Photography taken as an extra-curricular in 2007, French taken 1 year early in 2008)
Early life Education
Primary Schooling
UK, US, UK, CH
2005 - 1996
- 2003 - 2005 École Internationale de Genève (La Grande Boissière campus), (Geneva, Switzerland)
- 2000 - 2003 Cheddington Combined School (UK)
- 1999 – 2000 Osgood Elementary (Massachusetts, USA)
- 1997-1999 Cohasset Montessori (Massachusetts, USA)
- 1996-1997 Bagshot Montessori (UK)
‘Wet’ Lab Skills
Now Quite Rusty Molecular cloning (Multiple Techniques), DNA and RNA extraction and purification, PCR, Acrylamide and agarose gel electrophoresis, Basic chromatographic protein purification and hanging drop vapour diffusion crystallisation, Basic cell culture with transfection, staining and light microscopy.
Publications & Presentations
Publications
- FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction, in press Science Advances (2022)
- Spleen tyrosine kinase mediates innate and adaptive immune crosstalk in SARS-CoV-2 mRNA vaccinatio, in press EMBO Molecular Medicine (2022) 10.1101/2021.08.18.456709
- Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L, in press Cell Reports (pre-print 2021) 10.1101/2021.08.18.456709
- [First Author] The Genomic Loci of Specific Human tRNA Genes Exhibit Ageing-Related DNA Hypermethylation, Nature Communications (2021) 10.1038/s41467-021-22639-6
- Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci, Nature Communications (2018) 10.1038/s41467-017-01586-1 (journal-article)
- Cancer detection and tissue of origin determination with novel annotation and scoring of cell-free methylated DNA, AME Medical Journal (2017) 10.21037/amj.2017.08.02 (Comment)
Presentations
- (2019-01-16:17 - Advances at the interface between metabolism and epigenetics) Poster Presentation, Specific Isoacceptor and Isodecoder tRNA Genes Exhibit Increased DNA Methylation with Age.
- (2018-11-21 – Institute of Developmental Sciences Review) Oral Presentation, Ageing-Associated DNA Hypermethylation in tRNA genetic loci.
- (2018-01-31:02-02 - Healthy Ageing: From Molecules to Organisms) Lightning talk & Poster Presentation, Specific Isoacceptor and Isodecoder tRNA Genes Exhibit Increased DNA Methylation with Age.
- (2017-11-14:17 - Epigenomics of Common Disease) Poster Presentation – 1st Poster Prize, Specific Isoacceptor and Isodecoder tRNA Genes Exhibit Increased DNA Methylation with Age.
- (2017-11-08 - Institute of developmental sciences open day) Poster Presentation, Specific Isoacceptor and Isodecoder tRNA Genes Exhibit Increased DNA Methylation with Age.
Conferences, Meeting & Workshops
- 2019-08-20 R Package development with Hadley Wickham (Southampton)
- 2019-08-21 Boosting your productivity using Tidyverse with Hadley Wickham (Southampton)
- 2017-11-29 QMUL, London Epigenetic Club meeting
- 2017-06-05:07 Epigenetic Epidemiology Short Course (University of Bristol)
- 2017-03-08:10 Clinical Epigenetics Society (CLEPSO) meeting (Düsseldorf)
- 2017-03-03 London Epigenetics Club / London Chromatin Club joint meeting on Epigenetics and Metabolism
- 2016-11-25 Research Data management Workshop (Southampton)
- 2016-11-16 Galton institute conference (London)
- 2016-11-01:04 Epigenomics of Common Diseases (Cambridge)
Grants
BBSRC – Research Experience Placement grant
Project: Deletion, 2-hybrid vector creation and crystallography of the Bdellovibrio bacteriovorus Bd1483 gene.
Universities of Nottingham Birmingham
2014-08 - 2014-06
Supervisors: Professor Liz Sockett liz.sockett@nottingham.ac.uk, Dr. Andy Lovering a.lovering@bham.ac.uk
Footnotes
Scoring system* - A subjective assessment of my own skill level. 5 is ~ daily use of the language, extensive knowledge of its ecosystem as well as deep knowledge of its structure and experience of developing production apps in that language. 1 is occasional use with heavy reliance of reference material but with at least one real world task such as creating a website or pipline accomplished using that tool.
This resume was made with the R package pagedown.
Last updated on 2022-02-17.