Dr Sophie Shaw

Dr Sophie Shaw

Bioinformatician

Overview
Dr Sophie Shaw
Dr Sophie Shaw

Contact Details


Biography

Dr Shaw joined the CGEBM as a bioinformatician in May 2015 from the University of Exeter where she completed her PhD in Biological Sciences investigating the phenotypic impact of allele specific expression. Following her PhD, Dr Shaw undertook a post-doctoral position researching transcriptional responses during environmental inter-species interactions. She brings a background in ecological and environmental genomics (eDNA), with core expertise in RNA-seq and functional annotation, and whole genome sequencing and assembly, along with skills in fungal and plant molecular biology.

Her work for the CGEBM has covered a wide range of bioinformatics applications with analysis of data from both prokaryotic and eukaryotic species. Applications have included whole genome, single cell genome and  transcriptome assemblies, microbial community analysis using 16S rRNA sequencing and viral like particle sequencing, differential gene expression analysis, and ChIP sequencing analysis.

Dr Shaw has experience in the delivery of bioinformatics training modules in varied genomics analyses, including UNIX, short read genomics, assembly methods, transcriptomics, and shotgun whole genome and amplicon based metagenomics. Dr Shaw brings these skills to the training portfolio currently being delivered to the University of Aberdeen research community by CGEBM.


External Memberships and Affiliations

Dr. Shaw regularly contributes to the delivery of workshops covering the topics of genomics and bioinformatics internationally including:

Co-director of the Workshop on Genomics, Cesky Krumlov, Czech Republic, 2014-2020. 

Workshop on Microbiome and Transcriptome Analysis, Durban, South Africa, 2018.

ASM Microbe 2017-2019, Beginning Bioinformatics: An Introduction to the Command Line Workshop. New Orleans, USA, 2017. Atlanta, USA, 2018. San Francisco, USA, 2019.

ISCD Summer School 2017, Introduction to Sequence Analysis and Algorithms, Roscoff, France, 2017.

Workshop on Microbial Genomics, Harvard University, USA, 2016.

NERC Workshop on Metagenomics and Population Genomics, Totnes, UK, 2014.

Research

Research Areas

Specialisms

  • Bioinformatics
  • Genomics

Knowledge Exchange and Public Engagement

Dr Shaw regularly contributes to public engagement, providing and participating in various events throughout the year. This includes:

  • Recipient of the ISSF Wellcome Trust Public Engagement Fund. This is being used to develop an interactive two day workshop for secondary school pupils entitled "What's in my Pond?!". This will encompass DNA sequencing of the environmental DNA on campus using the Oxford Nanopore system. 
  • Cell Block Science - May 2019. The CGEBM team attended HMP Peterhead to provide a one-day interactive workshop for inmates on the topic of DNA and how DNA sequencing is used in everyday life. 
  • May Festival School's Programme - May 2017 & May 2019. Aimed at local primary schools, the CGEBM team presented Genes Unzipped! This interactive workshop aimed to teach children about DNA.
  • Doors Open Day - September 2018. This event sees hundreds of buildings open their doors for the public for free. The CGEBM team had fun activities on offer for all of the family including science puzzles, DNA putt-putt, "make-your-own" DNA bracelets, and real life samples to peer at under the microscope.  

Research Funding and Grants

  • Recipient of the ISSF Wellcome Trust Public Engagement Fund. 
Teaching

Teaching Responsibilities

Dr. Shaw currently contributes to the teaching of the following modules:

MB5021: Bioinformatics

MB5522: Advanced Bioinformatics and Genome Sequencing

ME40LB: Intercalated Medical Degree

MT5515: Basic Research Methods.

In addition, Dr. Shaw has supervised MSc students with bioinformatics-based final year research projects.

Publications

Publications 

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