Bio

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Summary

Daniel is a research bioinformatician for Cardiff University School of Biosciences, working within the Genomics Research Hub. This role involves collaboration on short to midterm projects with particular focus on groups that do not have a bioinformatic background, working on medical, environmental, and fundamental biology across a range of platforms and techniques (genomics/transcriptomics/micro* /chipseq/ChromatinSeq/other!).

Alongside this research role Daniel teaches the Masters(Res) and Masters(Sci) bioinformatics course, and has previously taught externally on the Wellcome Advanced course (Chromatin Structure and Function) and worked with the Bio-Linux development team in development and training.

Research

Previously, Daniel was a Research Associate investigating chromatin dynamics in the model plant Arabidopsis thalania. Studying both natural and altered growth states, and the changes occurring during the cell cycle allow for developing knowledge on the nucleosomal and subnucleosomal landscape of DNA-binding particles. This was based in Cardiff University with Jim Murray and Nick Kent.

He completed his PhD at Cardiff University joint with CEH-Walingford/NBAF, focused on eukaryotic host to microbial community interactions in invertebrates, with an aim to elucidate on the contribution that associated microbiota has to the host species. This was assessed primarily with Next Generation DNA Sequencing techniques investigating metagenomics and microbiomics in earthworms.

Simultaneously Daniel aims to develop novel bioinformatic processes to overcome obstacles and create new methods to investigate communities, processes and interactions. A prime interest is the development of methods to integrate differing datatypes towards a greater understanding of the holistic biotic system, something which often gets overlooked when focusing solely on one technique.

Skills

Daniel is highly experienced in performing data-intensive bioinformatic analysis in the linux environment with expertise using and managing High Performance Compute clusters.

Daniel is experienced in python coding both in my current bespoke analysis and development of software ad-hoc packages. He has good experience with R, perl and bash scripting, and have some hackability with html/php and MySQL. Some publicly available work can be found at https://github.com/passdan.

Daniel was commissioned by the Environment Agency (UK) in 2014 to develop the open source software, PROMpT (Primary Rapid Overview of Metagenomic Taxonomy), to support their use of NGS in community analysis through a web-interactive pipeline tool for non-informatic users.

Whilst being primarily concerned with bioinformatic analysis, Daniel also has extensive experience in the wet-lab, a skill which greatly aids communication with scientist without bioinformatic experience.

Education

2011-2015: PhD, Cardiff University
Title: The earthworm microbiome and its role in enabling host fitness and plasticity.

2006-2009: Genetics BSc. (Hons) 2:1, Cardiff University
Final year Project: Informatic transcriptome characterisation of Gammarus pulex.

2004-2006: A-levels, Churchill Sixth Form, Churchill, North Somerset
Biology, Chemistry, Maths

1999-2004: GCSEs, Priory Community School, Weston-super-Mare, North Somerset