Ewan Mollison

I have extensive experience in bioinformatics and working with large biological data sets, around 25 years in total, applied to a range of disciplines including studying protein-protein interaction networks in cancer research, cancer proteomics, genome assembly and analysis of non-model plant species and oomycete pathogens using next-generation sequencing techniques

Key Skills

• Extensive experience (15 years) with de novo genome assembly and annotation from NGS sequencing, mainly applied to non-model plant and protist species, using commercial and open-source tools. Experienced with Illumina and 454 sequencing since 2010 and PacBio since 2017
• Familiar with using and processing multiple data formats used in NGS analyses: FASTQ, SAM/BAM, BED, GTF, etc.
• Transcriptome assembly and RNA-Seq analysis using de novo (Trinity) and reference-guided (Bowtie-Tophat-Cufflinks, STAR, Salmon, DESeq) approaches, and GO enrichment analysis of differentially expressed genes
• Characterisation of gene families
• Bayesian phylogenetic analysis of targeted gene families
• Extensive Linux command line experience as both user and administrator in high-performance computing (HPC) clusters
• Job management in HPC environments (Platform LSF, Sun Grid Engine)
• Programming in Bash, Perl, Python and R to facilitate formatting and querying of data for analysis and visualization

PhD Thesis: Genome assembly of Lolium perenne and development of a genomic resource for targeted gene-mining studies

Key aspects of my research were:

• De novo assembly of a working-draft assembly of the Lolium perenne gene-space from next-generation sequencing data (Illumina)
• Annotation of this assembly using ab initio and reference-guided methods, assembly of a transcriptome from RNA-Seq data, and presentation of the genome assembly and annotations online through a JBrowse genome browser
• Use of the resources developed to aid in characterisation, and Bayesian phylogenetic analysis, of a family of high-affinity nitrate transporter (HAT) genes