London, England, United Kingdom
Analyzing biomedical data for all. Computational Biologist in Chronic Kidney Disease with Prof Eoin McKinney in the Cambridge-GSK collaboration. Handling Electronic Health Records and designing analyses. Python: pandas, numpy, polars. Bash top three commands: tmux, vim, sbatch. R current favourite packages: ggplot, tidyverse, data.table. Reproducibility: RMarkdown reports, Github version control, Nextflow (nf-core/rnaseq, sarek), Singularity, Docker, AWS cloud architecture. De novo genome assembly (PacBio, MinION, Illumina, HiC), genome annotation (genes, lncRNA, TE, VEP, ClinVar), variant calling (Deepvariant, Manta), GWAS, population genomics, ancestry analysis. RNAseq QC and Transcriptome analyses: DESeq2, WGCNA. Machine learning: Support Vector Machine. Database curation: MySQL. Contact me if you fancy a chat. And coffee. And cake.
Bioinformatician in the Department of Medicine of University of Cambridge, working with PI Chris Wallace on the INTREPID project. We are exploring molecular data from Primary Immuno Deficient patients (https://www.intrepidproject.info/).
Evolution of social organisation in wasps in Seirian Sumner's lab. Bioinformatics for population genetics & genome/transcriptome wrangling. I analysed and compared transcriptomes of 16 insect species for gene expression levels (QC, DESeq2, WGCNA) associated with sociality, using machine learning Support Vector Machine to predict caste from wasp RNAseq data. I have analysed more than 16 insect genomic datasets: de novo genome assembly (PacBio, MinION, Illumina, HiC), genome annotation (genes, lncRNA, TE), variant calling, GWAS, population genomics. I also defined the Data Management strategy for long-term data storage for the Sumner Lab, and developed a system for all members to safely save their data (genomes, transcriptomes, annotations) I produce large analyses on HPC cluster (bash top three commands: tmux, vim, qsub) with reproducibility in mind (Nextflow nf-core/rnaseq, Singularity, Docker, Github version control). I deliver clean annotated code, running statistics in R (ggplot, tidyverse, adegenet) and Python (matplotlib, pandas, numpy) with easy-to-read reports (RMarkdown reports, Jupyter notebooks).
Learning to be a researcher in the Environmental Sciences: the theory and the practice. Geology and biology fieldwork, extensive lab work (from entomology to Arduino), problem-based group work, R programming practicals. My Doctoral Training Program is based at UCL, but my research activities are at QMUL.
Practicing the art of researching: field work on 3 continents, PhD courses on Ant Identification in France (May 2016) and Social Evolution in Austria (November 2016), conference talks around the world (last invited talk: UC Davis, CA). At QMUL, you can find me at my desk wrangling data using the cluster, R and Unix commands, or in the lab pipetting ant DNA from extractions to whole-genome library preparations. My Doctoral Training Program is based at UCL, but my research activities are at QMUL.
Responsible for preparation of KS3 to A-level science practicals (Biology, Chemistry, Physics). Demonstration of Biology equipment and practicals. Woodlice rearing.
In the research group "Ants, Genomes & Evolution" (Dr Yannick Wurm, http://wurmlab.github.io/). - Research project in the fire ant (Solenopsis invicta) social chromosome. - Responsible for curating genes of fire ant social chromosome, improving user's experience of web interface for gene annotation (Afra), participating in the research team including creation of a journal club and networking events.