CV
Research positions
- Since May 2023: Bioinformatician in Rare Diseases in Prof Chris Wallace’s lab. Handling immuno-deficient patient data and designing analyses for 4 research groups.
- Statistical analysis of B cell data from immuno-deficient patients in the team of clinical academic Prof Siobhan Burns with Dr Luiza C. Campos.
- Mapping thousands of genomes to GRCh38 and calling variants for rare diseases in the team of biostatistician Dr Ernest Turro.
- Managing a reliable archiving solution to preserve patient data (flow cytometry, WGS, transcriptomics) for both secure storage and input to R&D.
- Calling variants and annotating their effects with VEP in the team of immunologist Prof Matthew Cook.
- Oct 2019 - April 2023: NERC-funded Postdoc in Seirian Sumner’s lab. Focused on understanding the origins of sociality in the wasps and the bees: comparative transcriptomics and genomics.
Education
- 2015 – 2019: PhD in ant genomics, QMUL. Supervisors: Yannick Wurm and Max Reuter. NERC-funded Doctoral Training Programme. Practiced in molecular DNA wet lab and dry lab (short and long reads).
- 2013 - 2014: MRes Biosystematics at Imperial College London & Natural History Museum, London (NHM).
- 2008 - 2011: BSc Environmental Sciences at Oxford Brookes University, Oxford 1st Class (Hons).
Technical
- Bioinformatics for population genetics & genome/transcriptome wrangling
- R current favourite packages: ggplot, tidyverse, adegenet
- Python: matplotlib, pandas, numpy
- Bash: tmux, vim, sbatch, qsub
- Database: MySQL (creating new schema, updating current database, extracting data for management and curation)
- Pipeline optimisation: HPC resource management to tailor Nextflow pipeline nf-core/sarek to a large re-mapping project
- Reproducibility: RMarkdown reports, Github version control, Nextflow (nf-core/rnaseq), Singularity, Docker
- De novo genome assembly (PacBio, MinION, Illumina, HiC), genome annotation (genes, lncRNA, TE), variant calling (SNP, SV, copy number variant), GWAS, population genomics
- RNAseq QC and Transcriptome analyses: DESeq2, WGCNA
- Machine learning: Support Vector Machine (to predict caste from wasp RNAseq data)
- Data Management: I defined the 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)
In the past, you could also find me in the wet lab (MinION, RNA, DNA, microsatellites) and in the field (sampling invertebrates worldwide).
Talks
- 2022: international invited talk for the GRIB group at IMIM-Pompeu Fabra (Barcelona)
- 2021: 2 talks (UCL CLOE and UCL CBER Seminars, London)
- 2020: 1 talk (UCL GEE Seminar, London)
- 2018: 2 international invited talks in USA (Ramírez’s group, UC Davis, California; Social Insect Research Group, Arizona State University, Arizona); 1 invited talk (UCL GEE Seminar, London); 1 international talk (IUSSI Brazil, in Guaruja); 1 international poster (ESEB and Evolution conference, Montpellier, France).
- 2017: 1 international talk (Evolution, Portland, Oregon, USA); 1 international poster (ESEB congress, Groningen, Netherlands); 1 talk (PopGroup, Cambridge)
- 2016: 1 talk (North-West section of IUSSI Winter Meeting, London)
Grants, honours & awards
- 2020: ESEB’s Godfrey Hewitt Mobility award - €1600
- 2019: Genetics Society grant to give a talk at PopGroup - £150
- 2018: QMUL PostGraduate Research Fund for Arizona & California fieldtrip - £1200
- 2018: IUSSI North-Western Section grant to organise a symposium at IUSSI Brazil – £1000
- 2018: Royal Entomological Society grant to organise a symposium at IUSSI Brazil - £450
- 2018: Royal Society of Biology grant to organise a symposium at IUSSI Brazil - £500 PDF report
- 2017: Genetics Society grant to give a talk at PopGroup - £150
- 2017: Genetics Society grant to present a poster at ESEB - £624
- 2015: PhD Scholarship from London NERC DTP - £7500
- 2014: Royal Entomological Society grant to present a poster at 2nd Young Natural History Scientists’ Meeting (2014, France)
- 2013: Scholarship awarded from Entente Cordiale (Masters of Research)
- 2013: Study grant from Ruby and Will George Trust (Masters of Research)
Teaching
- Nov 2020 and 2021: Teaching “Molecular Tools for Ecologists” to 80 UCL Undergraduate students. Lecture, exam preparation and marking.
- Nov 2019 - ongoing: mentoring students in Seirian Sumner’s lab.
- 1st year Undergraduate Summer project student Jadesada Schneider (bioinformatics)
- 3rd year Undergraduate Autumn project student Shin Khan (R)
- MRes Winter project student Phoebe Cunningham (R)
- Msci Winter project student Quinn Coxon (bioinformatics)
- Sept 2016 - Sept 2019: Teaching assistant for 8 cohorts of QMUL Undergraduates and Masters classes, including Fieldwork (Tropical Ecology in South Africa), Bioinformatics (R Basics, Advanced R, Bash for Genomics), Basic Biology lab skills (dilution, microscopy, PCR).
- Dec 2017: Lecturer during Undergraduate Tropical Ecology Module in South Africa (Wildlife and Human Interactions)
- Jan - Aug 2017: Design and Supervising Master student project. With Gino Brignoli, focussing on social organisation of yellow meadow ants, involving fieldwork and genetic analyses.
Outreach
- 2022: invited talk at Pint of Science for a London pub crowd
- 2021: Science expert on an episode of Exolore podcast: World of Migratory Wasps
- 2019-22: Science pen pal with a US-based student from Letters to a Pre-Scientist. Exchanging four letters a year.
- 2018: QMUL Festival of Communities in London
- 2017: Science SoapBox volunteer in Brighton
- 2014: NHM Researchers’ Night in London
- 2013: NHM Big Nature Day in London
Collaborative Project Organisation
- 2020: Postdoc representative for UCL GEE: setting up webpage and Slack forum for 200 postdocs.
- 2020: Principal coordinator of NWE IUSSI Winter Meeting in a small organising committee. The first of its kind online: Zoom, Slack, Twitter, Youtube for 200 participants from 4 continents.
- 2018: Organising the QMUL Festival of Communities outreach day among a small team of PhD students, specialising in equipment, transport, people logistics.
- 2017 – 18: Leading our conference committee to organise a symposium during the international congress IUSSI Brazil, specialising in writing symposium abstract, selecting and reaching out to all speakers including keynote speaker, co-chairing the symposium.
- 2016 – 2019: Leading the lab’s monthly review of published articles, in which each lab member is responsible to summarise 3 journals’ current issue.
Active Part in Research Communities
- Member of International Union for the Study of Social Insects, Genetics Society, Royal Entomological Society, European Society of Evolutionary Biology, Society of Systematics Biologists, Society of Molecular Biology and Evolution
- Reviewer for ERC grant, ProcB, PeerJ, Myrmecological News Blog, Insect Science,
More details on LinkedIn