Education
Ph.D. in Life Sciences, Imperial College London, South
Kensington, London, UK, 2013–2017
- Thesis: Exploring complex ecological patterns in hyper-diverse tropical canopy arthropod communities using modern genetic technologies
- Advisor: Prof. Alfried P. Vogler
- Focus: Tropical forest ecology, arthropod ecology, climate change, molecular ecology, bioinformatics
M.Res. in Ecology, Evolution and Conservation Research, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK, 2011–2012
- Pass with Distinction
- Recieved R.E.Southwood prize for highest Masters marks in the year
- Thesis 1: Drivers of heterogeneity in predictions of species responses to climate change: a meta-analysis
- Thesis 2: Responses of invertebrate communities to disturbance in a tropical montane cloud forest
B.A. (Hons) in Biological Sciences, University of Oxford, Oxford, Oxfordshire, UK, 2007–2010
- Upper Second Class Honours (Equivalent to approx. 3.8/4.0 GPA, A-)
- Recieved Orielton Balls prize for best research reports
Research experience
Senior Invertebrate Scientist, Honduras Terrestrial Expedition, Operation Wallacea, 2011 – present (currently an advisory role)
- Community ecology research and monitoring of Scarabaeinae dung beetles
- Deforestation monitoring and conservation
- Curation and statistical analysis of long-term ecological data
- Research team field management and equipment logistics (5-12 scientists)
- Focus: Tropical Invertebrate Ecology, Conservation, Biodiversity Assessment, Data management and analysis, Field logistics, Personnel management
Lead Field Scientist, Honduras Expedition, Biodiversity Initiative, Natural History Museum London, 2014
- Tropical Forest Invertebrate Biodiversity research
- Research team management and logistics
- Local and national permit negotiation,stakeholder management
- Focus: Biodiversity research, data management, Research design, expedition management, logistics
Field Scientist, French Guiana Expedition, Biodiversity Initiative, Natural History Museum London, 2013
- Tropical Forest Invertebrate Biodiversity research
- Teamwork and field planning
Teaching experience
Senior Field Supervisor,Invertebrate Research, Operation Wallacea 2011–present
- Advised research design, field methods and statistical analysis on invertebrate projects
- To date more than 15 undergraduate and masters students from UK, USA, Canada and other countries
Invited Practical Lecturer, Belgian Network for DNA Barcoding of Life workshop, Physalia Courses,
2017
- Intensive two-day course on practical mitochondrial genome assembly
- Around 30 PhD, Postdoc and Academic participants
Bioinformatics and Phylogenetics, Masters in Biodiversity and Systematics, Department of Life Sciences, Imperial College London, 2016 & 2017
- Practical Lecturer for week-long masters-level module
- Covered: linux CLI, basic bioinformatics pipeline, metabarcoding, mitochondrial genomes, phylogenetics
Undergraduate and Masters thesis supervisor, Vogler Lab, Department of Life Sciences, Imperial College London, 2015–2017
- Provided day-to-day supervision of several undergraduate and masters students
- Projects from freshwater meta-barcoding to mitochondrial genomics and phylogenetics
Lead Demonstrator, Silwood R Course, Department of Life Sciences, Imperial College London, 2013 & 2014
- Lead practical demonstrator for PhD students and Post-Docs
- Covered: basic R usage, parametric statistical analysis, GLM, ANOVA
Technical skills
Bioinformatics
- Languages: Linux Bash (intermediate), Perl (intermediate), Python (beginner)
- CLI: USEARCH pipeline, BLAST suite, swarm, Celera, Newbler,Ray, SpADEs, IDBA, bbmap, MIRA, NOVOplasty
- GUI: Geneious, UGENE, Megan
- Author of a range of perl scripts for bioinformatics, in particular the [NAPtime](https://github.com/tjcreedy/NAPtime) pipeline for metabarcoding
Phylogenetics
- Limited theoretical background, but good practical understanding of managing phylogenetic data
- Software: RAxML, BEAST/BEAUTi, Figtree,Dendroscope, R packages (e.g. picante, ape, adephylo, phytools)
- Author of several perl and R scripts for managing and manipulating phylogenetic data as Newick and other file formats
Data science
- Statistics software: R (GUI and CLI), Rstudio
- GIS software: ArcGIS, QGIS, R packages for GIS (maptools,rgeos,spatstat)
- Proficient and highly experienced in standard parametric statistics: ANOVA, GLM, etc
- Substantial experience managing large datasets, including sequence data and multi-decade ecological community data
- Experience with mixed effects modelling and multivariate statistics/ordination
- Some experience with machine learning and classification
General
- Office: LaTeX, Microsoft Office (Word, Excel, Powerpoint, Access), Libre Office and Google Docs equivalents
- Graphics: Adobe Photoshop and Indesign, Inkscape, GIMP
- Operating Systems: Windows, Linux (Ubuntu)
- Other: Amazon Web Services (EC2, S3), networking, OS installation and troubleshooting, computer assembly.
Publications
In press or published
Conferences
Suttle, K. B., Kiupel, S., Zhou, B., Creedy, T. J.(2014), “Probing heterogeneity in ecological responses to climate change,” 99th Ecological Society of America Annual Convention, Sacramento, California, USA.
Vogler, A. P., Linard, B., and Creedy, T. J.(2017), “Mitochondrial metagenomics: A one stop shop for evolutionary bioligy, ecology and population genetics,” Entomological Society of America, Denver, Colorado, USA.