About
I am a Robertson Fellow in Biomedical Data Science at the Big Data Institute, University of Oxford. I develop algorithms and software to tackle difficult problems in large-scale genomics, integrating with the Python data science stack.
Contact
| jerome.kelleher@bdi.ox.ac.uk | Me at the BDI
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| GitHub | @jeromekelleher | |
| Orcid | orcid.org/0000-0002-7894-5253 | |
| Google Scholar | profile |
Address:
Assoc Prof Jerome Kelleher
Big Data Institute
Li Ka Shing Centre for Health Information and Discovery
Old Road Campus
Oxford
OX3 7LF
UK
Activities
- I contribute to the sgkit-dev GitHub organisation, including leading work on the VCF Zarr paper and associated bio2zarr and vcztools utilities.
- I lead development of tskit, the tree sequence toolkit. Tskit is a Python and C API that allows us to work with genealogical histories at unprecedented scale.
- I also lead development of the msprime coalescent simulator, which is based on tskit, and can simulate of the exact coalescent with recombination over chromosome-sized regions with hundreds of thousands of samples.
- I co-organised Probabilistic Modelling in Genomics 2022 conference. Please see the ProbGen22 website for more details.
- I'm a member of the PopSim Consortium and lead development of its first product, stdpopsim.
- I'm part of the Data Working Group in the Global Alliance for Genomics and Health (GA4GH). I am currently participating in the design and client side implementation of the htsget data access protocol.
- During my postdoc in theoretical population genetics , I worked primarily on a new model for populations evolving in a spatial continuum. During this time I developed two Python simulation packages: one to simulate a general form of the model and another to simulate a more specialised form much more efficiently.
- I found some bugs in TAOCP volume 4A while it was still in beta-test fascicle form. I am therefore a proud saver at the The Bank of San Serriffe!
CV Sketch
- 2019-present
- Robertson Fellowship in Biomedical Data Science at the Big Data Institute, University of Oxford.
- 2014-2019
- Senior statistical programmer in the McVean Group at the Big Data Institute (and formerly at the Wellcome Centre for Human Genetics), University of Oxford.
- 2008-2014
- Postdoc, primarily at the Institute of Evolutionary Biology, University of Edinburgh and also at the Department of Statistics, University of Oxford.
- 2005-2008
- Senior Software Architect, MPSTOR
- 2002-2005
- PhD Computer Science, University College Cork (thesis).
- 1998-2002
- BSc Computer Science, University College Cork.
Publications
See my ORCID profile for an up-to-date list of my publications