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Research Interests


I am interested in decoding patterns of gene gain and loss in bacterial genomes. Specifically, the questions I am interested in are: 1) What kind of processes contribute to evolution by gene gain and loss and how frequently do these occur? 2) Is gene gain and loss important in shaping bacterial traits that interest us, such as antibiotic resistance or pathogenicity? 3) What is the connection between bacterial social behaviours and mobile genes?


In my previous post-doc I worked on developing methods for genome wide association studies using whole genome sequences from bacteria, in particular finding associations between the gain and loss of genes and clinically relevant traits such as antibiotic resistance. 2013-2016


Jane Charlesworth

Publications


Lewis J, Breeze C, Charlesworth J, Maclaren O, Cooper J (2016). Where next for the reproducibility agenda in computational biology? BMC Systems Biology (in press).


Earle SG, Wu C-H, Charlesworth J, Stoesser N, Gordon NC, Walker TM, Spencer CCA, Iqbal Z, Clifton DA, Hopkins KL, Woodford N, Smith EG, Ismail N, Llewelyn MJ, Peto TE, Crook DW, McVean G, Walker AS, Wilson DJ (2016). Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nature Microbiology 16041.


Everitt RG, Didelot X, Batty EM, Miller RR, Knox K, Young BC, Bowden R, Auton A, Votintseva A, Larner-Svensson H, Charlesworth J, Golubchik T, Ip CLC, Godwin H, Fung R, Peto TEA, Walker AS, Crook DW, Wilson DJ (2014). Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nat Commun 5 :3956.


Yao Y, Charlesworth J, Nair V & Watson M (2013). MicroRNA expression profiles in avian haemopoietic cells. Frontiers in genetics 4:153. doi:10.3389/fgene.2013.00153


Charlesworth J (2009). Genome hunters set their sights on creatures great and small. The Guardian.


Charlesworth J, Eyre-Walker A (2007). The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. PNAS 104: 16992-16997.


Charlesworth J, Eyre-Walker A (2006). The McDonald-Kreitman Test and Slightly Deleterious Mutations. Mol Biol Evol 25: 1007-1015.


J Charlesworth, A Eyre-Walker (2006). The rate of adaptive evolution in enteric bacteria. Molecular biology and evolution. 23:1348-1356. doi: 10.1093/molbev/msk025.


History


2016-present:      EBPOD fellowship, working both in the Department of Genetics

                            and with Prof. Nick Goldman at EBI  

2013-2016           Post-doc; Modernising Medical Microbiology group in Oxford.

2011-2013           ARK-Genomics, Royal (Dick) School of Veterinary Studies,

                            The Roslin Institute, University of Edinburgh.

2010-2011           Wellcome Trust Centre for Cell Biology in Edinburgh 

2007-2010           Science journalism

2003-2007           PhD, “genome-wide rates of adaptive substitution in bacteria” Adam Eyre-Walker.    

                            University of Sussex.

1999-2003           BSc (Genetics). University of Edinburgh.