Dr Richard Badge

Dr Richard Badge grew up in the historic port city of Plymouth, United Kingdom.

In 1989 Richard went to study pure and applied biology at Keble College, Oxford University, moving on to complete a PhD in the evolutionary population biology and molecular genetics of fruit fly transposable elements at the University of Nottingham.

After a postdoctoral period in Nottingham, Dr Badge secured a Wellcome Trust International Travelling Fellowship to work on human transposable elements at the University of Michigan in Ann Arbor, completing this fellowship at the Department of Genetics, University of Leicester, in the group of Professor Sir Alec Jeffreys FRS.

Now as an associate professor in bioinformatics in the Department of Genetics and Genome Biology, Dr Badge uses computational and molecular genomic methods to study human, rodent and primate transposable elements.

Activity of human retrotransposons in cultured cells, developing embryos and the germline.

L1 or LINE-1 retrotransposons are the ‘master’ transposons in the human genome providing the machinery required to mobilise not only themselves but also non-autonomous transposons and even human genes. The group uses genome-wide analyses, both in the lab and in silico, to investigate the dynamics and regulation of this unusual behaviour in cultured human cells and DNA from embryonic and germline sources.

Analysis of chimpanzee and gibbon specific active retrotransposons.

In collaboration with Twycross Zoo (The World Primate Centre) the group are developing tools to study the activity of L1 retrotransposons in humanity’s closest living relative: the chimpanzee. Chimpanzees at Twycross have been trained as part of their enrichment and healthcare regimen to allow collection of DNA by mouth swabs. These samples obtained in a stress-free manner are underpinning our exploration of L1 diversity and activity in chimpanzees. Gibbons are somewhat harder to train (and catch!) so the group mostly uses DNA extracted from hair to study their genomes. The group have developed tools to molecularly identify gibbon species and their hybrids, using DNA markers, which is vitally important in captive breeding programmes. These systems also have potential for application in the field, allowing conservation genetics to be used in helping to protect these critically endangered species.

Tufarelli, C., & Badge, R. M. (2017). Retrotransposon-driven transcription and cancer. In Human Retrotransposons in Health and Disease (pp. 259-273). doi:10.1007/978-3-319-48344-3_11
Ogeh, D., & Badge, R. (2017). A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. Bioinformatics, 33(5), 650-653. doi:10.1093/bioinformatics/btw687
Penzkofer, T., Jaeger, M., Figlerowicz, M., Badge, R., Mundlos, S., Robinson, P. N., & Zemojtel, T. (2017). L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Research, 45(D1), D68-D73. doi:10.1093/nar/gkw925 Altmetrics: 3, Citations: 10
Rahbari, R., & Badge, R. M. (2016). Combining amplification typing of L1 active subfamilies (ATLAS) with high-throughput sequencing. Methods Mol Biol. 2016;1400:95-106. doi:10.1007/978-1-4939-3372-3
Rahbari, R., Habibi, L., Garcia-Puche, J. L., Badge, R. M., & Garcia-Perez, J. (2015). LINE-1 retrotransposons and their role in cancer. In Epigenetics Territory and Cancer (pp. 51-99). doi:10.1007/978-94-017-9639-2_3
Macfarlane, C. M., & Badge, R. M. (2015). Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies. Retrovirology, 12, 17 pages. doi:10.1186/s12977-015-0162-8 Altmetrics: 2, Citations: 8
Ottolini, B., Hornsby, M. J., Abujaber, R., MacArthur, J. A. L., Badge, R. M., Schwarzacher, T., Hollox, E. J. (2014). Evidence of Convergent Evolution in Humans and Macaques Supports an Adaptive Role for Copy Number Variation of the beta-Defensin-2 Gene. Genome Biology and Evolution, 6(11), 3025-3038. doi:10.1093/gbe/evu236
Gray L.J., Leigh T., Davies M.J., Patel N., Stone M., Bonar M., Badge R., Khunti K. (2013). Systematic review of the development, implementation and availability of smart-phone applications for assessing Type2 diabetes risk. Diabetic Medicine, 30(6), 758-760. doi:10.1111/dme.12115
Macfarlane CM, Collier P, Rahbari R, Beck CR, Wagstaff JF, Igoe S, Moran JV, Badge RM. Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. Hum Mutat. 2013 Jul;34(7):974-85. doi:10.1002/humu.22327. Epub 2013 Apr 23. PubMed PMID: 23553801; PubMed Central PMCID: PMC3880804.
Gray LJ, Leigh T, Davies MJ, Patel N, Stone M, Bonar M, Badge R, Khunti K. Systematic review of the development, implementation and availability of smart-phone applications for assessing type 2 diabetes risk. Diabet Med. 2013 Jun;30(6):758-60. doi: 10.1111/dme.12115. Review. PubMed PMID: 23683104.
Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease.  Annu Rev Genomics Hum Genet. 2011 Sep 22;12:187-215. Review. PMID: 21801021
Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease.  Annu Rev Genomics Hum Genet. 2011 Sep 22;12:187-215. Review. PMID: 21801021

Bioinformatics

Genomics

Mobile DNA

Human genetic variation

Programme Director: Biological Sciences Foundation Year

Co-convenor: MSc Bioinformatics

Co-convenor: BS2040: Bioinformatics

Co-convenor: BS0011:

Co-convenor: BS0014: 

Genomics

Human genetic diversity

Ape evolution

BA Hons (Oxon)

PhD (Genetics)