People

Dr Richard Badge

Associate Professor in Bioinformatics

School/Department: Genetics and Genome Biology, Department of

Telephone: 0116(0) 252 4042

Email: rmb19@leicester.ac.uk

Profile

I grew up in the historic port city of Plymouth United Kingdom. In 1989 I went up to study Pure and Applied Biology at Keble College Oxford University. I then went 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 I secured a Wellcome Trust International Travelling Fellowship to work on human transposable elements at the University of Michigan in Ann Arbor. I completed this Fellowship in 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 I use computational and molecular genomic methods to study human rodent and primate transposable elements.

Research

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. . We use 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) we are developing tools to study the activity of L1 retrotransposons in our closest living relative: the chimpanzee. Chimpanzees at Twycross have been trained as part of their enrichment and health care 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 we mostly use DNA extracted from hair to study their genomes.

Publications

(0) 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.

Supervision

Bioinformatics genomics mobile DNA human genetic variation

Teaching

Programme Director: Biological Sciences Foundation Year

Co-convenor: MSc Bioinformatics

Co-convenor: BS2040: Bioinformatics

Co-convenor: BS0011:

Co-convenor: BS0014:

Contributor:

 

Press and media

Genomics human genetic diversity ape evolution

Awards

Senior Fellow of the HEA

Qualifications

BA Hons (Oxon)

PhD (Genetics)

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