Dr Richard Badge

Dr Richard Badge
Associate Professor in Bioinformatics


Tel: +44 (0)116 252 5042
Fax: +44 (0)116 252 3378

Email: rmb19@leicester.ac.uk

BA Hons (Oxon), PhD (Genetics)

Personal details

BA (Hons), PhD

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.


PhD.com Dr R.Badge

PhD Project page  Dr R.Badge


Other responsibilities

  • Programme Lead: Biological Sciences with a Foundation Year, BS


  • 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
  • Muñoz-Lopez M, Macia A, Garcia-Cañadas M, Badge RM, Garcia-Perez JL. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans.  Mob Genet Elements. 2011 Jul;1(2):122-127. Epub 2011 Jul 1. PMID: 22016860
  • Freeman P, Macfarlane C, Collier P, Jeffreys AJ, Badge RM. L1 hybridization enrichment: a method for directly accessing de novo L1 insertions in the human germline.  Hum Mutat. 2011 Aug;32(8):978-88. doi: 10.1002/humu.21533. Epub 2011 Jul 12. PMID: 21560187
  • Macia A, Muñoz-Lopez M, Cortes JL, Hastings RK, Morell S, Lucena-Aguilar G, Marchal JA, Badge RM, Garcia-Perez JL. Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol. 2010 Nov 1. [Epub ahead of print] PMID: 21041477
  • Ray A, Rahbari R, Badge RM. IAP Display: A Simple Method to Identify Mouse Strain Specific IAP Insertions. Mol Biotechnol. 2010 Sep 26. [Epub ahead of print] PMID: 20872285
  • Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. LINE-1 retrotransposition activity in human genomes. Cell. 2010 Jun 25;141(7):1159-70. PubMed PMID: 20602998.
  • Rahbari R, Sheahan T, Modes V, Collier P, Macfarlane C, Badge RM. A novel L1 retrotransposon marker for HeLa cell line identification. Biotechniques. 2009 Apr;46(4):277-84. PubMed PMID: 19450234; PubMed Central PMCID: PMC2696096.
  • Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M. Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics. 2007 Oct 26;8:392. PubMed PMID: 17963496; PubMed Central PMCID: PMC2176070.
  • Athanikar JN, Badge RM, Moran JV. A YY1-binding site is required for accurate  human LINE-1 transcription initiation. Nucleic Acids Res. 2004 Jul 22;32(13):3846-55. Print 2004. PubMed PMID: 15272086; PubMed Central PMCID:PMC506791.
  • Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH Jr. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5280-5. Epub 2003 Apr 7. PubMed PMID: 12682288; PubMed Central PMCID: PMC154336.
  • Badge RM, Alisch RS, Moran JV. ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet. 2003 Apr;72(4):823-38. Epub 2003 Mar 11. PubMed PMID: 12632328; PubMed Central PMCID: PMC1180347.
  • Cheng YC, Lee CJ, Badge RM, Orme AT, Scotting PJ. Sox8 gene expression identifies immature glial cells in developing cerebellum and cerebellar tumours. Brain Res Mol Brain Res. 2001 Aug 15;92(1-2):193-200. PubMed PMID: 11483257.
  • Badge RM, Yardley J, Jeffreys AJ, Armour JA. Crossover breakpoint mapping identifies a subtelomeric hotspot for male meiotic recombination. Hum Mol Genet. 2000 May 1;9(8):1239-44. PubMed PMID: 10767349.
  • Badge RM, Brookfield JF. A novel repressor of P element transposition in Drosophila melanogaster. Genet Res. 1998 Feb;71(1):21-30. PubMed PMID: 9674380.
  • Badge RM, Brookfield JF. The role of host factors in the population dynamics of selfish transposable elements. J Theor Biol. 1997 Jul 21;187(2):261-71. PubMed PMID: 9237896.
  • Brookfield JF, Badge RM. Population genetics models of transposable elements. Genetica. 1997;100(1-3):281-94. PubMed PMID: 9440281.


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

Human Cell growth in culture
Human cells growing in a culture

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. Understanding when and where these molecular parasites move has profound implications for their impact on human genome evolution. Recent studies have shown that while most transposons restrict their activity to the germline L1 retrotransposons may specifically target the early stages of development. 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 specific active retrotransposons

Gibbon & Chimpanzee, Twycross Zoo

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.

Genome dynamics and regulation of mouse IAP retrotranspons

Gel Align
Gel Align

IAP elements are virus-like transposons that cause a significant proportion of mutations in laboratory mice, by jumping into and disrupting essential genes. Their activity is strongly regulated by epigenetic changes, and sometimes their regulatory sequences are co-opted to drive mouse gene expression.

As such IAP transposons can be used as reporters of genome-wide epigenetic alterations, such as those that often occur in cancer.

Conversely by studying manipulations of mouse epigenetic marks they can become a model system to examine how transposon activity is regulated.

PhD projects

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Departmental PhD Project page for this Supervisor: Dr R.Badge

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Contact Details

Department of Genetics
University of Leicester

Adrian Building
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United Kingdom

Tel: +44 (0)116 252 3374
E Mail: genetics@le.ac.uk

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Professor Jacqui Shaw

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