Professor Simon Reed

2024

• Zuo, Y. et al. 2024. Long non-coding RNA LIP interacts with PARP-1 influencing the efficiency of base excision repair. Non-coding RNA Research 9(3), pp. 649-658. (10.1016/j.ncrna.2024.03.010)
• Mackay, H. L. et al. 2024. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication. Nature Communications 15, article number: 8102. (10.1038/s41467-024-52250-4)
• Klapwijk, J. C. et al. 2024. Improving the assessment of risk factors relevant to potential carcinogenicity of gene therapies: a consensus article. Human Gene Therapy 35(15-16), pp. 527-542. (10.1089/hum.2024.033)

2023

• Newton, M. D. et al. 2023. Negative DNA supercoiling induces genome-wide Cas9 off-target activity. Molecular Cell 83(19), pp. 3533-3545.e5. (10.1016/j.molcel.2023.09.008)
• Lynch, A. M. et al. 2023. Next Generation Sequencing Workshop at the Royal Society of Medicine (London, May 2022): how genomics is on the path to modernizing genetic toxicology. Mutagenesis (10.1093/mutage/gead012)
• Yancoskie, M. N., Maritz, C., van Eijk, P., Reed, S. H. and Naegeli, H. 2023. To incise or not and where: SET-domain methyltransferases know. Trends in Biochemical Sciences 48(4), pp. 321-330. (10.1016/j.tibs.2022.10.003)

2022

• Murat, P., Perez, C., Crisp, A., van Eijk, P., Reed, S. H., Guilbaud, G. and Sale, J. E. 2022. DNA replication initiation shapes the mutational landscape and expression of the human genome. Science Advances 8(45) (10.1126/sciadv.add3686)
• Dobbs, F. M., van Eijk, P., Fellows, M. D., Loiacono, L., Nitsch, R. and Reed, S. H. 2022. Precision digital mapping of endogenous and induced genomic DNA breaks by INDUCE-seq. Nature Communications 13, article number: 3989. (10.1038/s41467-022-31702-9)
• Fletcher, C. E. et al. 2022. A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer. Molecular Cancer 21, article number: 82. (10.1186/s12943-022-01540-w)

2021

• Menzies, G., Prior, I. A., Brancale, A., Reed, S. H. and Lewis, P. D. 2021. Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence. BMC Chemistry 15, article number: 51. (10.1186/s13065-021-00777-8)

2020

• Wang, D. et al. 2020. LRIK interacts with the Ku70–Ku80 heterodimer enhancing the efficiency of NHEJ repair. Cell Death and Differentiation 27, pp. 3337-3353. (10.1038/s41418-020-0581-5)

2018

• van Eijk, P., Nandi, S. P., Yu, S., Bennett, M., Leadbitter, M., Teng, Y. and Reed, S. H. 2018. Nucleosome remodeling at origins of global genome?nucleotide excision repair occurs at the boundaries of higher-order chromatin structure. Genome Research 29(1), pp. 74-84. (10.1101/gr.237198.118)
• Wang, D., Yang, H., Zhou, Z., Zhao, M., Chen, R. and Reed, S. 2018. XPF plays an indispensable role in relieving silver nanoparticle induced DNA damage stress in human cells. Toxicology Letters 288, pp. 44-54. (10.1016/j.toxlet.2018.02.022)
• Piasecka, A. et al. 2018. The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers. Journal of Molecular Biology 430(5), pp. 611-627. (10.1016/j.jmb.2017.11.016)

2017

• Van Eijk, P., Teng, Y., Bennet, M. R., Evans, K., Powell, J. R., Webster, R. and Reed, S. 2017. Integrated microarray-based tools for detection of genomic DNA damage and repair mechanisms. In: Muzi-Falconi, M. and Brown, G. W. eds. Genome Instability. Methods in Molecular Biology., Vol. 1672. New York, NY: Humana Press, pp. 77., (10.1007/978-1-4939-7306-4_7)

2016

• Yu, S. et al. 2016. Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin. Genome Research 26, pp. 1376-1387. (10.1101/gr.209106.116)

2015

• Waters, R., van Eijk, P. and Reed, S. 2015. Histone modification and chromatin remodeling during NER. DNA Repair 36, pp. 105-113. (10.1016/j.dnarep.2015.09.013)
• Menzies, G., Reed, S. H., Brancale, A. and Lewis, P. D. 2015. Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability. Nucleic Acids Research 43(19), pp. 9133-9146. (10.1093/nar/gkv910)
• Zhou, Z. et al. 2015. UV induced ubiquitination of the yeast Rad4–Rad23 complex promotes survival by regulating cellular dNTP pools. Nucleic Acids Research 43(15), pp. 7360-7370. (10.1093/nar/gkv680)
• Bennett, M. R. et al. 2015. Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure. Scientific Reports 5, article number: 13395. (10.1038/srep13395)
• Powell, J. R. et al. 2015. 3D-DIP-Chip: a microarray-based method to measure genomic DNA damage. Scientific Reports 5, article number: 7975. (10.1038/srep07975)

2013

• Colmont, C. S., Ben Ketah, A., Errington, R. J., Reed, S. H., Udey, M. C. and Patel, G. K. 2013. Human basal cell carcinoma tumor-initiating cells are resistant to etoposide [Letter]. Journal of Investigative Dermatology 134(3), pp. 867-870. (10.1038/jid.2013.377)
• Yu, Y., Deng, Y., Reed, S. H., Millar, C. B. and Waters, R. 2013. Histone variant Htz1 promotes histone H3 acetylation to enhance nucleotide excision repair in Htz1 nucleosomes. Nucleic Acids Research 41(19), pp. 9006-9019. (10.1093/nar/gkt688)
• Colmont, C. S. et al. 2013. CD200-expressing human basal cell carcinoma cells initiate tumor growth. Proceedings of the National Academy of Sciences of the United States of America 110(4), pp. 1434-1439. (10.1073/pnas.1211655110)
• Powell, J., Bennett, M., Waters, R., Skinner, N. and Reed, S. 2013. Functional genome-wide analysis: a technical review, its developments and its relevance to cancer research. Recent Patents on DNA and Gene Sequences 7(2), pp. 157-166. (10.2174/18722156113079990020)

2012

• Waters, R., Evans, K. E., Bennett, M. R., Yu, S. and Reed, S. H. 2012. Nucleotide excision repair in cellular chromatin: studies with yeast from nucleotide to gene to genome. International Journal of Molecular Sciences 13(9), pp. 11141-11164. (10.3390/ijms130911141)
• Waters, R., Teng, Y., Bennett, M. R., Evans, K. E., Zhuang-Jackson, H., Higgs, A. and Reed, S. H. 2012. Emerging technologies in genotoxicity testing: measuring DNA damage in entire genomes at high resolution [Abstract]. Mutagenesis 27(1), pp. 112. (10.1093/mutage/ger068)
• Bennett, M. R. et al. 2012. Bioinformatic analyses of genome wide nucleotide excision repair datasets in Saccharomyces cerevisiae [Abstract]. Mutagenesis 27(1), pp. 121. (10.1093/mutage/ger068)

2011

• Silver, H. R., Nissley, J. A., Reed, S. H., Hou, Y. and Johnson, E. S. 2011. A role for SUMO in nucleotide excision repair. DNA Repair 10(12), pp. 1243-1251. (10.1016/j.dnarep.2011.09.013)
• Yu, S., Teng, Y., Waters, R. and Reed, S. H. 2011. How chromatin is remodelled during DNA repair of UV-induced DNA damage in Saccharomyces cerevisiae. PLoS Genetics 7(6), article number: e1002124. (10.1371/journal.pgen.1002124)
• Teng, Y., Bennett, M. R., Evans, K. E., Zhuang Jackson, H., Higgs, A., Reed, S. H. and Waters, R. 2011. A novel method for the genome-wide high resolution analysis of DNA damage. Nucleic Acids Research 39(2), article number: e10. (10.1093/nar/gkq1036)
• Reed, S. H. 2011. Nucleotide excision repair in chromatin: damage removal at the drop of a HAT. DNA Repair 10(7), pp. 734-742. (10.1016/j.dnarep.2011.04.029)

2010

• Irizar, M. A., Yu, Y., Reed, S. H., Louis, E. J. and Waters, R. 2010. Silenced yeast chromatin is maintained by Sir2 in preference to permitting histone acetylations for efficient NER. Nucleic Acids Research 38(14), pp. 4675-4686. (10.1093/nar/gkq242)

2009

• Yu, S. et al. 2009. ABF1-binding sites promote efficient global genome nucleotide excision repair. Journal of Biological Chemistry 284(2), pp. 966-973. (10.1074/jbc.M806830200)
• Teng, Y., Yu, S., Reed, S. H. and Waters, R. 2009. Lux ex tenebris: Nucleotide resolution DNA repair and nucleosome mapping. Methods 48(1), pp. 23-34. (10.1016/j.ymeth.2009.02.017)
• Waters, R., Teng, Y., Yu, Y., Yu, S. and Reed, S. H. 2009. Tilting at windmills? The nucleotide excision repair of chromosomal DNA. DNA Repair 8(2), pp. 146-152. (10.1016/j.dnarep.2008.11.001)

2008

• Teng, Y., Liu, H., Gill, H., Yu, Y., Waters, R. and Reed, S. H. 2008. Saccharomyces cerevisiae Rad16 mediates ultraviolet-dependent histone H3 acetylation required for efficient global genome nucleotide-excision repair. EMBO Reports 9(1), pp. 97-102. (10.1038/sj.embor.7401112)

2007

• Teng, Y., Liu, H., Gill, H., Yu, Y., Waters, R. and Reed, S. H. 2007. Saccharomyces cerevisiae Rad16 mediates UV dependent histone H3 acetylation required for efficient global genome nucleotide excision repair. Technical Report.

2006

• Reed, S. H., Waters, R., Yu, S. and Gillette, T. 2006. Distinct functions of the ubiquitin-proteasome pathway influence nucleotide excision repair. Embo J 25, pp. 2529-2538. (10.1038/sj.emboj.7601120)

2005

• Yu, Y., Teng, Y., Liu, H., Reed, S. H. and Waters, R. 2005. UV irradiation stimulates histone acetylation and chromatin remodeling at a repressed yeast locus. Proceedings of the National Academy of Sciences 102(24), pp. 8650-8655. (10.1073/pnas.0501458102)

2004

• Yu, S., Owen-Hughes, T., Friedberg, E. C., Waters, R. and Reed, S. H. 2004. The yeast Rad7/Rad16/Abf1 complex generates superhelical torsion in DNA that is required for nucleotide excision repair. DNA repair 3(3), pp. 277-287. (10.1016/j.dnarep.2003.11.004)

2001

• Gillette, T. G., Huang, W., Russell, S. J., Reed, S. H., Johnston, S. A. and Friedberg, E. C. 2001. The 19S complex of the proteasome regulates nucleotide excision repair in yeast. Genes & Development 15(12), pp. 1528-1539. (10.1101/gad.869601)