Physiology of Mutagenesis
University of Cambridge & MRC Cancer Unit

Dr. Gene CC Koh

Research Associate

Gene obtained his MSc from Universität Heidelberg with a major in (Computational) Systems Biology and trained in mass spectrometry-based proteomics under Ruedi Aebersold at ETH Zürich. Bored of the snow in Switzerland, he traded it for the rain in the UK to pursue his PhD at the University of Cambridge/Wellcome Trust Sanger Institute. His research interests lie primarily in the fields of DNA damage & repair, mutagenesis, NGS sequencing, as well as CRISPR/Cas9-based genome editing technologies. His work employs experimental model systems to delineate how mutational processes leave characteristic patterns in the genome. Particularly, he’s passionate about combining molecular biology techniques, such as CRISPR/Cas9, with ‘multi-omic’ technologies to understand the interplay between DNA damage and repair processes, and their roles in shaping the mutational landscape in human cancers. When he’s not editing cells in the lab, he’s likely wrestling with a piece of R code in front of his computer. Get in touch should you wish to brainstorm project ideas or just to chitchat (: He collects and grows rare, beautiful aroids plants in his living room and might have a few pictures to show you.

Published Works

  • Koh, G., Degasperi, A., Zou, X., Momen, S., & Nik-Zainal, S. (2021). Mutational signatures: emerging concepts, caveats and clinical applications. Nature reviews. Cancer, 10.1038/s41568-021-00377-7. Advance online publication. https://doi.org/10.1038/s41568-021-00377-7
  • Xueqing Zou, Gene Ching Chiek Koh, Arjun Scott Nanda, Andrea Degasperi, Katie Urgo, Theodoros I. Roumeliotis, Chukwuma A. Agu, Cherif Badja, Sophie Momen, Jamie Young, Tauanne Dias Amarante, Lucy Side, Glen Brice, Vanesa Perez-Alonso, Daniel Rueda, Celine Gomez, Wendy Bushell, Rebecca Harris, Jyoti S. Choudhary, Genomics England Research Consortium, Josef Jiricny, William C. Skarnes & Serena Nik-Zainal . (2021). A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nature Cancer. https://www.nature.com/articles/s43018-021-00200-0
  • Georgakopoulos-Soares, I., Koh, G., Momen, S. E., Jiricny, J., Hemberg, M., & Nik-Zainal, S. (2020). Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nature communications, 11(1), 1980. https://doi.org/10.1038/s41467-020-15901-w
  • Degasperi, A., Amarante, T. D., Czarnecki, J., Shooter, S., Zou, X., Glodzik, D., Morganella, S., Nanda, A. S., Badja, C., Koh, G., Momen, S. E., Georgakopoulos-Soares, I., Dias, J., Young, J., Memari, Y., Davies, H., & Nik-Zainal, S. (2020). A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Nature cancer, 1(2), 249–263. https://doi.org/10.1038/s43018-020-0027-5
  • Koh, G., Zou, X., & Nik-Zainal, S. (2020). Mutational signatures: experimental design and analytical framework. Genome biology, 21(1), 37. https://doi.org/10.1186/s13059-020-1951-5
  • Li, L., Koh, C. C., Reker, D., Brown, J. B., Wang, H., Lee, N. K., Liow, H. H., Dai, H., Fan, H. M., Chen, L., & Wei, D. Q. (2019). Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. Scientific reports, 9(1), 7703. https://doi.org/10.1038/s41598-019-43125-6
  • Petljak, M., Alexandrov, L. B., Brammeld, J. S., Price, S., Wedge, D. C., Grossmann, S., Dawson, K. J., Ju, Y. S., Iorio, F., Tubio, J., Koh, C. C., Georgakopoulos-Soares, I., Rodríguez-Martín, B., Otlu, B., O'Meara, S., Butler, A. P., Menzies, A., Bhosle, S. G., Raine, K., Jones, D. R., … Stratton, M. R. (2019). Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis. Cell, 176(6), 1282–1294.e20. https://doi.org/10.1016/j.cell.2019.02.012
  • Caron, E., Kowalewski, D. J., Chiek Koh, C., Sturm, T., Schuster, H., & Aebersold, R. (2015). Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Molecular & cellular proteomics : MCP, 14(12), 3105–3117. https://doi.org/10.1074/mcp.O115.052431
  • Guo, T., Kouvonen, P., Koh, C. C., Gillet, L. C., Wolski, W. E., Röst, H. L., Rosenberger, G., Collins, B. C., Blum, L. C., Gillessen, S., Joerger, M., Jochum, W., & Aebersold, R. (2015). Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature medicine, 21(4), 407–413. https://doi.org/10.1038/nm.3807
  • Rosenberger, G., Koh, C. C., Guo, T., Röst, H. L., Kouvonen, P., Collins, B. C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., Faini, M., Schubert, O. T., Faridi, P., Ebhardt, H. A., Matondo, M., Lam, H., Bader, S. L., Campbell, D. S., Deutsch, E. W., Moritz, R. L., … Aebersold, R. (2014). A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific data, 1, 140031. https://doi.org/10.1038/sdata.2014.31

Contact Us

Dr. Serena Nik-Zainal
MRC Cancer Unit
University of Cambridge
Hutchison/MRC Research Centre
Box 197
Cambridge Biomedical Campus
Cambridge
United Kingdom
CB2 0XZ

signal@medschl.cam.ac.uk