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Department of Biochemistry profile

Dr Chun Shen Lim

PositionPostdoctoral Fellow
DepartmentDepartment of Biochemistry
Research summaryGenomics and bioinformatics

Research

My research interests focus on protein expression and RNA biology. I completed my PhD studying the roles of introns under the supervision of Dr Chris Brown in the Department of Biochemistry. I have joined Dr Paul Gardner's group recently to create smart software that designs DNA sequences with synonymous codon changes in order to improve protein expression of a gene of interest. This project is funded by an MBIE Smart Idea.

Publications

Lim, C. S., Weinstein, B. N., Roy, S. W., & Brown, C. M. (2021). Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Molecular Biology & Evolution. Advance online publication. doi: 10.1093/molbev/msab094

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Nucleic Acids Research. Advance online publication. doi: 10.1093/nar/gkab175

Lim, C. S., Sozzi, V., Littlejohn, M., Yuen, L. K. W., Warner, N., Betz-Stablein, B., … Brown, C. M. (2021). Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microbial Genomics. Advance online publication. doi: 10.1099/mgen.0.000492

Chapman, L. M., Spies, N., Pai, P., Lim, C. S., Carroll, A., Narzisi, G., … Zook, J. M. (2020). A crowdsourced set of curated structural variants for the human genome. PLoS Computational Biology, 16(6), e1007933. doi: 10.1371/journal.pcbi.1007933

Tan, L. P., Tan, G. W., Sivanesan, V. M., Goh, S. L., Ng, X. J., Lim, C. S., … the Malaysian Nasopharyngeal Carcinoma Study Group. (2020). Systematic comparison of plasma EBV DNA, anti-EBV antibodies and miRNA levels for early detection and prognosis of Nasopharyngeal Carcinoma. International Journal of Cancer, 146, 2336-2347. doi: 10.1002/ijc.32656

Journal - Research Article

Lim, C. S., Weinstein, B. N., Roy, S. W., & Brown, C. M. (2021). Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Molecular Biology & Evolution. Advance online publication. doi: 10.1093/molbev/msab094

Lim, C. S., Sozzi, V., Littlejohn, M., Yuen, L. K. W., Warner, N., Betz-Stablein, B., … Brown, C. M. (2021). Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microbial Genomics. Advance online publication. doi: 10.1099/mgen.0.000492

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Nucleic Acids Research. Advance online publication. doi: 10.1093/nar/gkab175

Chapman, L. M., Spies, N., Pai, P., Lim, C. S., Carroll, A., Narzisi, G., … Zook, J. M. (2020). A crowdsourced set of curated structural variants for the human genome. PLoS Computational Biology, 16(6), e1007933. doi: 10.1371/journal.pcbi.1007933

Tan, L. P., Tan, G. W., Sivanesan, V. M., Goh, S. L., Ng, X. J., Lim, C. S., … the Malaysian Nasopharyngeal Carcinoma Study Group. (2020). Systematic comparison of plasma EBV DNA, anti-EBV antibodies and miRNA levels for early detection and prognosis of Nasopharyngeal Carcinoma. International Journal of Cancer, 146, 2336-2347. doi: 10.1002/ijc.32656

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Solubility-Weighted Index: Fast and accurate prediction of protein solubility. Bioinformatics. Advance online publication. doi: 10.1093/bioinformatics/btaa578

Lim, C. S., Wardell, S. J. T., Kleffmann, T., & Brown, C. M. (2018). The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Research, 46(9), 4575-4591. doi: 10.1093/nar/gky282

Lim, C. S., & Brown, C. M. (2016). Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element. RNA Biology, 13(9), 743-747. doi: 10.1080/15476286.2016.1166330

Lim, C. S., Goh, S. L., Kariapper, L., Krishnan, G., Lim, Y.-Y., & Ng, C. C. (2015). Inclusion bodies of recombinant Epstein–Barr virus capsid antigen p18 as potential immobilized antigens in enzyme immunoassays for detection of nasopharyngeal carcinoma. Clinica Chimica Acta, 448, 206-210. doi: 10.1016/j.cca.2015.07.008

Lim, K.-S., Tan, A.-H., Lim, C.-S., Chua, K.-H., Lee, P.-C., Ramli, N., … Ng, C.-C. (2015). R54C mutation of NOTCH3 gene in the first Rungus family with CADASIL. PLoS ONE, 10(8), e0135470. doi: 10.1371/ journal.pone.0135470

Lim, C. S., Goh, S. L., Krishnan, G., & Ng, C. C. (2014). Recombinant production of Epstein-Barr virus BZLF1 trans-activator and characterization of its DNA-binding specificity. Protein Expression & Purification, 95, 8-12. doi: 10.1016/j.pep.2013.11.007

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Journal - Research Other

Lim, C. S., & Brown, C. M. (2018). Know your enemy: Successful bioinformatic approaches to predict functional RNA structures in viral RNAs. Frontiers in Microbiology, 8, 2582. doi: 10.3389/fmicb.2017.02582

Lim, C. S., & Brown, C. (2017). A new class of ribozyme from hepatitis B virus. FEBS Journal, 284(8), 1182-1183. doi: 10.1111/febs.14062

Lim, C. S., Krishnan, G., Sam, C. K., & Ng, C. C. (2013). On optimizing the blocking step of indirect enzyme-linked immunosorbent assay for Epstein-Barr virus serology [Short communication]. Clinica Chimica Acta, 415, 158-161. doi: 10.1016/j.cca.2012.08.031

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