DNA and RNA  Editing (DaRE) Lab

33) Nguyen T.A.*, Heng J.W.J.*, Ng Y.T., Sun R., Fisher S., Oguz G., Kaewsapsak P., Xue S., Reversade B., Ramasamy A., Eisenberg E., and Tan M.H. (2023) Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus. BMC Biology21(1): 251.32)

32) Tan M.H. (2023) Identification of bona fide RNA editing sites: History, challenges, and opportunities. Accounts of Chemical Research56(21): 3033-3044.

31 Lee B.C.A., Tan M.H., and Chai C. (2022) Small-molecule enhancers of CRISPR-induced homology-directed repair in gene therapy: a medicinal chemist’s perspective. Drug Discovery Today27(9):2510-2525.

30) Nguyen T.A., Heng J.W.J.*, Kaewsapsak P.*, Kok E.P.L., Stanojević D., Liu H., Cardilla A., Praditya A., Yi Z., Lin M., Aw J.G.A., Ho Y.Y., Peh K.L.E., Wang Y., Zhong Q., Heraud-Farlow J., Xue S., Reversade B., Walkley C., Ho Y.S., Šikić M., Wan Y., and Tan M.H. (2022) Direct identification of A-to-I editing sites with nanopore native RNA sequencing. Nature Methods19(7): 833-844.

29) Ooi K.H., Liu M.M., Moo J.R., Nimsamer P., Payungporn S., Kaewsapsak P., and Tan M.H. (2022) A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV-2 detection in clinical samples. ACS Synthetic Biology11(1): 448-463.​

28) Beal J.†, Baldwin G.S.†, Farny N.G.†, Gershater M.†, Haddock-Angelli T.†, Buckley-Taylor R., Dwijayanti A., Kiga D., Lizarazo M., Marken J., de Mora K., Rettberg R., Sanchania V., Selvarajah V., Sison A., Storch M., Workman C.T., and iGEM Interlab Study Contributors. (2021) Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs. PLoS ONE16(6): e0252263.

27) Ooi K.H.*, Liu M.M.*, Tay J.W.D.*, Teo S.Y.*, Kaewsapsak P.*, Jin S., Lee C.K., Maurer-Stroh S., Yan B., Yan G., Gao Y.-G., and Tan M.H. (2021) An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nature Communications12(1):1739. (Featured article)

26) Aw J.G.A.*, Lim S.W.*, Wang J.X.*, Lambert F.R.P., Tan W.T., Shen Y., Zhang Y., Kaewsapsak P., Li C., Ng S.B., Vardy L.A., Tan M.H., Nagarajan N.†, and Wan Y.† (2021) Determination of isoform-specific RNA structure with nanopore long reads. Nature Biotechnology39(3): 336-346.

25) Srinivasan H., Kok E.P.L., and Tan M.H. (2021) RNA editing in human and mouse tissues. Methods in Molecular Biology2181:163-176.

24) Chin C.L.*, Goh J.B.*, Srinivasan H., Liu K.I., Gowher A., Shanmugam R., Lim H.L., Choo M., Tang W.Q., Tan A.H.-M., Nguyen-Khuong T., Tan M.H. †, and Ng S.K. † (2019) A human expression system based on HEK293 for the stable production of recombinant erythropoietin. Scientific Reports9(1):16768. 

23) Liu K.I., Sutrisnoh N.A.B., Wang Y., and Tan M.H. (2019) Genome editing in mammalian cell lines using CRISPR-Cas. Journal of Visualized Experiments146. doi: 10.3791/59086.

22) Teh M.Y.*, Ooi K.H.*, Teo S.X.D., Mansoor M.E.B., Lim W.Z.S., and Tan M.H. (2019) An expanded synthetic biology toolkit for gene expression control in Acetobacteraceae. ACS Synthetic Biology8(4): 708-723.

21) Shanmugam R.*, Zhang F.*, Srinivasan H., Charles Richard J.L., Liu K.I., Zhang X., Woo C.W.A., Chua Z.H.M., Buschdorf J.P., Meaney M.J., and Tan M.H. (2018) SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Research46(14): 7379-7395.

20) Beal J.*, Haddock-Angelli T.*, Baldwin G.*, Gershater M., Dwijayanti A., Storch M., de Mora K., Lizarazo M., Rettberg R., and iGEM Interlab Study Contributors. (2018) Quantification of bacterial fluorescence using independent calibrants. PLoS ONE13(6): e0199432.

19) Wang Y.*, Liu K.I.*, Sutrisnoh N.A.B., Srinivasan H., Zhang J., Li J., Zhang F., Charles R.J.L., Xing H., Shanmugam R., Foo J.N., Yeo H.T., Ooi K.H., Bleckwehl T., Par Y.Y.R., Lee S.M., Ismail N.N.B., Sanwari N.A.B., Lee S.T.V., Lew J., and Tan M.H. (2018) Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells. Genome Biology19: 62.

18) Liu K.I., Ramli M.N.B., Sutrisnoh N.A.B., and Tan M.H. (2018) Rapid control of genome editing in human cells by chemical-inducible CRISPR-Cas systems. Methods in Molecular Biology1772: 267-288. ​

17) Tan M.H.*†, Li Q.*, Shanmugam R., Piskol R., Kohler J., Young A.N., Liu K.I., Zhang R., Ramaswami G., Ariyoshi K., Gupte A., Keegan L.P., George C.X., Ramu A., Huang N., Pollina E.A., Leeman D., Rustighi A., Goh Y.P.S., The GTEx Consortium, Chawla A., Del Sal G., Peltz G., Brunet A., Conrad D.F., Samuel C.E., O’Connell M.A., Walkley C.R., Nishikura K., and Li J.B.† (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550: 249-254.

16) Shi S., Choi Y.W., Zhao H., Tan M.H., and Ang E.L.. (2017) Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae. Bioresource Technology 245 (Part B): 1343-1351.

​15) Choi Y.J.*, Lin C.P.*, Risso D.*, Chen S., Kim T.A., Tan M.H., Li J.B., Wu Y., Chen C., Xuan Z., MacFarlan T., Peng W., Lloyd K.C., Kim S.Y., Speed T.P., and He L. (2017) Deficiency of miRNA miR-34a expands cell fate potential of pluripotent stem cells. Science 355(6325): eaag1927.

​14) Liu K.I., Ramli M.N.B., Woo C.W.A., Wang Y., Zhao T., Zhang X., Yim G.R.D., Chong B.Y., Gowher A., Chua M.Z.H., Jung J., Lee J.H.J., and Tan M.H. (2016) A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing. Nature Chemical Biology ​​12(11): 980-987. (Cover article)​​ ​

13) Zheng M., Zhang H., Dill D.L., Clark J.D., Tu S., Yablonovitch A.L., Tan M.H., Zhang R., Rujescu D., Wu M., Tessarollo L., Vieira W., Gottesman M.M., Deng S., Eberlin L.S., Zare R.N., Billard J.-M., Gillet J.-P., Li J.B., and Peltz G. (2015) The role of Abcb5 alleles in susceptibility to haloperidol-induced toxicity in mice and humans. PLoS Medicine 12(1): e1001782.

​12) Zheng Q.*, Cai X.*, Tan M.H., Schaffert S., Arnold C.P., Gong X., Chen C.-Z., and Huang S. (2014) Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells. BioTechniques 57(3): 115-124.

​11) Kukurba K.R., Zhang R., Li X., Smith K.S., Knowles D.A., Tan M.H., Piskol R., Lek M., Snyder M., MacArthur D.G., Li J.B., and Montgomery S.B. (2014) Allelic expression of deleterious protein-coding variants across human tissues. PLoS Genetics 10(5): e1004304.

10) Tan M.H. and Li J.B.. (2013) Identification of RNA editing sites: a Survey of the Past, Present, and Future. In RNA Editing: Current Research and Future Trends (editor S. Maas). Horizon Press: Norwich.

9) Tan M.H.*, Au K.F.*, Leong D.E., Foygel K., Wong W.H., and Yao M.W.M. (2013) An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo. Molecular Systems Biology 9: 632.

8) Tan M.H.*†, Au K.F.*, Yablonovitch A.L.*, Wills A.E., Chuang J., Baker J.C., Wong W.H., and Li J.B.†. (2013) RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Research 23: 201–216.

7) Ramaswami G.*, Lin W.*, Piskol R.*, Tan M.H., Davis C., and Li J.B.. (2012) Accurate identification of human Alu and non-Alu RNA editing sites. Nature Methods 9: 579-581.

6) Lin W.*, Piskol R.*, Tan M.H., and Li J.B.. (2012) Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”. Science 335(6074): 1302.

5) Tan M.H., Kozdon J.B., Shen X., Shapiro L., and McAdams H.H.. (2010) An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation. Proc. Natl. Acad. Sci. USA 107(44): 18985-18990.

4) Jedrusik A., Bruce A.W.*, Tan M.H.*, Leong D.E., Skamagki M., Yao M., and Zernicka-Goetz M.. (2010) Maernally and zygotically provided Cdx2 have novel and critical roles for early development of the mouse embryo. Developmental Biology 344: 66-78.

3) McGrath P.T., Lee H., Zhang L., Iniesta A.A., Hottes A.K., Tan M.H., Hillson N.J., Hu P., Shapiro L., and McAdams H.H. (2007) High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nature Biotechnology 25(5): 584-592.

2) El-Naggar M.Y.*, Klamo
J.T.*, Tan M.H.*, and Hornung H.G.. (2004) Experimental verification of the Mach-number field in a supersonic Ludwieg tube. AIAA Journal 42(8): 1721-1724.

1) O’Reilly O.M. and Tan M.H. (2004) Steady motions of an axisymmetric satellite: An atlas of their bifurcations. International Journal of Nonlinear Mechanics 39(6): 921-940.

* Equal contributions
† Co-corresponding authors