Selected publications
Computational Contributions
Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.
Tan, K.-T., Slevin, M.K., Leibowitz, M.L., Garrity-Janger, M., Li, H., and Meyerson, M. Cell Genomics (Accepted and in press). (2024).
Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres.
Tan, K.T., Slevin, M.K., Meyerson, M., and Li, H. Genome Biol. 23, 1–16. (2022).
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas.
Tan, K.T., Kim, H., Carrot-Zhang, J., Zhang, Y., Kim, W.J., Kugener, G., Wala, J.A., Howard, T.P., Chi, Y.Y., Beroukhim, R., Li, H., Ha, G., Alper, S.L., Perlman, E.J., Mullen, E.A., Hahn, W.C., Meyerson, M., and Hong, A.L. Genome Med. 13. (2021).
Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts.
Tan, K.T., Ding, L.W., Wu, C.S., Tenen, D.G., and Yang, H. Sci. Adv. 7. (2021).
Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines.
Tan, K.-T.*†, Ding, L.-W.*, Sun, Q.-Y.*, Lao, Z.-T., Chien, W., Ren, X., Xiao, J.-F., Loh, X.Y., Xu, L., Lill, M., Mayakonda, A., Lin, D.-C., Yang, H., and Koeffler, H.P. BMC Cancer 18. (2018).
Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement.
Ding, L.-W.*, Tan, K.-T.*†, Sun, Q.-Y.*, Lao, Z.-T., Yang, H., Jiang, N., Chien, W., Xiao, J.-F., Loh, X.-Y., Huang, M.-L., Lill, M., Lin, D.-C., Yeoh, A.E.J., and Koeffler, H.P. Br. J. Haematol. 184, 829–833. (2019).
Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD).
Sun, Q.Y.*, Ding, L.W.*, Tan, K.T.*†, Chien, W., Mayakonda, A., Lin, D.C., Loh, X.Y., Xiao, J.F., Meggendorfer, M., Alpermann, T., Garg, M., Lim, S.L., Madan, V., Hattori, N., Nagata, Y., Miyano, S., Yeoh, A.E.J., Hou, H.A., Jiang, Y.Y., Takao, S., Liu, L.Z., Tan, S.Z., Lill, M., Hayashi, M., Kinoshita, A., Kantarjian, H.M., Kornblau, S.M., Ogawa, S., Haferlach, T., Yang, H., and Koeffler, H.P. Leukemia 31. (2017).
Mutational profiling of a MonoMAC syndrome family with GATA2 deficiency.
Ding, L.W.*, Ikezoe, T.*, Tan, K.T.*†, Mori, M., Mayakonda, A., Chien, W., Lin, D.C., Jiang, Y.Y., Lill, M., Yang, H., Sun, Q.Y., and Koeffler, H.P. Leukemia 31. (2017).
Mutational landscape of pediatric acute lymphoblastic leukemia.
Ding, L.W.*, Sun, Q.Y.*, Tan, K.T.*†, Chien, W., Thippeswamy, A.M., Yeoh, A.E.J., Kawamata, N., Nagata, Y., Xiao, J.F., Loh, X.Y., Lin, D.C., Garg, M., Jiang, Y.Y., Xu, L., Lim, S.L., Liu, L.Z., Madan, V., Sanada, M., Fernández, L.T., Preethi, H., Lill, M., Kantarjian, H.M., Kornblau, S.M., Miyano, S., Liang, D.C., Ogawa, S., Shih, L.Y., Yang, H., and Koeffler, H.P. Cancer Res. 77. (2017).
Experimental contributions
RNA-binding protein RBM24 is required for sarcomere assembly and heart contractility.
Poon, K.L., Tan, K.T., Wei, Y.Y., Ng, C.P., Colman, A., Korzh, V., and Xu, X.Q. Cardiovasc. Res. 94, 418–427. (2012).3
Efficient production of superior dumbbell-shaped DNA minimal vectors for small hairpin RNA expression.
Yu, H., Jiang, X., Tan, K.T., Hang, L., and Patzel, V. Nucleic Acids Res. 43, e120–e120. (2015).
Global profiling of Rbm24 bound RNAs uncovers a multi-tasking RNA binding protein.
Lin, Y.*, Tan, K.T.*, Liu, J., Kong, X., Huang, Z., and Xu, X.Q. Int. J. Biochem. & Cell Biol. 94, 10–21. (2018).
Full publication list
[30] Human telomere length is chromosome specific and conserved across individuals.
Karimian, K., Groot, A., Huso, V., Kahidi, R., Tan, K.-T., Sholes, S., Keener, R., McDyer, J.F., Alder, J.K., Li, H., Rechtsteiner, A., and Greider, C.W. bioRxiv . (2024).
[29] Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly.
Mostovoy, Y., Boone, P.M., Huang, Y., Garimella, K. V, Tan, K.-T., Russell, B.E., Salani, M., Curall, B., Lucente, D., Bowers, T., DeSmet, T., Gabriel, S., Morton, C.C., Meyerson, M., Gusella, J., Quintero-Rivera, F., Brand, H., and Talkowski, M.E. bioRxiv. (2023).
[28] Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.
Tan, K.-T., Slevin, M.K., Leibowitz, M.L., Garrity-Janger, M., Li, H., and Meyerson, M. Cell Genomics (Accepted and in press) (2024).
[27] The genome sequence of the Large Scabious Mining Bee, Andrena hattorfiana (Fabricius, 1775).
Falk, S., Tan, K.-T., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, and Darwin Tree of Life Consortium Wellcome open Res. 8, 224. (2023).
[26] Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres.
Tan, K.T., Slevin, M.K., Meyerson, M., and Li, H. Genome Biol. 23, 1–16. (2022).
[25] Haplotype-resolved germline and somatic alterations in renal medullary carcinomas.
Tan, K.T., Kim, H., Carrot-Zhang, J., Zhang, Y., Kim, W.J., Kugener, G., Wala, J.A., Howard, T.P., Chi, Y.Y., Beroukhim, R., Li, H., Ha, G., Alper, S.L., Perlman, E.J., Mullen, E.A., Hahn, W.C., Meyerson, M., and Hong, A.L. Genome Med. 13. (2021).
[24] Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts.
Tan, K.T., Ding, L.W., Wu, C.S., Tenen, D.G., and Yang, H. Sci. Adv. 7. (2021).
[23] CSI NGS portal: an online platform for automated NGS data analysis and sharing.
An, O., Tan, K.-T., Li, Y., Li, J., Wu, C.-S., Zhang, B., Chen, L., and Yang, H. Int. J. Mol. Sci. 21, 3828. (2020).
[22] Profiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination.
Toh, J., Hoppe, M.M., Thakur, T., Yang, H., Tan, K.T., Pang, B., Ho, S., Roy, R., Ho, K.Y., Yeoh, K.G., Tan, P., Sundar, R., and Jeyasekharan, A. BMJ open Gastroenterol. 7, e000452. (2020).
[21] Next generation sequencing reveals novel mutations in mismatch repair genes and other cancer predisposition genes in Asian patients with suspected Lynch syndrome.
Ow, S.G.W., Tan, K.T., Yang, H., Yap, H.-L., Sapari, N.S.B., Ong, P.Y., Soong, R., and Lee, S.-C. Clin. Colorectal Cancer 18, e324–e334. (2019).
[20] Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm.
Kubota, S., Tokunaga, K., Umezu, T., Yokomizo-Nakano, T., Sun, Y., Oshima, M., Tan, K.T., Yang, H., Kanai, A., Iwanaga, E., and others Nat. Commun. 10, 1653. (2019).
[19] Mutational and transcriptomic profiling of acute leukemia of ambiguous lineage reveals obscure but clinically important lineage bias.
Lao, Z.-T., Ding, L.-W., An, O., Hattori, N., Sun, Q.-Y., Tan, K.-T., Mayakonda, A., Chuan, W.G., Madan, V., Lin, D.-C., and others Haematologica 104, e200. (2019).
[18] Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines.
Tan, K.-T.*†, Ding, L.-W.*, Sun, Q.-Y.*, Lao, Z.-T., Chien, W., Ren, X., Xiao, J.-F., Loh, X.Y., Xu, L., Lill, M., Mayakonda, A., Lin, D.-C., Yang, H., and Koeffler, H.P. BMC Cancer 18. (2018).
[17] Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement.
Ding, L.-W.*, Tan, K.-T.*†, Sun, Q.-Y.*, Lao, Z.-T., Yang, H., Jiang, N., Chien, W., Xiao, J.-F., Loh, X.-Y., Huang, M.-L., and others Br. J. Haematol. 184, 829–833. (2018).
[16] Global profiling of Rbm24 bound RNAs uncovers a multi-tasking RNA binding protein.
Lin, Y.*, Tan, K.T.*, Liu, J., Kong, X., Huang, Z., and Xu, X.Q. Int. J. Biochem. & Cell Biol. 94, 10–21. (2018).
[15] The c-MYC–BMI1 axis is essential for SETDB1-mediated breast tumourigenesis.
Xiao, J.F., Sun, Q.Y., Ding, L.W., Chien, W., Liu, X.Y., Mayakonda, A., Jiang, Y.Y., Loh, X.Y., Ran, X. Bin, Doan, N.B., Castor, B., Chia, D., Said, J.W., Tan, K.T., Yang, H., Fu, X.Y., Lin, D.C., and Koeffler, H.P. J. Pathol. 246, 89–102. (2018).
[14] Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD).
Sun, Q.Y.*, Ding, L.W.*, Tan, K.T.*†, Chien, W., Mayakonda, A., Lin, D.C., Loh, X.Y., Xiao, J.F., Meggendorfer, M., Alpermann, T., Garg, M., Lim, S.L., Madan, V., Hattori, N., Nagata, Y., Miyano, S., Yeoh, A.E.J., Hou, H.A., Jiang, Y.Y., Takao, S., Liu, L.Z., Tan, S.Z., Lill, M., Hayashi, M., Kinoshita, A., Kantarjian, H.M., Kornblau, S.M., Ogawa, S., Haferlach, T., Yang, H., and Koeffler, H.P. Leukemia 31. (2017).
[13] Mutational profiling of a MonoMAC syndrome family with GATA2 deficiency.
Ding, L.W.*, Ikezoe, T.*, Tan, K.T.*†, Mori, M., Mayakonda, A., Chien, W., Lin, D.C., Jiang, Y.Y., Lill, M., Yang, H., Sun, Q.Y., and Koeffler, H.P. Leukemia 31. (2017).
[12] Mutational landscape of pediatric acute lymphoblastic leukemia.
Ding, L.W.*, Sun, Q.Y.*, Tan, K.T.*†, Chien, W., Thippeswamy, A.M., Yeoh, A.E.J., Kawamata, N., Nagata, Y., Xiao, J.F., Loh, X.Y., Lin, D.C., Garg, M., Jiang, Y.Y., Xu, L., Lim, S.L., Liu, L.Z., Madan, V., Sanada, M., Fernández, L.T., Preethi, H., Lill, M., Kantarjian, H.M., Kornblau, S.M., Miyano, S., Liang, D.C., Ogawa, S., Shih, L.Y., Yang, H., and Koeffler, H.P. Cancer Res. 77. (2017).
[11] An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer.
Qi, L., Song, Y., Chan, T.H.M., Yang, H., Lin, C.H., Tay, D.J.T., Hong, H., Tang, S.J., Tan, K.T., Huang, X.X., and others Nucleic Acids Res. 45, 10436–10451. (2017).
[10] Diagnosis and relapse: cytogenetically normal acute myelogenous leukemia without FLT3-ITD or MLL-PTD.
Chien, W., Sun, Q.-Y., Ding, L.-W., Mayakonda, A., Takao, S., Liu, L., Lim, S.L., Tan, K.T., Garg, M., De Sousa Maria Varela, A., and others Leukemia 31, 762–766. (2017).
[9] Mutational profiling of acute lymphoblastic leukemia with testicular relapse.
Ding, L.-W., Sun, Q.-Y., Mayakonda, A., Tan, K.-T., Chien, W., Lin, D.-C., Jiang, Y.-Y., Xu, L., Garg, M., Lao, Z.-T., Lill, M., Yang, H., Yeoh, A.E.J., and Koeffler, H.P. J. Hematol. Oncol. 10, 65. (2017).
[8] ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer.
Chan, T.H.M., Qamra, A., Tan, K.T., Guo, J., Yang, H., Qi, L., Lin, J.S., Ng, V.H.E., Song, Y., Hong, H., Tay, S.T., Liu, Y., Lee, J., Rha, S.Y., Zhu, F., So, J.B.Y., Teh, B.T., Yeoh, K.G., Rozen, S., Tenen, D.G., Tan, P., and Chen, L. Gastroenterology 151, 637-650.e10. (2016).
[7] Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia.
Madan, V., Shyamsunder, P., Han, L., Mayakonda, A., Nagata, Y., Sundaresan, J., Kanojia, D., Yoshida, K., Ganesan, S., Hattori, N., Fulton, N., Tan, K.T., Alpermann, T., Kuo, M.C., Rostami, S., Matthews, J., Sanada, M., Liu, L.Z., Shiraishi, Y., Miyano, S., Chendamarai, E., Hou, H.A., Malnassy, G., Ma, T., Garg, M., Ding, L.W., Sun, Q.Y., Chien, W., Ikezoe, T., Lill, M., Biondi, A., Larson, R.A., Powell, B.L., Lübbert, M., Chng, W.J., Tien, H.F., Heuser, M., Ganser, A., Koren-Michowitz, M., Kornblau, S.M., Kantarjian, H.M., Nowak, D., Hofmann, W.K., Yang, H., Stock, W., Ghavamzadeh, A., Alimoghaddam, K., Haferlach, T., Ogawa, S., Shih, L.Y., Mathews, V., and Koeffler, H.P. Leukemia 30, 1672–1681. (2016).
[6] CEACAM6 is upregulated by Helicobacter pylori CagA and is a biomarker for early gastric cancer.
Roy, R.K., Hoppe, M.M., Srivastava, S., Samanta, A., Sharma, N., Tan, K.T., Yang, H., Voon, D.C., Pang, B., Teh, M., and others Oncotarget 7, 55290. (2016).
[5] Efficient production of superior dumbbell-shaped DNA minimal vectors for small hairpin RNA expression.
Yu, H., Jiang, X., Tan, K.T., Hang, L., and Patzel, V. Nucleic Acids Res. 43, e120–e120. (2015).
[4] Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse.
Garg, M., Nagata, Y., Kanojia, D., Mayakonda, A., Yoshida, K., Haridas Keloth, S., Zang, Z.J., Okuno, Y., Shiraishi, Y., Chiba, K., Tanaka, H., Miyano, S., Ding, L.-W., Alpermann, T., Sun, Q.-Y., Lin, D.-C., Chien, W., Madan, V., Liu, L.-Z., Tan, K.-T., Sampath, A., Venkatesan, S., Inokuchi, K., Wakita, S., Yamaguchi, H., Chng, W.J., Kham, S.-K.Y., Yeoh, A.E.-J., Sanada, M., Schiller, J., Kreuzer, K.-A., Kornblau, S.M., Kantarjian, H.M., Haferlach, T., Lill, M., Kuo, M.-C., Shih, L.-Y., Blau, I.-W., Blau, O., Yang, H., Ogawa, S., and Koeffler, H.P. Blood 126, 2491–2501. (2015).
[3] Establishment and characterization of novel human primary and metastatic anaplastic thyroid cancer cell lines and their genomic evolution over a year as a primagraft.
Garg, M., Okamoto, R., Nagata, Y., Kanojia, D., Venkatesan, S., M T, A., Braunstein, G.D., Said, J.W., Doan, N.B., Ho, Q., Akagi, T., Gery, S., Liu, L.-Z., Tan, K.T., Chng, W.J., Yang, H., Ogawa, S., and Koeffler, H.P. J. Clin. Endocrinol. Metab. 100, 725–735. (2015).
[2] Cardiomyocytes from Human Embryonic Stem Cells.
Xu, X.Q., Nandihalli, M., Tan, K.T., and Sun, W. Encycl. Mol. Cell Biol. Mol. Med. (2013). In Encyclopedia of Molecular Cell Biology and Molecular Medicine (Wiley-VCH Verlag GmbH & Co. KGaA).
[1] RNA-binding protein RBM24 is required for sarcomere assembly and heart contractility.
Poon, K.L., Tan, K.T., Wei, Y.Y., Ng, C.P., Colman, A., Korzh, V., and Xu, X.Q. Cardiovasc. Res. 94, 418–427. (2012).
*Equal contributions
†Led computational analysis
Full publication list: Google Scholar