PE-Assembler: De novo assembler using short paired-end reads

by Ariyaratne, P.N., Sung, W.-K.
Published 2013

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

by Li, G., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.-S., Sung, W.-K., Fullwood, M.J., Wei, C.-L., Ruan, Y., Tennakoon, C.
Published 2011

Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

by Yao, F., Ariyaratne, P.N., Hillmer, A.M., Lee, W.H., Li, G., Teo, A.S.M., Woo, X.Y., Zhang, Z., Chen, J.P., Poh, W.T., Zawack, K.F.B., Chan, C.S., Leong, S.T., Neo, S.C., Choi, P.S.D., Gao, S., Nagarajan, N., Thoreau, H., Shahab, A., Ruan, X., Cacheux-Rataboul, V., Wei, C.-L., Bourque, G., Sung, W.-K., Liu, E.T., Ruan, Y.
Published 2014

Detection of chromosomal breakpoints in patients with developmental delay and speech disorders

by Utami K.H., Hillmer A.M., Aksoy I., Chew E.G.Y., Teo A.S.M., Zhang Z., Lee C.W.H., Chen P.J., Seng C.C., Ariyaratne P.N., Rouam S.L., Soo L.S., Yousoof S., Prokudin I., Peters G., Collins F., Wilson M., Kakakios A., Haddad G., Menuet A., Perche O., Tay S.K.H., Sung K.W.K., Ruan X., Ruan Y., Liu E.T., Briault S., Jamieson R.V., Davila S., Cacheux V.
Published 2018

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

by Sung, W.-K., Zheng, H., Li, S., Chen, R., Liu, X., Li, Y., Lee, N.P., Lee, W.H., Ariyaratne, P.N., Tennakoon, C., Mulawadi, F.H., Wong, K.F., Liu, A.M., Poon, R.T., Fan, S.T., Chan, K.L., Gong, Z., Hu, Y., Lin, Z., Wang, G., Zhang, Q., Barber, T.D., Chou, W.-C., Aggarwal, A., Hao, K., Zhou, W., Zhang, C., Hardwick, J., Buser, C., Xu, J., Kan, Z., Dai, H., Mao, M., Reinhard, C., Wang, J., Luk, J.M.
Published 2013

Whole-genome reconstruction and mutational signatures in gastric cancer

by Nagarajan N., Bertrand D., Hillmer A.M., Zang Z.J., Yao F., Jacques P., Teo A.S., Cutcutache I., Zhang Z., Lee W.H., Sia Y.Y., Gao S., Ariyaratne P.N., Ho A., Woo X.Y., Veeravali L., Ong C.K., Deng N., Desai K.V., Khor C.C., Hibberd M.L., Shahab A., Rao J., Wu M., Teh M., Zhu F., Chin S.Y., Pang B., So J.B., Bourque G., Soong R., Sung W.-K., Tean Teh B., Rozen S., Ruan X., Yeoh K.G., Tan P.B., Ruan Y.
Published 2018

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

by Hillmer, A.M., Yao, F., Inaki, K., Lee, W.H., Ariyaratne, P.N., Teo, A.S.M., Woo, X.Y., Zhang, Z., Zhao, H., Ukil, L., Chen, J.P., Zhu, F., So, J.B.Y., Salto-Tellez, M., Poh, W.T., Zawack, K.F.B., Nagarajan, N., Gao, S., Li, G., Kumar, V., Lim, H.P.J., Sia, Y.Y., Chan, C.S., Leong, S.T., Neo, S.C., Choi, P.S.D., Thoreau, H., Tan, P.B.O., Shahab, A., Ruan, X., Bergh, J., Hall, P., Cacheux-Rataboul, V., Wei, C.-L., Yeoh, K.G., Sung, W.-K., Bourque, G., Liu, E.T., Ruan, Y.
Published 2014

An oestrogen-receptor-α-bound human chromatin interactome

by Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., Chew, E.G.Y., Huang, P.Y.H., Han, Y., Ooi, H.S., Ariyaratne, P.N., Vega, V.B., Luo, Y., Tan, P.Y., Choy, P.Y., Wansa, K.D.S.A., Zhao, B., Lim, K.S., Leow, S.C., Yow, J.S., Joseph, R., Li, H., Desai, K.V., Thomsen, J.S., Lee, Y.K., Karuturi, R.K.M., Herve, T., Bourque, G., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Liu, E.T., Wei, C.-L., Cheung, E., Ruan, Y., Welboren, W.-J., Stunnenberg, H.G.
Published 2011

An oestrogen-receptor-α-bound human chromatin interactome

by Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., Chew, E.G.Y., Huang, P.Y.H., Welboren, W.-J., Han, Y., Ooi, H.S., Ariyaratne, P.N., Vega, V.B., Luo, Y., Tan, P.Y., Choy, P.Y., Wansa, K.D.S.A., Zhao, B., Lim, K.S., Leow, S.C., Yow, J.S., Joseph, R., Li, H., Desai, K.V., Thomsen, J.S., Lee, Y.K., Karuturi, R.K.M., Herve, T., Bourque, G., Stunnenberg, H.G., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Liu, E.T., Wei, C.-L., Cheung, E., Ruan, Y.
Published 2014

A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer

by Ng, K.P., Hillmer, A.M., Chuah, C.T.H., Juan, W.C., Ko, T.K., Teo, A.S.M., Ariyaratne, P.N., Takahashi, N., Sawada, K., Fei, Y., Soh, S., Lee, W.H., Huang, J.W.J., Allen Jr., J.C., Woo, X.Y., Nagarajan, N., Kumar, V., Thalamuthu, A., Poh, W.T., Ang, A.L., Mya, H.T., How, G.F., Yang, L.Y., Koh, L.P., Chowbay, B., Chang, C.-T., Nadarajan, V.S., Chng, W.J., Than, H., Lim, L.C., Goh, Y.T., Zhang, S., Poh, D., Tan, P., Seet, J.-E., Ang, M.-K., Chau, N.-M., Ng, Q.-S., Tan, D.S.W., Soda, M., Isobe, K., Nöthen, M.M., Wong, T.Y., Shahab, A., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Tan, E.H., Yatabe, Y., Mano, H., Soo, R.A., Chin, T.M., Lim, W.-T., Ruan, Y., Ong, S.T.
Published 2014

Assemblathon 1: A competitive assessment of de novo short read assembly methods

by Earl, D., Bradnam, K., St. John, J., Darling, A., Lin, D., Fass, J., Yu, H.O.K., Buffalo, V., Zerbino, D.R., Diekhans, M., Nguyen, N., Ariyaratne, P.N., Sung, W.-K., Ning, Z., Haimel, M., Simpson, J.T., Fonseca, N.A., Birol, I., Docking, T.R., Ho, I.Y., Rokhsar, D.S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M.C., Kelley, D.R., Phillippy, A.M., Koren, S., Yang, S.-P., Wu, W., Chou, W.-C., Srivastava, A., Shaw, T.I., Ruby, J.G., Skewes-Cox, P., Betegon, M., Dimon, M.T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F.J., Sharpe, T., Hall, G., Kersey, P.J., Durbin, R., Jackman, S.D., Chapman, J.A., Huang, X., DeRisi, J.L., Caccamo, M., Li, Y., Jaffe, D.B., Green, R.E., Haussler, D., Korf, I., Paten, B.
Published 2013