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High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos.
Mukashyaka, Patience; Kumar, Pooja; Mellert, David J; Nicholas, Shadae; Noorbakhsh, Javad; Brugiolo, Mattia; Courtois, Elise T; Anczukow, Olga; Liu, Edison T; Chuang, Jeffrey H Nature communications 2023 Dec;14(1):8406
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FANCM regulates repair pathway choice at stalled replication forks.
Panday, Arvind; Willis, Nicholas A; Elango, Rajula; Menghi, Francesca; Duffey, Erin E; Liu, Edison T; Scully, Ralph Molecular cell 2021 Apr;
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Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia.
Wang, Ping; Tang, Zhonghui; Lee, Byoungkoo; Zhu, Jacqueline Jufen; Cai, Liuyang; Szalaj, Przemyslaw; Tian, Simon Zhongyuan; Zheng, Meizhen; Plewczynski, Dariusz; Ruan, Xiaoan; Liu, Edison T; Wei, Chia-Lin; Ruan, Yijun Genome biology 2020 May;21(1):110
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Tumor Origins Through Genomic Profiles.
Liu, Edison T; Mockus, Susan M JAMA oncology 2019 Nov;
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High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts.
Kim, Hyunsoo; Kumar, Pooja; Menghi, Francesca; Noorbakhsh, Javad; Cerveira, Eliza; Ryan, Mallory; Zhu, Qihui; Ananda, Guruprasad; George, Joshy; Chen, Henry C; Mockus, Susan; Zhang, Chengsheng; Yang, Yan; Keck, James; Karuturi, R Krishna Murthy; Bult, Carol J; Lee, Charles; Liu, Edison T; Chuang, Jeffrey H Scientific reports 2018 Dec;8(1):17937
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Picky comprehensively detects high-resolution structural variants in nanopore long reads.
Gong, Liang; Wong, Chee-Hong; Cheng, Wei-Chung; Tjong, Harianto; Menghi, Francesca; Ngan, Chew Yee; Liu, Edison T; Wei, Chia-Lin Nature methods 2018 Apr;15455-460
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The tandem duplicator phenotype as a distinct genomic configuration in cancer.
Menghi, Francesca; Inaki, Koichiro; Woo, XingYi; Kumar, Pooja A; Grzeda, Krzysztof R; Malhotra, Ankit; Yadav, Vinod; Kim, Hyunsoo; Marquez, Eladio J; Ucar, Duygu; Shreckengast, Phung T; Wagner, Joel P; MacIntyre, George; Murthy Karuturi, Krishna R; Scully, Ralph; Keck, James; Chuang, Jeffrey H; Liu, Edison T Proceedings of the National Academy of Sciences of the United States of America 2016 Apr;113(17):E2373-82
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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun Cell 2015 Dec;163(7):1611-27
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Genomic alterations in BCL2L1 and DLC1 contribute to drug sensitivity in gastric cancer.
Park, Hansoo; Cho, Sung-Yup; Kim, Hyerim; Na, Deukchae; Han, Jee Yun; Chae, Jeesoo; Park, Changho; Park, Ok-Kyoung; Min, Seoyeon; Kang, Jinjoo; Choi, Boram; Min, Jimin; Kwon, Jee Young; Suh, Yun-Suhk; Kong, Seong-Ho; Lee, Hyuk-Joon; Liu, Edison T; Kim, Jong-Il; Kim, Sunghoon; Yang, Han-Kwang; Lee, Charles Proceedings of the National Academy of Sciences of the United States of America 2015 Oct;112(40):12492-12497
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Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.
Bertrand, Denis; Chng, Kern Rei; Sherbaf, Faranak Ghazi; Kiesel, Anja; Chia, Burton K H; Sia, Yee Yen; Huang, Sharon K; Hoon, Dave S B; Liu, Edison T; Hillmer, Axel; Nagarajan, Niranjan Nucleic acids research 2015 Jan;43(7):e44
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Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.
Buisine, Nicolas; Ruan, Xiaoan; Bilesimo, Patrice; Grimaldi, Alexis; Alfama, Gladys; Ariyaratne, Pramila; Mulawadi, Fabianus; Chen, Jieqi; Sung, Wing-Kin; Liu, Edison T; Demeneix, Barbara A; Ruan, Yijun; Sachs, Laurent M PloS one 2015 Jan;10(9):e0137526
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Systems consequences of amplicon formation in human breast cancer.
Inaki, Koichiro; Menghi, Francesca; Woo, Xing Yi; Wagner, Joel P; Jacques, Pierre-Étienne; Lee, Yi Fang; Shreckengast, Phung Trang; Soon, Wendy WeiJia; Malhotra, Ankit; Teo, Audrey S M; Hillmer, Axel M; Khng, Alexis Jiaying; Ruan, Xiaoan; Ong, Swee Hoe; Bertrand, Denis; Nagarajan, Niranjan; Karuturi, R Krishna Murthy; Miranda, Alfredo Hidalgo; Liu, Edison T Genome research 2014 Sep;24(10):1559-71
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Telomerase directly regulates NF-κB-dependent transcription.
Ghosh, Arkasubhra; Saginc, Gaye; Leow, Shi Chi; Khattar, Ekta; Shin, Eun Myong; Yan, Ting Dong; Wong, Marc; Zhang, Zhizhuo; Li, Guoliang; Sung, Wing-Kin; Zhou, Jianbiao; Chng, Wee Joo; Li, Shang; Liu, Edison; Tergaonkar, Vinay Nature cell biology 2012 Dec;14(12):1270-81
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Large-scale functional organization of long-range chromatin interaction networks.
Sandhu, Kuljeet Singh; Li, Guoliang; Poh, Huay Mei; Quek, Yu Ling Kelly; Sia, Yee Yen; Peh, Su Qin; Mulawadi, Fabianus Hendriyan; Lim, Joanne; Sikic, Mile; Menghi, Francesca; Thalamuthu, Anbupalam; Sung, Wing Kin; Ruan, Xiaoan; Fullwood, Melissa Jane; Liu, Edison; Csermely, Peter; Ruan, Yijun Cell reports 2012 Nov;2(5):1207-19
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Heterogeneous epigenetic regulation of TIMP3 in prostate cancer.
Shinojima, Toshiaki; Yu, Qiang; Huang, Sharon K; Li, Michelle; Mizuno, Ryuichi; Liu, Edison T; Hoon, Dave S B; Lessard, Laurent Epigenetics 2012 Nov;7(11):1279-89
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PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse.
Pott, Sebastian; Kamrani, Nima K; Bourque, Guillaume; Pettersson, Sven; Liu, Edison T PloS one 2012 Oct;7(10):e48102
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Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.
Yao, Fei; Ariyaratne, Pramila N; Hillmer, Axel M; Lee, Wah Heng; Li, Guoliang; Teo, Audrey S M; Woo, Xing Yi; Zhang, Zhenshui; Chen, Jieqi P; Poh, Wan Ting; Zawack, Kelson F B; Chan, Chee Seng; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D; Gao, Song; Nagarajan, Niranjan; Thoreau, Hervé; Shahab, Atif; Ruan, Xiaoan; Cacheux-Rataboul, Valère; Wei, Chia-Lin; Bourque, Guillaume; Sung, Wing-Kin; Liu, Edison T; Ruan, Yijun PloS one 2012 Sep;7(9):e46152
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Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells.
Györy, Ildiko; Boller, Sören; Nechanitzky, Robert; Mandel, Elizabeth; Pott, Sebastian; Liu, Edison; Grosschedl, Rudolf Genes & development 2012 Apr;26(7):668-82
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Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion.
Xu, Shuhua; Pugach, Irina; Stoneking, Mark; Kayser, Manfred; Jin, Li; Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Cutiongco-de la Paz, Eva Maria C; De Ungria, Maria Corazon A; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; San Lai, Poh; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi Proceedings of the National Academy of Sciences of the United States of America 2012 Mar;109(12):4574-9
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Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Li, Guoliang; Ruan, Xiaoan; Auerbach, Raymond K; Sandhu, Kuljeet Singh; Zheng, Meizhen; Wang, Ping; Poh, Huay Mei; Goh, Yufen; Lim, Joanne; Zhang, Jingyao; Sim, Hui Shan; Peh, Su Qin; Mulawadi, Fabianus Hendriyan; Ong, Chin Thing; Orlov, Yuriy L; Hong, Shuzhen; Zhang, Zhizhuo; Landt, Steve; Raha, Debasish; Euskirchen, Ghia; Wei, Chia-Lin; Ge, Weihong; Wang, Huaien; Davis, Carrie; Fisher-Aylor, Katherine I; Mortazavi, Ali; Gerstein, Mark; Gingeras, Thomas; Wold, Barbara; Sun, Yi; Fullwood, Melissa J; Cheung, Edwin; Liu, Edison; Sung, Wing-Kin; Snyder, Michael; Ruan, Yijun Cell 2012 Jan;148(1-2):84-98
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JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer.
Lee, Yi Fang; Miller, Lance David; Chan, Xiu Bin; Black, Michael A; Pang, Brendan; Ong, Chee Wee; Salto-Tellez, Manuel; Liu, Edison T; Desai, Kartiki V Breast cancer research : BCR 2012 Jan;14(3):R85
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HUGO Pan-Asian SNP Consortium. PanSNPdb: the Pan-Asian
SNP genotyping database.
Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, *Liu E, Tongsima S PLoS One 2011 Jun;6(6):e21451
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Self-assembled monolayer-assisted silicon nanowire biosensor for detection of protein-DNA interactions in nuclear extracts from breast cancer cell.
Zhang, Guo-Jun; Huang, Min Joon; Ang, Jun'An Jason; Liu, Edison T; Desai, Kartiki Vasant Biosensors & bioelectronics 2011 Mar;26(7):3233-9
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Identification of close relatives in the HUGO Pan-Asian SNP database.
Yang, Xiong; Xu, Shuhua; Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Paz, Eva Maria C Cutiongco-de la; Ungria, Maria Corazon A De; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi; Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Paz, Eva Maria C Cutiongco-de la; Ungria, Maria Corazon A De; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi PloS one 2011 Jan;6(12):e29502
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PanSNPdb: the Pan-Asian SNP genotyping database.
Ngamphiw, Chumpol; Assawamakin, Anunchai; Xu, Shuhua; Shaw, Philip J; Yang, Jin Ok; Ghang, Ho; Bhak, Jong; Liu, Edison; Tongsima, Sissades PloS one 2011 Jan;6(6):e21451
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Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.
Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi; Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Cutiongco-de la Paz, Eva Maria C; De Ungria, Maria Corazon A; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi PloS one 2011 Jan;6(4):e18312
