2025
1. Sharon Pei Yi Chan, Janice Jia Ni Goh, Wai Yee Wong, Nur Nadiah Bite Ismail, Baiwen Luo, Benjamin Jieming Chen, Brandon Xue Ming Phua, Xing Yi Woo, Tan Boon Toh, Edward Kai-Hua Chow, Valerie Shiwen Yang. Ex vivo drug testing identifies a novel drug pair in targeting soft tissue sarcoma. NPJ Precision Oncology 9: 83 (2025). https://doi.org/10.1038/s41698-025-00851-7
2024
1. Mark Yong Siang See*, Janice Jia Ni Goh*, Chen Ee Low, Chun En Yau, Whee Sze Ong, Ru Xin Wong, Nur Fazlin Mohamed Noor, Mohamed Haniffa Bin Hasan Mohamed, Jannatul Tajrin Suha, Alisa Noor Hidayah Sairi, Go Wei Lin, Xing Yi Woo, Valerie Shiwen Yang. Head and Neck Sarcoma Assessor (HaNSA) for treatment decisions using real-world data. ESMO Real World Data and Digital Oncology 5: 100069 (2024). DOl: 10.1016/j.esmorw.2024.100069
2. Sharon Pei Yi Chan, Baiwen Luo, Benjamin Jieming Chen, Andre Villanueva, Sam Xin Xiu, Benjamin Livingstone Farah, Nicholas Shannon, Chin-Ann Johnny Ong, Claramae Shulyn Chia, Ming-Hui Yong, Krishan Kumar, London Lucien Ooi, Timothy Kwang Yong Tay, Xing Yi Woo, Tan Boon Toh, Edward Kai-Hua Chow, Valerie Shiwen Yang. Ex vivo drug testing in an ultra-rare sarcoma reveals therapeutic vulnerability and resistance. medRxiv 2022.08.03.22278327; doi: https://doi.org/10.1101/2022.08.03.22278327
3. Brian S White, Xing Yi Woo*, Soner Koc, Todd Sheridan, Steven B Neuhauser, Shidan Wang, Yvonne A Evrard, John David Landua, R Jay Mashl, Sherri R Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W Evans, Matthew H Bailey, Yeging Chen, Min Xiao, Jill Rubinstein, Ali Foroughi pour, Lacey Elizabeth Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C Fields, Jacqueline L Mudd, Xiaowei Xu, Melinda G Hollingshead, Shahanawaz Jiwani, PDXNet consortium, Brandi Davis-Dusenbery, Tiffany A Wallace, Jeffrey A Moscow, James H Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S Chen Jr, Luis G Carvajal-Carmona, Alana L Welm, Bryan E Welm, Ramaswamy Govindan, Shunqiang Li, Michael A Davies, Jack A Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T Lewis, Carol J Bult, Dennis A Dean II, Jeffrey H Chuang. A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis. Cancer Research 84 (13): 2060-2072 (2024). https://doi.org/10.1158/0008-5472.CAN-23-1349
2022
1. Xing Yi Woo*, Anuj Srivastava*, Philip C. Mack*, Joel H. Graber*, Brian J. Sanderson, Michael W. Lloyd, Mandy Chen, Sergii Domanskyi, Regina Gandour-Edwards, Rebekah A. Tsai, James Keck, Mingshan Cheng, Margaret Bundy, Emily L. Jocoy, Jonathan W. Riess, William Holland, Stephen C. Grubb, James G. Peterson, Grace A. Stafford, Carolyn Paisie, Steven B. Neuhauser, R. Krishna Murthy Karuturi, Joshy George, Allen K. Simons, Margaret Chavaree, Clifford G. Tepper, Neal Goodwin, Susan D. Airhart, Primo N. Lara Jr., Thomas H. Openshaw, Edison T. Liu, David R. Gandara, Carol J. Bult. A Genomically and Clinically Annotated Patient Derived Xenograft (PDX) Resource for Preclinical Research in Non-Small Cell Lung Cancer. Cancer Research 82(22): 4126–4138 (2022). https://doi.org/10.1158/0008-5472.CAN-22-0948
2. Jennifer K Sargent, Mark A Warner, Benjamin E Low, Willian H Schott, Todd Hoffert, David Coleman, Xing Yi Woo, Todd Sheridan, Sonia Erattupuzha, Philipp P Henrich, Vivek M Philip, Jeffrey H. Chuang, Michael V. Wiles, and Muneer G Hasham. Genetically Diverse Mouse Platform to Xenograft Cancer Cells. Disease Models & Mechanisms 15(9): dmm049457 (2022). https://doi.org/10.1242/dmm.049457
3. Soner Koc, Michael W Lloyd, Jeffrey W Grover, Nan Xiao, Sara Seepo, Sai Lakshmi Subramanian, Manisha Ray, Christian Frech, John DiGiovanna, Phillip Webster, Steven Neuhauser, Anuj Srivastava, Xing Yi Woo, Brian J Sanderson, Brian White, Paul Lott, Lacey E Dobrolecki, Heidi Dowst, PDXNet Consortium, Yvonne A Evrard, Tiffany A Wallace, Jeffrey A Moscow, James H Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S Chen, Luis Carvajal-Carmona, Alana L Welm, Bryan E Welm, Michael T Lewis, Ramaswamy Govindan, Li Ding, Shunqiang Li, Meenhard Herlyn, Michael A Davies, Jack Roth, Funda Meric-Bernstam, Peter N Robinson, Carol J Bult, Brandi Davis-Dusenbery, Dennis A Dean, II, Jeffrey H Chuang. PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery, NAR Cancer 4(2), zcac014 (2022). https://doi.org/10.1093/narcan/zcac014
4. Katrin P Guillen, Maihi Fujita, Andrew J Butterfield, Sandra D Scherer, Matthew H Bailey, Zhengtao Chu, Yoko S DeRose, Ling Zhao, Emilio Cortes-Sanchez, Chieh-Hsiang Yang, Jennifer Toner, Guoying Wang, Yi Qiao, Xiaomeng Huang, Jeffery A Greenland, Jeffery M Vahrenkamp, David H Lum, Rachel E Factor, Edward W Nelson, Cindy B Matsen, Jane M Poretta, Regina Rosenthal, Anna C Beck, Saundra S Buys, Christos Vaklavas, John H Ward, Randy L Jensen, Kevin B Jones, Zheqi Li, Steffi Oesterreich, Lacey E Dobrolecki, Satya S Pathi, Xing Yi Woo, Kristofer C Berrett, Mark E Wadsworth, Jeffrey H Chuang, Michael T Lewis, Gabor T Marth, Jason Gertz, Katherine E Varley, Bryan E Welm, Alana L Welm. A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology. Nature Cancer 3, 232–250 (2022). https://doi.org/10.1038/s43018-022-00337-6
2021
1. Hua Sun, Song Cao, R. Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael Wendl, Sherri Davies, Matthew Bailey, Tina Primeau, Jeremy Hoog, Jacqueline Mudd, Dennis Dean,II, Rajesh Patidar, Lily Chen, Matthew Wyczalkowski, Reyka Jayasinghe, Fernanda Rodrigues, Nadezhda Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Van Tine, Cynthia Ma, Rebecca Aft, Katherine Fuh, Julie Schwarz, Jose Zevallos, Sidharth Puram, John DiPersio, The NCI PDXNet Consortium, Brandi Davis-Dusenbery, Matthew Ellis, Michael Lewis, Michael Davies, Meenhard Herlyn, Bingliang Fang, Jack Roth, Alana L Welm, Bryan Welm, Funda Meric-Bernstam, Feng Chen, Ryan Fields, Shunqiang Li, Ramaswamy Govindan, James Doroshow, Jeffrey Moscow, Yvonne Evrard, Jeffrey Chuang, Benjamin Raphael, and Li Ding. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment. Nature Communications 12, 5086 (2021). https://doi.org/10.1038/s41467-021-25177-3
2. Xing Yi Woo*, Jessica Giordano*, Anuj Srivastava, Zi-Ming Zhao, Michael W Lloyd, Roebi de Bruijn, Yun-Suhk Suh, Rajesh Patidar, Li Chen, Sandra Scherer, Matthew H Bailey, Chieh-Hsiang Yang, Emilio Cortes-Sanchez, Yuanxin Xi, Jing Wang, Jayamanna Wickramasinghe, Andrew V Kossenkov, Vito W Rebecca, Hua Sun, R Jay Mashl, Sherri R Davies, Ryan Jeon, Christian Frech, Jelena Randjelovic, Jacqueline Rosains, Francesco Galimi, Andrea Bertotti, Adam Lafferty, Alice C O’Farrell, Elodie Modave, Diether Lambrechts, Petra Ter Brugge, Violeta Serra, Elisabetta Marangoni, Rania El Botty, Hyunsoo Kim, Jong-Il Kim, Han-Kwang Yang, Charles Lee, Dennis A Dean, Brandi Davis-Dusenbery, Yvonne A Evrard, James H Doroshow, Alana L Welm, Bryan E Welm, Michael T Lewis, Bingliang Fang, Jack A Roth, Funda Meric-Bernstam, Meenhard Herlyn, Michael A Davies, Li Ding, Shunqiang Li, Ramaswamy Govindan, Claudio Isella, Jeffrey A Moscow, Livio Trusolino, Annette T Byrne, Jos Jonkers, Carol J Bult, Enzo Medico, Jeffrey H Chuang, PDXNET Consortium & EurOPDX Consortium. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nature Genetics 53, 86–99 (2021). https://doi.org/10.1038/s41588-020-00750-6
2020
1. Yvonne A. Evrard, Anuj Srivastava, Jelena Randjelovic, James H. Doroshow, Dennis A. Dean II, Jeffrey S. Morris and Jeffrey H. Chuang, The NCI PDXNet Consortium. Systematic establishment of robustness and standards in patient-derived xenograft experiments and analysis. Cancer Research 80(11):2286-2297 (2020). DOI: 10.1158/0008-5472.CAN-19-3101
2019
1. Xing Yi Woo*, Anuj Srivastava*, Joel H Graber*, Vinod Yadav, Vishal Kumar Sarsani, Al Simons, Glen Beane, Stephen Grubb, Guruprasad Ananda, Rangjiao Liu, Grace Stafford, Jeffrey H Chuang, Susan D Airhart, R Krishna Murthy Karuturi, Joshy George, Carol J Bult. Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. BMC Medical Genomics 12(1):92 (2019).
2017
1. Mo Jiang, Nicholas C. S. Kee, Xing Yi Woo, Li May Goh, Joshua D. Tice, Lifang Zhou, Reginald B. H. Tan, Charles F. Zukoski, Mitsuko Fujiwara, Zoltan K. Nagy, Paul J. A. Kenis, Richard D. Braatz. Role of Automatic Process Control in Quality by Design. Book chapter in Comprehensive Quality by Design for Pharmaceutical Product Development and Manufacture (2017).
2016
1. Francesca Menghi, Koichiro Inaki, Xing Yi Woo, Pooja A Kumar, Krzysztof R Grzeda, Ankit Malhotra, Vinod Yadav, Hyunsoo Kim, Eladio J Marquez, Duygu Ucar, Phung T Shreckengast, Joel P Wagner, George MacIntyre, Krishna R Murthy Karuturi, Ralph Scully, James Keck, Jeffrey H Chuang, Edison T Liu. The tandem duplicator phenotype as a distinct genomic configuration in cancer. Proceedings of the National Academy of Sciences 113(17): E2373-E2382 (2016). https://doi.org/10.1073/pnas.1520010113
2015
1. Yao F, Kausalya JP, Sia YY, Teo AS, Lee WH, Ong AG, Zhang Z, Tan JH, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S, Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PS, Chew EG, Nagarajan N, Jacques PÉ, So JB, Ruan X, Yeoh KG, Tan P, Sung WK, Hunziker W, Ruan Y, Hillmer AM. Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity. Cell Reports 12(2):272-285 (2015).
2. Sebastian Ribi, Daniel Baumhoer, Kristy Lee, Audrey SM Teo, Babita Madan, Kang Zhang, Wendy K Kohlmann, Fei Yao, Wah Heng Lee, Qiangze Hoi, Shaojiang Cai, Xing Yi Woo, Patrick Tan, Gernot Jundt, Jan Smida, Michaela Nathrath, Wing-Kin Sung, Joshua D Schiffman, David M Virshup, Axel M Hillmer. TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome. Oncotarget 6(10):7727-40 (2015).
2014
1. Koichiro Inaki*, Francesca Menghi*, Xing Yi Woo*, Joel P Wagner, Pierre-Étienne Jacques, Yi Fang Lee, Phung Trang Shreckengast, Wendy WeiJia Soon, Ankit Malhotra, Audrey SM Teo, Axel M Hillmer, Alexis Jiaying Khng, Xiaoan Ruan, Swee Hoe Ong, Denis Bertrand, Niranjan Nagarajan, R Krishna Murthy Karuturi, Alfredo Hidalgo Miranda, Edison T Liu. Systems consequences of amplicon formation in human breast cancer. Genome research 24(10): 1559-1571 (2014). http://www.genome.org/cgi/doi/10.1101/gr.164871.113
2012
1. N. Nagarajan, D. Bertrand, A.M. Hillmer, Z.J. Zang, F. Yao, P.-E. Jacques, A.S.M. Teo, I. Cutcutache, Z. Zhang, W.H. Lee, Y.Y. Sia, S. Gao, P.N. Ariyaratne, A. Ho, X.Y. Woo, L. Veeravali, C.K. Ong, N. Deng, K.V. Desai, C.C. Khor, M.L. Hibberd, A. Shahab, J. Rao, M. Wu, M. Teh, F. Zhu, S. Y Chin, B. Pang, J.B.Y. So, G. Bourque, R. Soong, W.-K. Sung, B.T. Teh, S. Rozen, X. Ruan, K.G. Yeoh, P.B.O. Tan, Y. Ruan. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biology 13(12):R115 (2012).
2. F. Yao, P.N. Ariyaratne, A.M. Hillmer, W.H. Lee, G. Li, A.S.M. Teo, X.Y. Woo, Z. Zhang, J.P. Chen, W. T. Poh, K.F.B. Zawack, C.S. Chan, S.T. Leong, S.C. Neo, P.S.D. Choi, S. Gao, N. Nagarajan, H. Thoreau, A. Shahab, X. Ruan, V. Cacheux-Rataboul, C.L. Wei, G. Bourque, W.-K. Sung, E.T. Liu, Y. Ruan. Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS ONE 7(9):e46152 (2012).
3. K.P. Ng, A.M. Hillmer, C.T.H. Chuah, W.C. Juan, T.K. Ko, A.S.M. Teo, P.N. Ariyaratne, N. Takahashi, K. Sawada, F. Yao, S. Soh, W.H. Lee, J.W.J. Huang, J.C. Allen Jr, X.Y. Woo, N. Nagarajan, V. Kumar, A. Thalamuthu, W.T. Poh, A.L. Ang, H.T. Mya, G.F. How, L.Y. Yang, L.P. Koh, B. Chowbay, C.-T. Chang, V.S. Nadarajan, W. J. Chng, H. Than, L.C. Lim, Y.T. Goh, S. Zhang, D. Poh, P. Tan, J.-E. Seet, M.-K. Ang, N.-M. Chau, Q.-S. Ng, D.S.W. Tan, M. Soda, K. Isobe, M.M. Nöthen, T.Y. Wong, A. Shahab, X. Ruan, V.Cacheux-Rataboul, W.-K. Sung, E.H. Tan, Y. Yatabe, H. Mano, R.A. Soo, T.M. Chin, W.-T. Lim, Y. Ruan and S.T. Ong. A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nature Medicine 18:521–528 (2012). https://doi.org/10.1038/nm.2713
2011
1. X.Y. Woo, R.B.H. Tan, and R.D. Braatz. Precise tailoring of the crystal size distribution by controlled growth and continuous seeding from impinging jet crystallizers. CrystEngComm 13:2006-2014 (2011).
2. A.M. Hillmer, F. Yao, K. Inaki, W.H. Lee, P.N. Ariyaratne, A.S. Teo, X.Y. Woo, Z. Zhang, H. Zhao, L. Ukil, J.P. Chen, F. Zhu, J.B. So, M. Salto-Tellez, W.T. Poh, K.F. Zawack, N. Nagarajan, S. Gao, G. Li, V. Kumar, H.P. Lim, Y.Y. Sia, C.S. Chan, S.T. Leong, S.C. Neo, P.S. Choi, H. Thoreau, P.B. Tan, A. Shahab, X. Ruan, J. Bergh, P. Hall, V. Cacheux-Rataboul, C.L. Wei, K.G. Yeoh, W.K. Sung, G. Bourque, E.T. Liu, Y. Ruan. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Research 21:676-687 (2011).
3. K. Inaki, A.M. Hillmer, L. Ukil, F. Yao, X.Y. Woo, L.A. Vardy, K.F. Zawack, C.W. Lee, P.N. Ariyaratne, Y.S. Chan, K.V. Desai, J. Bergh, P. Hall, T.C. Putti, W.L. Ong, A. Shahab, V. Cacheux-Rataboul, R.K. Karuturi, W.K. Sung, X. Ruan, G. Bourque, Y. Ruan, E.T. Liu. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Research 21:665-675 (2011).
2009
1. V.B. Vega, X.Y. Woo, H. Hamidi, H.C. Yeo, Z.X. Yeo, G. Bourque, ND Clarke. Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge. Annals of the New York Academy of Sciences 1158:215-23 (2009).
2. X.Y. Woo, Z.K. Nagy, R.B.H. Tan, and R.D. Braatz. Adaptive concentration control of cooling and antisolvent crystallization with laser backscattering measurement. Crystal Growth & Design 9:182-191 (2009).
3. X.Y. Woo, R.B.H. Tan, and R.D. Braatz. Modeling and computational fluid dynamics-population balance equation-micromixing simulation of impinging jet crystallizers. Crystal Growth & Design 9:156-164 (2009).
2008
1. N.C.S. Kee, X.Y. Woo, L.M. Goh, E. Rusli, G. He, V. Bhamidi, R.B.H. Tan, P.J.A. Kenis, C.F. Zukoski, and R.D. Braatz. Design of crystallization processes from laboratory research and development to the manufacturing scale: Parts I and II. American Pharmaceutical Review 11(6):110-115 and 11(7):66-74 (2008).
2. Z.K. Nagy, M. Fujiwara, X.Y. Woo, and R.D. Braatz. Determination of the kinetic parameters for the crystallization of paracetamol from water using metastable zone width experiments. Industrial & Engineering Chemistry Research 47:1245-1252 (2008).
2007
1. M.W. Hermanto, X.Y. Woo, R.D. Braatz and M.-S. Chiu. Robust optimal control of polymorphic transformation in batch crystallization. AIChE Journal, 53:2643-2650 (2007).
2006
1. X.Y. Woo, R.B.H. Tan, P.S. Chow, and R.D. Braatz. Simulation of mixing effects in antisolvent crystallization using a coupled CFD-PDF-PBE approach. Crystal Growth & Design, 6:1291-1303 (2006).
2. G.X. Zhou, M. Fujiwara, X.Y. Woo, E. Rusli, H.-H. Tung, C. Starbuck, O. Davidson, Z. Ge and R.D. Braatz. Direct design of pharmaceutical antisolvent crystallization through concentration control. Crystal Growth & Design, 6:892-898 (2006).