RESEARCH DATA INTEGRATION

Data science is an important component of biomedical and translational research, where data of multiple modalities are being constantly generated at unprecedented scale. The Research Data Integration group in the Biomedical Datahub Division aims to bridge the complexity of computational biology and data science with the needs of biologists and clinicians to drive biological discoveries and predict translational outcomes. To achieve this goal, we are developing capabilities to analyze and integrate multi-omics, imaging and clinical data generated by biomedical institutes in A*STAR, clinical institutions and national platforms in Singapore to improve the usability and interpretability of large-scale multimodal datasets of cancer and other diseases.

Cancer is one of our disease focus in the Biomedical Datahub. Our group uses a wide range of computational, statistical, annotation and machine learning approaches to analyze largescale multi-modal datasets generated from cancer patients, xenografts, organoids and cell lines. We work closely with cancer biologists, bioinformaticians and clinicians to build clinical and experimental cancer data resources that can drive research analysis and inform treatment options in the clinic, thereby improving patient outcomes.

• Data coordination and infrastructure building for large-scale biomedical projects
  
• Development of analysis workflows, databases, visualization with disease expert knowledge for clinical data in a secured computing environment
  
• Protein structure analysis of cancer mutations
  
• AI analysis of cancer images
  
• Analysis and database development of public cancer datasets
  
• Harmonization of disease and drug vocabulary

• 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).


• 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). 


• 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). 


• 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).


• 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


• 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, ChiehHsiang 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).


• Yvonne A Evrard, Anuj Srivastava, Jelena Randjelovic, James H Doroshow, Dennis A Dean II, Jeffrey S Morris, Jeffrey H Chuang and 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


• 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).


• 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). DOI: 10.1073/pnas.1520010113


• 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). DOI: 10.1101/gr.164871.113