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2. Supplementary Table 1 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Summary of Patients and Clinical Data.

Published
2023

3. Supplementary Figures 1-6 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Supplementary Figure 1. Unsupervised Clustering on CCA samples. Supplementary Figure 2. Alterations Found in CCA Clusters. Supplementary Figure 3. MAP2K4 Homozygous Deletions and ERBB2 Amplifications. Supplementary Figure 4. Alterations Related to Structural Variations Found in CCAs. Supplementary Figure 5. FIREFLY Analysis of Pathways Systematically Dysregulated by Somatic Promoter Mutations that Alter Transcription Factor Binding. Supplementary Figure 6. Epigenetic Clusters and Mutation Signatures.

Published
2023

4. Supplementary Table 4 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Structural Variations across 71 WGS CCAs.

Published
2023

5. Supplementary Table 3 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Summary of CCA Alterations.

Published
2023

6. Supplementary Methods and Supplementary Figure and Table Legends from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Further details of methods, in addition to the supplementary figure and table legends.

Published
2023

7. Supplementary Table 2 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Alterations in CCA Clusters.

Published
2023

8. Supplementary Table 5 from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Author

Patrick Tan, Bin Tean Teh, Chawalit Pairojkul, Tatsuhiro Shibata, Steven G. Rozen, Raluca Gordân, Ludmil B. Alexandrov, Young Nyun Park, Hyungjin Rhee, André Luiz Vettore, André Lopes Carvalho, Di-Xian Luo, Jiaming Lai, Aldo Scarpa, Ming-Chin Yu, Sen-Yung Hsieh, Philippe Broet, Irinel Popescu, Dan G. Duda, Simona Dima, Kiat Hon Lim, London Lucien Peng Jin Ooi, Alexander Yaw Fui Chung, Pierce Kah-Hoe Chow, Satoshi Yamasaki, Yasuhito Arai, Hiromi Nakamura, Yasushi Totoki, Sopit Wongkham, Puangrat Yongvanit, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, John R. McPherson, Jia Liang Loh, Jing Tan, Tse Hui Lim, Alvin Soon Tiong Lim, Stefanus Lie, Vikneswari Rajasegaran, Choon Kiat Ong, Mo Liu, Arnoud Boot, Cedric Chuan Young Ng, Weng Khong Lim, Sanjanaa Nagarajan, Raynoo Thanan, Swe Swe Myint, Su Pin Choo, Ley Moy Ng, Alvin Wei Tian Ng, Sarinya Kongpetch, Vishwa Nellore, Nisha Padmanabhan, Mi Ni Huang, Jing Quan Lim, Chern Han Yong, Ioana Cutcutache, and Apinya Jusakul

Abstract

Coverage Statistics and List of Genes for Targeted Sequencing.

Published
2023

9. Modeling and Experimental Validation of Large Scale Fluorescence Sensor Networks

Author

Chris Dwyer and Vishwa Nellore

Subjects
0301 basic medicine, Fluorescence sensor, Computer science, Scale (descriptive set theory), 02 engineering and technology, Experimental validation, 021001 nanoscience & nanotechnology, Fluorescence, Signature (logic), 03 medical and health sciences, 030104 developmental biology, Histogram, Fluorescence microscope, 0210 nano-technology, Biological system, Spatial analysis
Abstract

Fluorescence microscopy is by far the dominant assay used to measure molecular scale interactions in a wide range of disciplines including biochemistry, biophysics, bioengineering, biomedical imaging and clinical diagnostics. However, the technique can probe only a small number of molecular interactions with previous attempts at detecting more than 11 fluorophores simultaneously resulting in barcodes that are too big for in vivo analysis, expensive and involve time-consuming detection schemes. Here, we create DNA self-assembled Resonance Energy Transfer networks that generate a unique time-resolved fluorescence signature when probed by a series of light pulses. An experimentally informed theoretical model predicts that networks containing up to 125 fluorophores may be distinguished from other extremely similar networks. Through the largest experimental survey of RET networks, we demonstrate that minor changes made to the RET network result in a unique, experimentally resolvable optical signature. We show that we can generate over 300 unique signatures using only 3 fluorophores. Furthermore, from 1296 time-resolved fluorescence signatures, we show that the optical signatures are reproducible 99.48% of the time. The ability to simultaneously detect multiple biological entities, the high spatial information density and the high repeatability of the synthetic RET networks will potentially find use in many biological and clinical applications.

Published
2017

10. Self-Assembled Resonance Energy Transfer Keys for Secure Communication over Classical Channels

Author

Vishwa Nellore, Chris Dwyer, and Sam Likun Xi

Subjects
Key generation, Authentication, Computer science, business.industry, Key space, General Engineering, General Physics and Astronomy, Key distribution, Nanotechnology, Quantum key distribution, Secure communication, General Materials Science, business, Key management, Communications protocol, Computer network
Abstract

Modern authentication and communication protocols increasingly use physical keys in lieu of conventional software-based keys for security. This shift is primarily driven by the ability to derive a unique, unforgeable signature from a physical key. The sole demonstration of an unforgeable key, thus far, has been through quantum key distribution, which suffers from limited communication distances and expensive infrastructure requirements. Here, we show a method for creating unclonable keys by molecular self-assembly of resonance energy transfer (RET) devices. It is infeasible to clone the RET-key due to the inability to characterize the key using current technology, the large number of input-output combinations per key, and the variation of the key's response with time. However, the manufacturer can produce multiple identical devices, which enables inexpensive, secure authentication and communication over classical channels, and thus any distance. Through a detailed experimental survey of the nanoscale keys, we demonstrate that legitimate users are successfully authenticated 99.48% of the time and the false-positives are only 0.39%, over two attempts. We estimate that a legitimate user would have a computational advantage of more than 10(340) years over an attacker. Our method enables the discovery of physical key based multiparty authentication and communication schemes that are both practical and possess unprecedented security.

Published
2015

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