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2023 Journal Article Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinomaNguyen, Van-Chu, Nguyen, Trong Hieu, Phan, Thanh Hai, Tran, Thanh-Huong Thi, Pham, Thu Thuy Thi, Ho, Tan Dat, Nguyen, Hue Hanh Thi, Duong, Minh-Long, Nguyen, Cao Minh, Nguyen, Que-Tran Bui, Bach, Hoai-Phuong Thi, Kim, Van-Vu, Pham, The-Anh, Nguyen, Bao Toan, Nguyen, Thanh Nhan Vo, Huynh, Le Anh Khoa, Tran, Vu Uyen, Tran, Thuy Thi Thu, Nguyen, Thanh Dang, Phu, Dung Thai Bieu, Phan, Boi Hoan Huu, Nguyen, Quynh-Tho Thi, Truong, Dinh-Kiet, Do, Thanh-Thuy Thi, Nguyen, Hoai-Nghia, Phan, Minh-Duy, Giang, Hoa and Tran, Le Son (2023). Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinoma. BMC Cancer, 23 (1) 233, 1-17. doi: 10.1186/s12885-023-10681-0 |
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2023 Journal Article Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndromeThomson, Ella, Tran, Minh, Robevska, Gorjana, Ayers, Katie, van der Bergen, Jocelyn, Bhaskaran, Prarthna Gopalakrishnan, Haan, Eric, Cereghini, Silvia, Vash-Margita, Alla, Margetts, Miranda, Hensley, Alison, Nguyen, Quan, Sinclair, Andrew, Koopman, Peter and Pelosi, Emanuele (2023). Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome. Human Molecular Genetics, 32 (6), 1032-1047. doi: 10.1093/hmg/ddac262 |
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2023 Conference Publication Adversarial online multi-task reinforcement learningNguyen, Quan and Mehta, Nishant A. (2023). Adversarial online multi-task reinforcement learning. 34th International Conference on Algorithmic Learning Theory (ALT), Singapore, Singapore, 20-23 February 2023. San Diego, CA USA: Journal of Machine Learning Research. |
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2023 Other Outputs STimage datasetXiao Tan, Onkar Mulay and Quan Nguyen (2023). STimage dataset. The University of Queensland. (Dataset) doi: 10.48610/4fb74a9 |
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2023 Journal Article IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational studyShojaei, Maryam, Shamshirian, Amir, Monkman, James, Grice, Laura, Tran, Minh, Tan, Chin Wee, Teo, Siok Min, Rodrigues Rossi, Gustavo, McCulloch, Timothy R., Nalos, Marek, Raei, Maedeh, Razavi, Alireza, Ghasemian, Roya, Gheibi, Mobina, Roozbeh, Fatemeh, Sly, Peter D., Spann, Kirsten M., Chew, Keng Yih, Zhu, Yanshan, Xia, Yao, Wells, Timothy J., Senegaglia, Alexandra Cristina, Kuniyoshi, Carmen Lúcia, Franck, Claudio Luciano, dos Santos, Anna Flavia Ribeiro, Noronha, Lucia de, Motamen, Sepideh, Valadan, Reza, Amjadi, Omolbanin ... Tang, Benjamin (2023). IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study. Frontiers in Immunology, 13 1060438, 1-14. doi: 10.3389/fimmu.2022.1060438 |
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2023 Other Outputs A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung TissuesTan, Xiao and Nguyen, Quan (2023). A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung Tissues. The University of Queensland. (Dataset) doi: 10.48610/1bfc10c |
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2023 Journal Article Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblastsSathe, Anuja, Mason, Kaishu, Grimes, Susan M., Zhou, Zilu, Lau, Billy T., Bai, Xiangqi, Su, Andrew, Tan, Xiao, Lee, HoJoon, Suarez, Carlos J., Nguyen, Quan, Poultsides, George, Zhang, Nancy R. and Ji, Hanlee P. (2023). Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts. Clinical Cancer Research, 29 (1), 244-260. doi: 10.1158/1078-0432.ccr-22-2041 |
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2022 Journal Article Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y |
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2022 Conference Publication Exploratory data analysis of TCGA skin cutaneous melanoma RNA-seq dataZhang, Min, Arief, Vivi, McLachlan, Geoffrey, Nguyen, Quan and Basford, Kaye (2022). Exploratory data analysis of TCGA skin cutaneous melanoma RNA-seq data. Australasian Applied Statistics Conference (AASC), Inverloch, VIC Australia, 28 November - 2 December 2022. |
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2022 Journal Article Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of VietnamPham, Duy, Truong, Buu, Tran, Khai, Ni, Guiyan, Nguyen, Dat, Tran, Trang T. H., Tran, Mai H., Thuy, Duong Nguyen, Vo, Nam S. and Nguyen, Quan (2022). Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam. Briefings in Bioinformatics, 23 (6) bbac459. doi: 10.1093/bib/bbac459 |
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2022 Journal Article A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populationsNguyen, Dat Thanh, Tran, Trang T. H., Tran, Mai Hoang, Tran, Khai, Pham, Duy, Duong, Nguyen Thuy, Nguyen, Quan and Vo, Nam S. (2022). A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations. Scientific Reports, 12 (1) 17556, 1-13. doi: 10.1038/s41598-022-22215-y |
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2022 Journal Article The association between peptic ulcer disease and gastric cancer: results from the Stomach Cancer Pooling (StoP) Project ConsortiumParagomi, Pedram, Dabo, Bashir, Pelucchi, Claudio, Bonzi, Rossella, Bako, Abdulaziz T., Sanusi, Nabila Muhammad, Nguyen, Quan H., Zhang, Zuo-Feng, Palli, Domenico, Ferraroni, Monica, Vu, Khanh Truong, Yu, Guo-Pei, Turati, Federica, Zaridze, David, Maximovitch, Dmitry, Hu, Jinfu, Mu, Lina, Boccia, Stefania, Pastorino, Roberta, Tsugane, Shoichiro, Hidaka, Akihisa, Kurtz, Robert C., Lagiou, Areti, Lagiou, Pagona, Camargo, M. Constanza, Curado, Maria Paula, Lunet, Nuno, Vioque, Jesus, Boffetta, Paolo ... Luu, Hung N. (2022). The association between peptic ulcer disease and gastric cancer: results from the Stomach Cancer Pooling (StoP) Project Consortium. Cancers, 14 (19) 4905, 1-14. doi: 10.3390/cancers14194905 |
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2022 Journal Article A robust experimental and computational analysis framework at multiple resolutions, modalities and coveragesTran, M., Yoon, S., Teoh, M., Andersen, S., Lam, PY., Purdue, B. W., Raghubar, A., Hanson, S.J., Devitt, K., Jones, K., Walters, S., Monkman, J., Kulasinghe, A., Tuong, Z.K., Soyer, H.P., Frazer, I. H. and Nguyen, Q. (2022). A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Frontiers in Immunology, 13 911873, 911873. doi: 10.3389/fimmu.2022.911873 |
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2022 Journal Article Spatially resolved transcriptomes of mammalian kidneys illustrate the molecular complexity and interactions of functional nephron segmentsRaghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Crawford, Joanna, Lam, Pui Yeng, Andersen, Stacey B., Yoon, Sohye, Teoh, Siok Min, Matigian, Nicholas A., Stewart, Anne, Francis, Leo, Ng, Monica S. Y., Healy, Helen G., Combes, Alexander N., Kassianos, Andrew J., Nguyen, Quan and Mallett, Andrew J. (2022). Spatially resolved transcriptomes of mammalian kidneys illustrate the molecular complexity and interactions of functional nephron segments. Frontiers in Medicine, 9 873923, 873923. doi: 10.3389/fmed.2022.873923 |
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2022 Journal Article Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin RegionsNaval-Sanchez, Marina, Deshpande, Nikita, Tran, Minh, Zhang, Jingyu, Alhomrani, Majid, Alsanie, Walaa, Nguyen, Quan and Nefzger, Christian M. (2022). Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Frontiers in Molecular Biosciences, 9 900323, 1-15. doi: 10.3389/fmolb.2022.900323 |
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2022 Journal Article LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arraysNguyen, Dat Thanh, Nguyen, Quan Hoang, Duong, Nguyen Thuy and Vo, Nam S. (2022). LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays. Briefings in Bioinformatics, 23 (4) bbac252, 1-12. doi: 10.1093/bib/bbac252 |
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2022 Conference Publication Abstract 3817: A single-cell, spatial multiomics atlas and cellular interactome of all major skin cancer typesGrice, Laura, Ni, Guiyan, Jin, Xinnan, Tran, Minh, Killingbeck, Emily, Gregory, Mark, Mulay, Onkar, Teoh, Siok-Min, Kulasinghe, Arutha, Leon, Michael, Murphy, Sarah, Warren, Sarah, Kim, Youngmi and Nguyen, Quan (2022). Abstract 3817: A single-cell, spatial multiomics atlas and cellular interactome of all major skin cancer types. American Association for Cancer Research Annual Meeting, Philadelphia, PA, United States, 8-13 April 2022. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2022-3817 |
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2022 Conference Publication MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibitionVo, Tuan, Balderson, Brad, Jones, Kahli, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Ruitenberg, Marc, Robertson, Thomas, Bhuva, Dharmesh, Davis, Melissa, Wainwright, Brandon, Nguyen, Quan and Genovesi, Laura (2022). MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition. International Symposium on Pediatric Neuro-Oncology, Hamburg, Germany, 12–15 June 2022. Cary, NC, United States: Oxford University Press. doi: 10.1093/neuonc/noac079.381 |
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2022 Journal Article A deep learning model for molecular label transfer that enables cancer cell identification from histopathology imagesSu, Andrew, Lee, HoJoon, Tan, Xiao, Suarez, Carlos J., Andor, Noemi, Nguyen, Quan and Ji, Hanlee P. (2022). A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images. npj Precision Oncology, 6 (1) 14, 14. doi: 10.1038/s41698-022-00252-0 |
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2022 Conference Publication Cellular heterogeneity of pluripotent stem cell derived cardiomyocyte grafts is mechanistically linked to treatable arrhythmiasSelvakumar, D., Clayton, Z., Prowse, A., Dingwall, S., George, J., Shah, H., Paterson, H., Jeyaprakesh, P., Wu, Z., Campbell, T., Kotake, Y., Turnbull, S., Nguyen, Q., Grieve, S., Palpant, N., Pathan, F., Kizana, E., Kumar, S., Gray, P. and Chong, J. (2022). Cellular heterogeneity of pluripotent stem cell derived cardiomyocyte grafts is mechanistically linked to treatable arrhythmias. 70th Annual Scientific Meeting of the Cardiac Society of Australia and New Zealand, Gold Coast, QLD Australia, 11-14 August 2022. Chatswood, NSW Australia: Elsevier. doi: 10.1016/j.hlc.2022.06.004 |
