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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 |
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2021 Journal Article Resolving the immune landscape of human prostate at a single-cell level in health and cancerTuong, Zewen Kelvin, Loudon, Kevin W., Berry, Brendan, Richoz, Nathan, Jones, Julia, Tan, Xiao, Nguyen, Quan, George, Anne, Hori, Satoshi, Field, Sarah, Lynch, Andy G., Kania, Katarzyna, Coupland, Paul, Babbage, Anne, Grenfell, Richard, Barrett, Tristan, Warren, Anne Y., Gnanapragasam, Vincent, Massie, Charlie and Clatworthy, Menna R. (2021). Resolving the immune landscape of human prostate at a single-cell level in health and cancer. Cell Reports, 37 (12) 110132, 110132. doi: 10.1016/j.celrep.2021.110132 |
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2021 Journal Article Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkGrapotte, 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 (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7 |
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2021 Journal Article A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasiaTuong, Zewen K., Lukowski, Samuel W., Nguyen, Quan H., Chandra, Janin, Zhou, Chenhao, Gillinder, Kevin, Bashaw, Abate A., Ferdinand, John R., Stewart, Benjamin J., Teoh, Siok Min, Hanson, Sarah J., Devitt, Katharina, Clatworthy, Menna R., Powell, Joseph E. and Frazer, Ian H. (2021). A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia. iScience, 24 (11) 103326, 103326. doi: 10.1016/j.isci.2021.103326 |
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2021 Journal Article Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiationShen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006 |
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2021 Journal Article Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney diseaseTran, Ngan K., Lea, Rodney A., Holland, Samuel, Nguyen, Quan, Raghubar, Arti M., Sutherland, Heidi G., Benton, Miles C., Haupt, Larisa M., Blackburn, Nicholas B., Curran, Joanne E., Blangero, John, Mallett, Andrew J. and Griffiths, Lyn R. (2021). Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. Scientific reports, 11 (1) 19425, 19425. doi: 10.1038/s41598-021-98935-4 |
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2021 Journal Article Spatial omics and multiplexed imaging to explore cancer biologyLewis, Sabrina M., Asselin-Labat, Marie-Liesse, Nguyen, Quan, Berthelet, Jean, Tan, Xiao, Wimmer, Verena C., Merino, Delphine, Rogers, Kelly L. and Naik, Shalin H. (2021). Spatial omics and multiplexed imaging to explore cancer biology. Nature Methods, 18 (9), 997-1012. doi: 10.1038/s41592-021-01203-6 |
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2021 Journal Article scGPS: determining cell states and global fate potential of subpopulationsThompson, Michael, Matsumoto, Maika, Ma, Tianqi, Senabouth, Anne, Palpant, Nathan J., Powell, Joseph E. and Nguyen, Quan (2021). scGPS: determining cell states and global fate potential of subpopulations. Frontiers in Genetics, 12 666771, 666771. doi: 10.3389/fgene.2021.666771 |
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2021 Conference Publication Understanding the tumour immune microenvironment of stage III colorectal cancer using multiplexed imaging mass cytometryTran, Minh, Su, Andrew, Lee, HoJoon, Cruz, Richard, Pflieger, Lance, Dean, Ashely, Nguyen, Quan, Ji, Hanlee P. and Rhodes, Terence (2021). Understanding the tumour immune microenvironment of stage III colorectal cancer using multiplexed imaging mass cytometry. Royal College of Pathologists of Australasia - Pathology Update 2021, Sydney, NSW Australia, 2-4 July 2021. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.pathol.2021.06.063 |
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2021 Journal Article Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cellsSun, Xuan, Cao, Benjamin, Naval-Sanchez, Marina, Pham, Tony, Sun, Yu Bo Yang, Williams, Brenda, Heazlewood, Shen Y, Deshpande, Nikita, Li, Jinhua, Kraus, Felix, Rae, James, Nguyen, Quan, Yari, Hamed, Schröder, Jan, Heazlewood, Chad K, Fulton, Madeline, Hatwell-Humble, Jessica, Das Gupta, Kaustav, Kapetanovic, Ronan, Chen, Xiaoli, Sweet, Matthew J, Parton, Robert G, Ryan, Michael T, Polo, Jose M, Nefzger, Christian M and Nilsson, Susan K (2021). Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells. Nature Communications, 12 (1) 2665, 1-17. doi: 10.1038/s41467-021-22863-0 |
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2021 Journal Article Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cellsNeavin, Drew, Nguyen, Quan, Daniszewski, Maciej S., Liang, Helena H., Chiu, Han Sheng, Wee, Yong Kiat, Senabouth, Anne, Lukowski, Samuel W., Crombie, Duncan E., Lidgerwood, Grace E., Hernández, Damián, Vickers, James C., Cook, Anthony L., Palpant, Nathan J., Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2021). Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biology, 22 (1) 76, 1-19. doi: 10.1186/s13059-021-02293-3 |
