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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 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 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 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 |
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2021 Book Chapter scIVA: single cell database and tools for interactive visualisation and analysisCrowhurst, Liam M., Mulay, Onkar, Palpant, Nathan and Nguyen, Quan H. (2021). scIVA: single cell database and tools for interactive visualisation and analysis. Practical guide to life science databases. (pp. 191-205) edited by Imad Abugessaisa and Takeya Kasukawa. Singapore: Springer. doi: 10.1007/978-981-16-5812-9_10 |
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2021 Journal Article Prognostic value of early leukocyte fluctuations for recovery from traumatic spinal cord injuryJogia, Trisha, Lübstorf, Tom, Jacobson, Esther, Scriven, Elissa, Atresh, Sridhar, Nguyen, Quan H., Liebscher, Thomas, Schwab, Jan M., Kopp, Marcel A., Walsham, James, Campbell, Kate E. and Ruitenberg, Marc J. (2021). Prognostic value of early leukocyte fluctuations for recovery from traumatic spinal cord injury. Clinical and Translational Medicine, 11 (1) e272, e272. doi: 10.1002/ctm2.272 |
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2020 Journal Article Conserved epigenetic regulatory logic infers genes governing cell identityShim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001 |
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2020 Conference Publication 665 Spatial single-cell analysis of colorectal cancer tumour using multiplexed imaging mass cytometryTran, Minh, Su, Andrew, Lee, HoJoon, Cruz, Richard, Pflieger, Lance, Dean, Ashely, Nguyen, Quan, Ji, Hanlee and Rhodes, Terence (2020). 665 Spatial single-cell analysis of colorectal cancer tumour using multiplexed imaging mass cytometry. 35th Anniversary Annual Meeting (SITC 2020), Virtual, 11-14 November 2020. London, United Kingdom: BMJ Group. doi: 10.1136/jitc-2020-sitc2020.0665 |
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2020 Conference Publication Spatial Transcriptomics (ST): Integrating Molecular Profiles with Histomorphology in Kidney Tissue SectionsRaghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Lam, Pui Yeng, Crawford, Joanna, Andersen, Stacey, Yoon, Sohye, Holland, Samuel E., Francis, Leo, Combes, Alexander N., Kassianos, Andrew J., Healy, Helen G., Nguyen, Quan and Mallett, Andrew J. (2020). Spatial Transcriptomics (ST): Integrating Molecular Profiles with Histomorphology in Kidney Tissue Sections. Kidney Week, Online, 19-25 October 2020. Washington, DC United States: American Society of Nephrology. doi: 10.1681/asn.20203110s112b |
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2020 Journal Article Applying machine learning for integration of multi-modal genomics data and imaging data to quantify heterogeneity in tumour tissuesTan, Xiao, Su, Andrew T., Hajiabadi, Hamideh, Tran, Minh and Nguyen, Quan (2020). Applying machine learning for integration of multi-modal genomics data and imaging data to quantify heterogeneity in tumour tissues. Methods in Molecular Biology, 2190, 209-228. doi: 10.1007/978-1-0716-0826-5_10 |
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2020 Journal Article Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencingSenabouth, Anne, Andersen, Stacey, Shi, Qianyu, Shi, Lei, Jiang, Feng, Zhang, Wenwei, Wing, Kristof, Daniszewski, Maciej, Lukowski, Samuel W., Hung, Sandy S. C., Nguyen, Quan, Fink, Lynn, Beckhouse, Anthony, Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2020). Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing. NAR Genomics and Bioinformatics, 2 (2) lqaa034, 1-10. doi: 10.1093/nargab/lqaa034 |
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2020 Journal Article stLearn integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissuesPham, Duy, Tan, Xiao, Xu, Jun, Grice, Laura F., Lam, Pui Yeng, Raghubar, Arti, Vukovic, Jana, Ruitenberg, Marc J. and Nguyen, Quan (2020). stLearn integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues. Biorxiv, 1-18. doi: 10.1101/2020.05.31.125658v1 |
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2020 Journal Article Repopulating Microglia Promote Brain Repair in an IL-6-Dependent MannerWillis, Emily F., MacDonald, Kelli P. A., Nguyen, Quan H., Garrido, Adahir Labrador, Gillespie, Ellen R., Harley, Samuel B. R., Bartlett, Perry F., Schroder, Wayne A., Yates, Abi G., Anthony, Daniel C., Rose-John, Stefan, Ruitenberg, Marc J. and Vukovic, Jana (2020). Repopulating Microglia Promote Brain Repair in an IL-6-Dependent Manner. Cell, 180 (5), 833-846.e16. doi: 10.1016/j.cell.2020.02.013 |
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2019 Journal Article Genotype-free demultiplexing of pooled single-cell RNA-seqXu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7 |
