Publications

Michael G Leeming, Andrew P Isaac, Luke Zappia, Richard A J O’Hair, William A Donald, Bernard J Pope (2020). HiTIME: An efficient model-selection approach for the detection of unknown drug metabolites in LC-MS data. SoftwareX.

Malte D Luecken, Maren Buttner, Kridsadakorn Chaichoompu, Anna Danese, Marta Interlandi, Michaela F Mueller, Daniel C Strobl, Luke Zappia, Martin Dugas, Maria Colome-Tatche, Fabian J Theis (2020). Benchmarking atlas-level data integration in single-cell genomics. bioRxiv.

Shanika L Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E Ritchie, Quentin Gouil (2020). Opportunities and challenges in long-read sequencing data analysis. Genome biology.

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Luke Zappia (2019). Tools and techniques for single-cell RNA sequencing data. PhD Thesis.

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Alexander N Combes, Belinda Phipson, Kynan T Lawlor, Aude Dorison, Ralph Patrick, Luke Zappia, Richard P Harvey, Alicia Oshlack, Melissa H Little (2019). Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development.

Santhosh V Kumar, Pei X Er, Kynan T Lawlor, Ali Motazedian, Michelle Scurr, Irene Ghobrial, Alexander N Combes, Luke Zappia, Alicia Oshlack, Edouard G Stanley, Melissa H Little (2019). Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells. Development.

Joel Z Ma, Wy Ching Ng, Luke Zappia, Linden J Gearing, Moshe Olshansky, Kym Pham, Karey Cheong, Arthur Hsu, Stephen J Turner, Odilia Wijburg, Sarah L Londrigan, Andrew G Brooks, Patrick C Reading (2019). Unique transcriptional architecture in airway epithelial cells and macrophages shapes distinct responses following influenza virus infection ex vivo. Journal of virology.

Alexander N Combes^, Luke Zappia^, Pei Xuan Er, Alicia Oshlack, Melissa H Little (2019). Single-cell analysis reveals congruence between kidney organoids and human fetal kidney. Genome medicine.

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Kynan T Lawlor, Luke Zappia, James Lefevre, Joo-Seop Park, Nicholas A Hamilton, Alicia Oshlack, Melissa H Little, Alexander Nicholas Combes (2019). Nephron progenitor commitment is a stochastic process influenced by cell migration. eLife.

Belinda Phipson, Pei X Er, Alexander N Combes, Thomas A Forbes, Sara E Howden, Luke Zappia, Hsan-Jan Yen, Kynan T Lawlor, Lorna J Hale, Jane Sun, Ernst Wolvetang, Minoru Takasato, Alicia Oshlack, Melissa H Little (2018). Evaluation of variability in human kidney organoids. Nature methods.

Luke Zappia, Alicia Oshlack (2018). Clustering trees: a visualization for evaluating clusterings at multiple resolutions. GigaScience.

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Luke Zappia, Belinda Phipson, Alicia Oshlack (2018). Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS computational biology.

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Luke Zappia, Belinda Phipson, Alicia Oshlack (2017). Splatter: simulation of single-cell RNA sequencing data. Genome Biology.

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Belinda Phipson, Luke Zappia, Alicia Oshlack (2017). Gene length and detection bias in single cell RNA sequencing protocols. F1000Research.

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