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2024 Journal Article Applying hypergraphs to studies in quantitative biologyBarton, Samuel, Coster, Adelle, Donovan, Diane and Lefevre, James (2024). Applying hypergraphs to studies in quantitative biology. LIFE: International Journal of Health and Life-Sciences, 9, 21-33. doi: 10.20319/lijhls.2024.9.2133 |
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2023 Journal Article Hypergraphs and centrality measures identifying key features in gene expression dataBarton, Samuel, Broad, Zoe, Ortiz-Barrientos, Daniel, Donovan, Diane and Lefevre, James (2023). Hypergraphs and centrality measures identifying key features in gene expression data. Mathematical Biosciences, 366 109089, 1-14. doi: 10.1016/j.mbs.2023.109089 |
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2021 Journal Article Characterization of tissue types in basal cell carcinoma images via generative modeling and concept vectorsThomas, S. M., Lefevre, J. G., Baxter, G. and Hamilton, N. A. (2021). Characterization of tissue types in basal cell carcinoma images via generative modeling and concept vectors. Computerized Medical Imaging and Graphics, 94 101998, 101998. doi: 10.1016/j.compmedimag.2021.101998 |
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2021 Journal Article Non-melanoma skin cancer segmentation for histopathology datasetThomas, Simon M., Lefevre, James G., Baxter, Glenn and Hamilton, Nicholas A. (2021). Non-melanoma skin cancer segmentation for histopathology dataset. Data in Brief, 39 107587, 107587. doi: 10.1016/j.dib.2021.107587 |
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2021 Journal Article LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodiaLefevre, James G., Koh, Yvette W. H., Wall, Adam A., Condon, Nicholas D., Stow, Jennifer L. and Hamilton, Nicholas A. (2021). LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia. BMC Bioinformatics, 22 (1) 410, 1-26. doi: 10.1186/s12859-021-04324-z |
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2021 Journal Article Interpretable deep learning systems for multi-class segmentation and classification of non-melanoma skin cancerThomas, Simon M., Lefevre, James G., Baxter, Glenn and Hamilton, Nicholas A. (2021). Interpretable deep learning systems for multi-class segmentation and classification of non-melanoma skin cancer. Medical Image Analysis, 68 101915, 101915. doi: 10.1016/j.media.2020.101915 |
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2019 Journal Article Nephron progenitor commitment is a stochastic process influenced by cell migrationLawlor, Kynan T, Zappia, Luke, Lefevre, James, Park, Joo-Seop, Hamilton, Nicholas A, Oshlack, Alicia, Little, Melissa H and Combes, Alexander N (2019). Nephron progenitor commitment is a stochastic process influenced by cell migration. eLife, 8 e41156. doi: 10.7554/elife.41156 |
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2019 Journal Article Use of surrogate species to cost-effectively prioritize conservation actionsWard, Michelle, Rhodes, Jonathan R., Watson, James E.M., Lefevre, James, Atkinson, Scott and Possingham, Hugh P. (2019). Use of surrogate species to cost-effectively prioritize conservation actions. Conservation Biology, 34 (3) cobi.13430, 600-610. doi: 10.1111/cobi.13430 |
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2018 Journal Article Branching morphogenesis in the developing kidney 1 is not impacted by nephron formation or integrationShort, Kieran M., Combes, Alexander N., Lisnyak, Valerie, Lefevre, James G., Jones, Lynelle K., Little, Melissa H., Hamilton, Nicholas A. and Smyth, Ian M. (2018). Branching morphogenesis in the developing kidney 1 is not impacted by nephron formation or integration. eLife, 7 e38992. doi: 10.7554/eLife.38992 |
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2017 Journal Article Branching morphogenesis in the developing kidney is governed by rules that pattern the ureteric treeLefevre, James, Short, Kieran M, Lamberton, Timothy O, Michos, Odyssé, Graf, Daniel, Smyth, Ian M and Hamilton, Nicholas A (2017). Branching morphogenesis in the developing kidney is governed by rules that pattern the ureteric tree. Development (Cambridge, England), 144 (23), 4377-4385. doi: 10.1242/dev.153874 |
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2017 Journal Article Self-organisation after embryonic kidney dissociation is driven via selective adhesion of ureteric epithelial cellsLefevre, James G., Chiu, Han S., Combes, Alexander N., Vanslambrouck, Jessica M., Ju, Ali, Hamilton, Nicholas A. and Little, Melissa H. (2017). Self-organisation after embryonic kidney dissociation is driven via selective adhesion of ureteric epithelial cells. Development, 144 (6), 1087-1096. doi: 10.1242/dev.140228 |
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2016 Journal Article Analysed cap mesenchyme track data from live imaging of mouse kidney developmentLefevre, James G., Combes, Alexander N., Little, Melissa H. and Hamilton, Nicholas A. (2016). Analysed cap mesenchyme track data from live imaging of mouse kidney development. Data in Brief, 9, 149-154. doi: 10.1016/j.dib.2016.08.053 |
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2016 Journal Article Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tipCombes, Alexander N., Lefevre, James G., Wilson, Sean, Hamilton, Nicholas A. and Little, Melissa H. (2016). Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip. Developmental Biology, 418 (2), 297-306. doi: 10.1016/j.ydbio.2016.06.028 |
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2015 Journal Article A spatially-averaged mathematical model of kidney branching morphogenesisZubkov, V. S., Combes, A. N., Short, K. M., Lefevre, J. G., Hamilton, N. A., Smyth, I. M., Little, M. H. and Byrne, H. M. (2015). A spatially-averaged mathematical model of kidney branching morphogenesis. Journal of Theoretical Biology, 379, 24-37. doi: 10.1016/j.jtbi.2015.04.015 |
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2015 Journal Article Further biembeddings of twofold triple systemsDonovan, Diane M., Griggs, Terry S., Lefevre, James G. and McCourt, Thomas A. (2015). Further biembeddings of twofold triple systems. Ars Mathematica Contemporanea, 8 (2), 267-273. doi: 10.26493/1855-3974.415.ecd |
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2015 Journal Article Comparing and distinguishing the structure of biological branchingLamberton, Timothy O., Lefevre, James, Short, Kieram M., Smyth, Ian M. and Hamilton, Nicholas A. (2015). Comparing and distinguishing the structure of biological branching. Journal of Theoretical Biology, 365, 226-237. doi: 10.1016/j.jtbi.2014.10.001 |
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2014 Journal Article An integrated pipeline for the multidimensional analysis of branching morphogenesisCombes, Alexander N., Short, Kieran M., Lefevre, James, Hamilton, Nicholas A., Little, Melissa H. and Smyth, Ian M. (2014). An integrated pipeline for the multidimensional analysis of branching morphogenesis. Nature Protocols, 9 (12), 2859-2879. doi: 10.1038/nprot.2014.193 |
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2014 Journal Article Global quantification of tissue dynamics in the developing mouse kidneyShort, Kieran M., Combes, Alexander N., Lefevre, James, Ju, Adler L., Georgas, Kylie M., Lamberton, Timothy, Cairncross, Oliver, Rumballe, Bree A., McMahon, Andrew P., Hamilton, Nicholas A., Smyth, Ian M. and Little, Melissa H. (2014). Global quantification of tissue dynamics in the developing mouse kidney. Developmental Cell, 29 (2), 188-202. doi: 10.1016/j.devcel.2014.02.017 |
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2014 Journal Article Cortical F-actin stabilization generates apical–lateral patterns of junctional contractility that integrate cells into epitheliaWu, Selwin K., Gomez, Guillermo A., Michael, Magdalene, Verma, Suzie, Cox, Hayley L., Lefevre, James G., Parton, Robert G., Hamilton, Nicholas A., Neufeld, Zoltan and Yap, Alpha S. (2014). Cortical F-actin stabilization generates apical–lateral patterns of junctional contractility that integrate cells into epithelia. Nature Cell Biology, 16 (2), 167-178. doi: 10.1038/ncb2900 |
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2013 Journal Article Modelling cell turnover in a complex tissue during developmentLefevre, J., Marshall, D. J., Combes, A. N., Ju, A. L., Little, M. H. and Hamilton, N. A. (2013). Modelling cell turnover in a complex tissue during development. Journal of Theoretical Biology, 338, 66-79. doi: 10.1016/j.jtbi.2013.08.033 |
