Journal Article: Applying hypergraphs to studies in quantitative biology
Barton, 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
Journal Article: Hypergraphs and centrality measures identifying key features in gene expression data
Barton, 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
Journal Article: Characterization of tissue types in basal cell carcinoma images via generative modeling and concept vectors
Thomas, 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
A study of combinatorial problems and their applications
Doctor Philosophy
Pure and Applied Applications of Combinatorial Mathematics
Doctor Philosophy
Modelling Biological Systems using Mathematical Networks
Doctor Philosophy
Applying hypergraphs to studies in quantitative biology
Barton, 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
Hypergraphs and centrality measures identifying key features in gene expression data
Barton, 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
Thomas, 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
Non-melanoma skin cancer segmentation for histopathology dataset
Thomas, 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
Lefevre, 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
Thomas, 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
Nephron progenitor commitment is a stochastic process influenced by cell migration
Lawlor, 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
Use of surrogate species to cost-effectively prioritize conservation actions
Ward, 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
Short, 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
Branching morphogenesis in the developing kidney is governed by rules that pattern the ureteric tree
Lefevre, 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
Lefevre, 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
Analysed cap mesenchyme track data from live imaging of mouse kidney development
Lefevre, 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
Combes, 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
A spatially-averaged mathematical model of kidney branching morphogenesis
Zubkov, 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
Further biembeddings of twofold triple systems
Donovan, 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
Comparing and distinguishing the structure of biological branching
Lamberton, 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
An integrated pipeline for the multidimensional analysis of branching morphogenesis
Combes, 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
Global quantification of tissue dynamics in the developing mouse kidney
Short, 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
Wu, 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
Modelling cell turnover in a complex tissue during development
Lefevre, 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
Cyclic Biembeddings of Twofold Triple Systems
Donovan, Diane M., Griggs, Terry S., Lefevre, James G. and McCourt, Thomas A. (2013). Cyclic Biembeddings of Twofold Triple Systems. Annals of Combinatorics, 18 (1), 57-74. doi: 10.1007/s00026-013-0211-8
Defining Sets of Full Designs with Block Size Three II
Donovan, Diane, Lefevre, James, Waterhouse, Mary and Yazici, Emine Sule (2012). Defining Sets of Full Designs with Block Size Three II. Annals of Combinatorics, 16 (3), 507-515. doi: 10.1007/s00026-012-0143-8
Independent contrasts and PGLS regression estimators are equivalent
Blomberg, Simon P., Lefevre, James G., Wells, Jessie A. and Waterhouse, Mary (2012). Independent contrasts and PGLS regression estimators are equivalent. Systematic Biology, 61 (3), 382-391. doi: 10.1093/sysbio/syr118
Distinct equilateral triangle dissections of convex regions
Donovan, Diane M., Lefevre, James G., McCourt, Thomas A. and Cavenagh, Nicholas J. (2012). Distinct equilateral triangle dissections of convex regions. Commentationes Mathematicae Universitatis Carolinae, 53 (2), 189-210.
Identifying flaws in the security of critical sets in latin squares via triangulations
Donovan, Diane M., Lefevre, James G., McCourt, Thomas A., Cavenagh, Nicholas J. and Khodkar, Abdollah (2012). Identifying flaws in the security of critical sets in latin squares via triangulations. Australasian Journal of Combinatorics, 52, 243-268.
The spectrum of non-polychromatic equitable edge colored Steiner triple systems
Abueida, Atif A., Lefevre, James and Waterhouse, Mary (2012). The spectrum of non-polychromatic equitable edge colored Steiner triple systems. Journal of Combinatorial Mathematics and Combinatorial Computing, 80, 405-414.
The triangle intersection problem for nested Steiner triple systems
Billington, Elizabeth J., Donovan, Diane, Lefevre, James, McCourt, Thomas and Lindner, C. C. (2011). The triangle intersection problem for nested Steiner triple systems. Australasian Journal of Combinatorics, 51, 221-233.
Equitable edge colored Steiner triple systems
Abueida, Atif A., Lefevre, James and Waterhouse, Mary (2011). Equitable edge colored Steiner triple systems. Australasian Journal of Combinatorics, 50, 155-163.
The disjoint m-flower intersection problem for latin squares
Lefevre, James G. and McCourt, Thomas A. (2011). The disjoint m-flower intersection problem for latin squares. Electronic Journal of Combinatorics, 18 (1). doi: 10.37236/529
Self-embeddings of cyclic and projective Steiner quasigroups
Donovan, Diane M., Grannell, Mike J., Griggs, Terry S., Lefevre, James G. and McCourt, Thomas (2011). Self-embeddings of cyclic and projective Steiner quasigroups. Journal of Combinatorial Designs, 19 (1), 16-27. doi: 10.1002/jcd.20258
On defining sets of full designs
Lefevre, James and Waterhouse, Mary (2010). On defining sets of full designs. Discrete Mathematics, 310 (21), 3000-3006. doi: 10.1016/j.disc.2010.07.010
On parity vectors of Latin squares
Donovan, D. M., Grannell, M. J., Griggs, T. S. and Lefevre, J. G. (2010). On parity vectors of Latin squares. Graphs and Combinatorics, 26 (5), 673-684. doi: 10.1007/s00373-010-0942-9
Quarter-regular biembeddings of Latin squares
Donovan, D. M., Drápal, A., Grannell, M. J., Griggs, T. S. and Lefevre, J. G. (2010). Quarter-regular biembeddings of Latin squares. Discrete Mathematics, 310 (4), 692-699. doi: 10.1016/j.disc.2009.08.020
On defining sets of full designs with block size three
Donovan, D., Lefevre, J., Waterhouse, M. and Yazici, E. S. (2009). On defining sets of full designs with block size three. Graphs and Combinatorics, 25 (6), 825-839. doi: 10.1007/s00373-010-0882-4
A constraint on the biembedding of Latin squares
Lefevre, J. G., Donovan, D. M., Grannell, M. J. and Griggs, T. S. (2009). A constraint on the biembedding of Latin squares. European Journal of Combinatorics, 30 (2), 380-386. doi: 10.1016/j.ejc.2008.05.007
Some results on 2-perfect cube decompositions
Adams, Peter, Lefevre, James and Waterhouse, Mary (2009). Some results on 2-perfect cube decompositions. Australasian Journal of Combinatorics, 44, 95-103.
The volume and foundation of star trades
Lefevre, James G. (2008). The volume and foundation of star trades. Discrete Mathematics, 308 (11), 2059-2066. doi: 10.1016/j.disc.2007.04.054
Some 2-coloured 5-cycle decompositions
Waterhouse, Mary and Lefevre, James (2008). Some 2-coloured 5-cycle decompositions. The Journal of Combinatorial Mathematics and Combinatorial Computing, 64, 187-202.
On the spectrum of critical sets in latin squares of order 2n
Donovan, D. M., Lefevre, J. G. and Van Rees, G. H. J. (2008). On the spectrum of critical sets in latin squares of order 2n. Journal of Combinatorial Designs, 16 (1), 25-43. doi: 10.1002/jcd.20144
Six-cycle trades and a lower bound on the trade volumes of weakly connected graphs
Lefevre, James G. (2007). Six-cycle trades and a lower bound on the trade volumes of weakly connected graphs. Utilitas Mathematica, 72, 251-266.
Minimal and minimum size latin bitrades of each genus
Lefevre, J. G., Donovan, D. M., Cavenagh, N. and Drapal, A. (2007). Minimal and minimum size latin bitrades of each genus. Commentationes Mathematicae Universitatis Carolinae, 48 (2), 189-203.
Lefevre, James (2006). Graphical trades. Bulletin of The Australian Mathematical Society, 73 (3), 477-478. doi: 10.1017/S0004972700035486
Maximal triangle trades with foundation 5 (mod 6) - the final case
Lefevre, JG (2006). Maximal triangle trades with foundation 5 (mod 6) - the final case. Ars Combinatoria, 81 (-), 325-342.
Some equitably 3-colourable cycle decompositions of complete equipartite graphs
Lefevre, J and Waterhouse, M (2005). Some equitably 3-colourable cycle decompositions of complete equipartite graphs. Discrete Mathematics, 297 (-), 60-77. doi: 10.1016/j.disc.2005.03.021
Lefevre, JG (2005). Trade spectrum of K4-e. Graphs And Combinatorics, 21 (4), 475-488. doi: 10.1007/s00373-005-0633-0
Some equitably 3-colourable cycle decompositions
Adams, P, Bryant, D, Lefevre, J and Waterhouse, M (2004). Some equitably 3-colourable cycle decompositions. Discrete Mathematics, 284 (1-3), 21-35. doi: 10.1016/j.disc.2003.11.019
Steiner trade spectra of complete partite graphs
Lefevre, J. G. (2004). Steiner trade spectra of complete partite graphs. Discrete Mathematics, 288 (1-3), 89-98. doi: 10.1016/j.disc.2004.06.021
An integrated cell, tissue and whole organ profile of kidney morphogenesis
Combes, Alexander, Lefevre, James, Short, Kieran, Ju, Adler, Georgas, Kylie, Lamberton, Timothy, Cairncross, Oliver, Rumballe, Bree, McMahon, Andrew, Little, Melissa, Hamilton, Nicholas and Smyth, Ian (2017). An integrated cell, tissue and whole organ profile of kidney morphogenesis. 18th International Congress of Developmental Biology, Singapore, 18-22 June 2017. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.mod.2017.04.432
Disruption of cortical tension patterning drives the outgrowth of oncogenic cells
Wu, S., Gomez, G. A., Michael, M., Verma, S., Cox, H., Lefevre, J. G., Parton, R. G., Hamilton, N. A. and Yap, A. S. (2014). Disruption of cortical tension patterning drives the outgrowth of oncogenic cells. EACR-23: 23rd Biennial Congress of the European Association for Cancer Research, Munich, Germany, 5-8 July 2014. Oxford, United Kingdom: Elsevier. doi: 10.1016/S0959-8049(14)50251-1
An Integrated Cell, Tissue and Whole Organ Profile of Kidney Morphogenesis
Combes, A., Short, K., Lefevre, J., Ju, A., Georgas, K., Rumballe, B., Mcmahon, A., Hamilton, N., Smyth, I. and Little, M. (2013). An Integrated Cell, Tissue and Whole Organ Profile of Kidney Morphogenesis. 49th Annual Scientific Meeting of the Australian and New Zealand Society of Nephrology, Brisbane Australia, 9-11 September 2013. Richmond, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/nep.12121
Cavenagh, Nicholas, Hmlinen, Carlo, Lefevre, James G. and Stones, Douglas S. (2011). Multi-latin squares. 22nd British Combinatorial Conference, St Andrews Scotland, 6 - 10 July 2009. Amsterdam, The Netherlands: Elsevier BV * North-Holland. doi: 10.1016/j.disc.2010.06.026
Donovan, D. M., Lefevre, J. G. and Simpson, L. (2008). A discussion of constrained binary embeddings with applications to cryptanalysis of irregularly clocked stream ciphers. International Conference on Discrete Mathematics (ICDM 2006), Bangalore, India, 15-18 December 2006. Bangalore, India: Ramanujan Mathematical Society.
Permutation Representation of 3 and 4-Homogenous Latin Bitrades
Lefevre, J. G., Donovan, D. M. and Drapal, A. (2008). Permutation Representation of 3 and 4-Homogenous Latin Bitrades. Netherlands: IOS Press.
Donovan, D M, Lefevre, J G and Simpson, L (2006). A discussion of constrained binary embeddings with applications to cryptanalysis of irregularly clocked stream ciphers. International Conference on Discrete Mathematics 2006 (ICDM 2006), Banglaore, India, 15-18 December 2006. Bangalore: Indian Institute of Science.
Demonstration data for LLAMA open source analysis pipeline and visualiser publication
Lefevre, James and Cairncross, Oliver (2021). Demonstration data for LLAMA open source analysis pipeline and visualiser publication. The University of Queensland. (Dataset) doi: 10.14264/3084db2
Machine Learning Macropinocytosis
Lefevre, James (2019). Machine Learning Macropinocytosis. The University of Queensland. (Dataset) doi: 10.48610/dc2f523
Lefevre, James (2005). Graphical trades. PhD Thesis, School of Physical Sciences, The University of Queensland. doi: 10.14264/2c5082b
A study of combinatorial problems and their applications
Doctor Philosophy — Principal Advisor
Other advisors:
Pure and Applied Applications of Combinatorial Mathematics
Doctor Philosophy — Associate Advisor
Other advisors:
Modelling Biological Systems using Mathematical Networks
Doctor Philosophy — Associate Advisor
Other advisors:
Assessment of machine learning methods to discover novel models of gene networks to improve genomic prediction for plant breeding
Doctor Philosophy — Associate Advisor
Other advisors:
Deep Learning Methods For The Characterisation of Non-Melanoma Skin Cancer
(2022) Doctor Philosophy — Associate Advisor
(2010) Doctor Philosophy — Associate Advisor
Other advisors: