The University of Queensland

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, 109089. doi: 10.1016/j.mbs.2023.109089

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

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

LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia

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

Interpretable deep learning systems for multi-class segmentation and classification of non-melanoma skin cancer

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

Branching morphogenesis in the developing kidney 1 is not impacted by nephron formation or integration

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

Self-organisation after embryonic kidney dissociation is driven via selective adhesion of ureteric epithelial cells

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

Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip

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

Cortical F-actin stabilization generates apical–lateral patterns of junctional contractility that integrate cells into epithelia

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.

Graphical trades

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

Trade spectrum of K4-e

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

Multi-latin squares

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

A discussion of constrained binary embeddings with applications to cryptanalysis of irregularly clocked stream ciphers

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.

A discussion of constrained binary embeddings with applications to cryptanalysis of irregularly clocked stream ciphers

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

Graphical trades

Lefevre, James (2005). Graphical trades. PhD Thesis, School of Physical Sciences, The University of Queensland. doi: 10.14264/2c5082b