Journal articles and book chapters
K.J. Foster, S.J. Miklavcic (2014) On the competitive uptake and transport of ions through differentiated root tissues, Journal of Theoretical Biology, v340, p1-10.
K. Ip, N. Donoghue, M. K. Kim, and D. S. Lun, Constraint-based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids in Escherichia coli. Biotechol. Bioeng., to appear.
P. Kumar, C. Huang, J. Cai, S.J. Miklavcic (2014) Root phenotyping by root tip detection and classification through statistical learning, Plant and Soil, 380(1), 193-209.
P. Kumar, J. Cai, S.J. Miklavcic (2014) A complete system for 3D reconstruction of roots for phenotypic analysis, in Signal and Image Analysis for Biomedical and Life Sciences, Book Series: Advances in Experimental Medicine and Biology, Editors: C. Sun, T. Bednarz, T.D. Pham, P. Vallotton, and D. Wang, Springer.
H. Laga (2014) 3D Shape Classification and Retrieval Using Heterogeneous Features and Supervised Learning, in Machine Learning, Chapter 15, pp. 305-324. ISBN 978-953-7619-56-1, Hard cover,450 pages, Edited by: Abdelhamid Mellouk and Abdennacer Chebira, Publisher: IN-TECH, Jan 2009.
S.J. Miklavcic, M Nyden, J. Linden, J. Schulz (2014) Mathematically modelling competitive ion absorption in a polymer matrix, RSC Advances, 4, 60349–60362.
J. J. Kelley, A. Lane, X. Li, B. Mutthoju, S. Maor, D. Egen, and D. S. Lun. (2014) MOST: A software environment for constraint-based metabolic modeling and strain design. Bioinformatics, in press.
H. Laga, S. Kurtek, A. Srivastava, S.J. Miklavcic (2014) Landmark-free statistical analysis of the shape of plant leaves, Journal of Theoretical Biology, 363, 41-52.
F. Chevalier, K. Nieminen, J.C. Sánchez-Ferrero, M.L. Rodríguez, M. Chagoyen, C.S. Hardtke, P. Cubas (2014) Strigolactone Promotes Degradation of DWARF14, an α/β Hydrolase Essential for Strigolactone Signaling in Arabidopsis, The Plant Cell.
M.K. Kim, D.S. Lun (2014) Methods for integration of transcriptomic data in genome-scale metabolic models, Computational and Structural Biotechnology Journal, Available online 3 September 2014.
O. D. Makinde, R. J. Moitsheki, R. N. Jana, B. H. Bradshaw-Hajek, W. A. Khan (2014) Nonlinear fluid flow and heat transfer (editorial), Advances in Mathematical Physics, Art ID 719102, 2 pages.
C.S. Byrt, B. Xu, M. Krishnan, D.J. Lightfoot, A. Athman, A. K. Jacobs, N.S. Watson‐Haigh, D. Plett, R. Munns, M. Tester, M. Gilliham (2014), The Na+ transporter, TaHKT1; 5‐D, limits shoot Na+ accumulation in bread wheat, The Plant Journal, 80, 516-526.
Z. Jeknić, K. A Pillman, T. Dhillon, J. S Skinner, O. Veisz, A. Cuesta-Marcos, P. M Hayes, A. K. Jacobs, T. HH Chen, E. J Stockinger (2014), Hv-CBF2A overexpression in barley accelerates COR gene transcript accumulation and acquisition of freezing tolerance during cold acclimation, Plant molecular biology, 84, 67-82.
G. Safonova , E. Vinogradova, Y. Tuchkin (2014), Accurate impedance calculations for transmission lines with adjustable inner conductor, Microwave and Optic al Technology Letters, 56, 2066-2070.
C.Y.K. Fung, R. Sedev, J.N. Connor (2014), Wetting films: a technique for probing the microscopic meniscus using white light interferometry, Advanced Powder Technology, 25, 1171-1176.
O. Octoman, S. McLean, J.A. Sleep (2014) Children in foster care: What behaviours do carers find challenging?, Clincial Psychologist, 18 (1), p 10-20.
M Razzaghmanesh, S Beecham, C.J. Brien (2014) Developing resilient green roofs in a dry climate, Science of The Total Environment 490, 579-589.
A. Torokhti, A. Grant, S.J. Miklavcic (2014) Efficient compression of distributed information in estimation fusion, Electronic Notes of Discrete Mathematics (published online).
Refereed Conference Proceedings
A. L. Diaby, S.J. Miklavcic, J. Addai-Mensah (2014) “Planning and optimisation of scheduled cleaning of fouled heat exchanger networks under ageing using the genetic algorithm”, CHEMECA 2014, September 2014, Perth.
A. L. Diaby, S.J. Miklavcic, J. Addai-Mensah (2014) “Optimal cleaning schedule of fouled heat exchanger networks under the effect of ageing using the genetic algorithm: a modelling framework”, CHEMECA 2014, September 2014, Perth.
J. Cai (2014) The integration of images and Kinect depth maps for better quality of 3Dsurface reconstruction, ICARCV.
J. Cai (2014) Automatic lens distortion correction using single images by finding reliable lines for rectification, ICARCV.
P. Kumar, R. Matheyarasu, N. S. Bolan, S.J. Miklavcic (2014) “Phenotyping earthworms by image analysis” International Conference on Robotics and Computer Vision (ICARCV2014), December 2014, Singapore.
R. Matheyarasu, P. Kumar, R. Matheyarasu, B. Seshadri, N. S. Bolan, R.Naidu, S.J. Miklavcic (2014) Influence of abattoir wastewater irrigation on soil fertility and root phenotypes of two different plant species, 한국토양비료학회 학술발표회 초록집, 401-401.
P. Kumar, J. Connor, S.J. Miklavcic (2014) “Analysis of high-throughput 3D reconstruction of plant shoots for phenotyping” International Conference on Robotics and Computer Vision (ICARCV2014), December 2014, Singapore.
H. Laga, F. Shahinnia, and D. Fleury (2014) Image-based Plant Stomata Phenotyping. International Conference on Control, Automation, Robotics and Computer Vision (ICARCV) 2014.
L. Qiongyan, J. Cai, B. Berger, S.J. Miklavcic (2014) “Study on spike detection on cereal plants” International Conference on Robotics and Computer Vision (ICARCV2014), December 2014, Singapore.
U. Eck, F. Pankratz, G. Klinker, C. Sandor, H. Laga (2014) Comprehensive Workspace Calibration for Visuo-Haptic Augmented Reality. International Symposium on Mixed and Augmented Reality 2014.
S. Biasotti, H. Laga, M. Mortara, M. Spagnuolo (2014) Reasoning About Shape in Complex Datasets: Geometry, Structure and Semantics. Eurographics (Tutorials), t3, 2014.
S. Kurtek, H. Laga, Q. Xie (2014) Elastic Analysis of Boundaries of Planar Objects with Multiple Components and Arbitrary Topologies. Asian Conference on Computer Vision (ACCV) 2014.
S. Kurtek, M. Shen, H. Laga (2014) Elastic Reflection Symmetry Based Shape Descriptors. IEEE Winter Conference on Applications of Computer Vision WACV2014, pp. 293-300, 2014.
H. Tabia, H. Laga, D. Picard, P.-H. Gosselin (2014) Covariance Descriptors for 3D Shape Matching and Retrieval. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), 2014.
B.H. Bradshaw-Hajek, S.J. Miklavcic, D.A. Ward (2013) A composite Level Set and Extended-Domain-Eigenfunction Method for simulating 2D Stokes flow involving a free surface, Journal of Computational and Applied Mathematics, 237 (1), 389-402.
C.J. Brien, B. Berger, H. Rabie, M. Tester (2013) Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems, Plant Methods 9 (5).
J. Cai, S.J. Miklavcic (2013) Surface fitting for individual image thresholding and beyond, IET Image Processing, vol.7,no.6, pp.596-605.
J. Cai, S.J. Miklavcic (2013) Automatic curve selection for lens distortion correction using Hough transform energy, Proceedings of the IEEE Workshop on Applications of Computer Vision (WACV).
J. Cai (2013) Noise Estimation Using an MVDR-LIKE Approach for Acoustic Signal Enhancement, IET International Conference on Information and Communications Technologies, pp.150-158.
K.J. Foster, S.J. Miklavcic (2013) Mathematical modelling of the uptake and transport of salt in plant roots, Journal of Theoretical Biology, v336, pp 132-143.
P. Kumar, A. Dick (2013) Adaptive Earth Movers Distance based Bayesian Multi-Target Tracking, Journal of IET Computer Vision, Volume 7, Issue 4, p. 246 – 257.
P. Kumar, J. Cai, S.J. Miklavcic, 3D Reconstruction, Modelling and Analysis of in Situ Root Architecture, accepted MODSIM 2013.
P. Kumar, J. Cai, S.J. Miklavcic, Improved Ellipse Fitting By Considering the Eccentricity of Data Point Sets, Published International Conference on Image Processing, 2013.
H. Laga (2013) Graspable parts recognition in man-made 3d shapes, Computer Vision–ACCV 2012, Lecture Notes in Computer Science Volume 7725, pp 552-564.
H. Laga, M. Mortara, M. Spagnuolo (2013) Geometry and Context for Semantic Correspondences and Functionality Recognition in Manmade 3D Shapes. ACM Transactions on Graphics (presented at Siggraph 2014), 32(5).
H. Laga, S.J. Miklavcic. Curve-based Stereo Matching for 3D Modeling of Plants. Accepted for publication at the International Congress on Modelling and Simulation (MODSIM) 2013.
H. Laga, S. Kurtek, A. Srivastava, S.J. Miklavcic, Statistical Shape Models of Plant Leaves. International Conference on Image Processing (ICIP) 2013.
H. Rabie, N Flournoy (2013) Optimal designs for contingent response models with application to toxicity–efficacy studies, Journal of Statistical Planning and Inference, 143 (8).
J.A. Sleep, A.W. Schreiber, U. Baumann (2013) Sequencing error correction without a reference genome, BMC Bioinformatics, 14, 367.
J. Aarao, S.J. Miklavcic, D.A. Ward, (2013) Extended-domain-eigenfunction method (EDEM): a study of ill-posedness and regularization, J. Phys. A: Math. Theor. 46
C.G.B. Demétrio, J.F.M. Menten, R.A. Leandro and C.J. Brien. (2013) Experimental power considerations - justifying replication for animal care and use committees. Poultry Science, 92 (9): 2490-2497.
S. Kurtek, A. Srivastava, E. Klassen, and H. Laga. (2013) Landmark-Guided Elastic Shape Analysis of Spherically-Parameterized Surfaces. Computer Graphics Forum, (Proceedings of Eurographics 2013). 32(2), pp. 429-438, 2013.
R.J. Moitsheki, B.H. Bradshaw-Hajek (2013) Symmetry analysis of a heat conduction model for heat transfer in a longitudinal rectangular fin of a heterogeneous material, Communications in Nonlinear Science and Numerical Simulation, Volume 18, Issue 9, Pages 2374-2387
H Tabia, D Picard, H. Laga, P.-H. Gosselin, Compact Vectors of Locally Aggregated Tensors for 3D shape retrieval, Eurographics Workshop on 3D Object Retrieval (3DOR), pp. 17-24, 2013.
H. Tabia, D. Picard, H. Laga, P.-H. Gosselin. 3D Shape Similarity Computing Using Vectors of Locally Aggregated Tensors. International Conference on Image Processing (ICIP) 2013.
H. Tabia, D. Picard, H. Laga, P.-H. Gosselin. Fast Approximation of Distance Between Elastic Curves using Kernels. British Machine Vision Conference (BMVC) 2013.
A. Torokhti, P. Howlett, and H. Laga. Robust Estimation of Large Data Sets: an Almost Blind Case. European Conference on Data Analysis (ECDA) 2013.
A. Torokhti, P. Howlett, and H. Laga . Filtering of Large Signal Sets: an Almost Blind Case. The Eighth International Multi-Conference on Computing in Global Information Technology ICCGI, pp. 101-105, 2013.
C.J. Brien, R.A. Bailey, T.T. Tran, and J. Boland, (2012) Quasi-Latin designs. Electronic Journal of Statistics, 6, 1900-1925.
C.J. Brien, (2012) Comments on 'Therapist variation within randomized trials of psychotherapy: Implications for precision, internal and external validity', Statistical Methods in Medical Research, April 2012, vol. 21 no. 2 215-216
C.J. Brien, (2012) Contribution to the discussion of Optimum design of experiments for statistical inference. Journal of the Royal Statistical Society, Series C, 61, 379.
J. Cai, (2012) Integration of Optical Flow and Dynamic Programming for Stereo Matching, IET Image Processing, 6 (3), 205-212.
J. Cai, (2012) Robust Filtering-Based Thinning Algorithm for Pattern Recognition, The Computer Journal, v55
J. Cai, M. Cespedes, (2012) Plant temperature measurement and analysis from infrared images, Proceedings of the 27th Conference on Image and Vision Computing New Zealand IVCNZ 2012, 406-411.
J. Cai, S.J. Miklavcic, (2012) Automated extraction of three-dimensional cereal plant structures from two-dimensional orthographic images, IET Image Processing,6 (6), 687-696.
J. Cai, S.J. Miklavcic, (2012) The Generation of Digital Terrain Models from LiDAR Data using Seeding and Filtering and Its Application to Flood Modelling, Proceedings of the International Conference on Multimedia Technology, 2011.
M.R. Golzarian, M.-K. Lee, J.M.A. Desbiolles, (2012) Evaluation of color indices for improved segmentation of plant images. Transactions of the ASABE, v55(1): 261-273.
B-.L. Huynh, D.E. Mather, A.W. Schreiber, et al. (2012) Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley, Plant Molecular Biology
P. Kumar, J. Cai, S.J. Miklavcic (2012) Automated detection of root crowns using Gaussian Mixture Models and Bayesian classification, accepted for publication in the proceedings of DICTA 2012.
P. Kumar, J. Cai, S.J. Miklavcic(2012) High-throughput 3D modelling of plants for phenotypic analysis, was accepted for publication in the proceedings of IVCNZ 2012.
P. Kumar, J. Cai, S.J. Miklavcic(2012) Root crown detection using statistics of Zernike moments, was accepted for publication in the proceedings of ICARCV 2012.
H. Laga, S. Kurtek, A. Srivastava, M.R. Golzarian, and S.J. Miklavcic (2012) A Riemannian elastic metric for shape-based plant leaf classification, Proceedings of DICTA2012.
H. Laga. (2012). Graspable parts recognition in man-made 3D shapes, Proceedings of the Asian Conference on Computer Vision (ACCV) 2012.
H. Rabie, and Saunders, I (2012) A simulation study to assess a variable selection method for selecting single nucleotide polymorphisms associated with disease, Journal of Computational Biology.
P. Sanchez, G. Glonek, A. Metcalfe, (2012) Pareto simulated annealing for the design of experiments: illustrated by a gene expression study, Foundations of Computing and Decision Sciences, v 37(3), p199-221.
G. P. Bisson, C. Mehaffy, C. Broeckling, J. Prenni, D. Rifat, D. S. Lun, M. Burgos, D. Weissman, P. C. Karakousis, and K. Dobos (2012). Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampicin-resistant, rpoB-mutant Mycobacterium tuberculosis. J. Bacteriol., 2012.
A. Brandes, D.S. Lun, K. Ip, J. Zucker, C. Colijn, B. Weiner, and J.E. Galagan (2012) Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS ONE, 7 (5).
Demétrio, C. G.B., Menten, J. F. M., Leandro, R. A. and C.J. Brien (2012) Experimental power considerations — justifying replication for animal care and use committees. Poultry Science, accepted
D. Egen and D.S. Lun. Truncated branch and bound achieves efficient constraint-based genetic design. Bioinformatics, in press.
M.G. Niepielko, K. Ip, J.S. Kanodia, D.S. Lun, and N. Yakoby. Evolution of BMP signaling in Drosophila oogenesis: A receptor-based mechanism. Biophys. J., 102(8):1722-1730, April 2012.
G. Smith, C.J. Brien and H. Ashman (2012) Evaluating implicit judgements from image search click-through data. Accepted for publication in the Journal of the American Society for Information Science and Technology.
A. Torokhti, S.J. Miklavcic (2012) Piecewise interpolation filter for effective processing of large signal sets. International Conference on Electrical, Computer, Electronics and Communication Engineering (ICECECE 2012), Zurich, Switzerland July 5-6, 2012
A. Torokhti, S.J. Miklavcic (2012) Matrix approximation by a sum of rank-constrained matrices. International Congress on Computational and Applied Mathematics (CCAM 2012), Ghent, Belgium July 9-13, 2012
A. Torokhti, S.J. Miklavcic (2012) Best rank constrained operator approximation. International Congress on Computational and Applied Mathematics (CCAM 2012), Ghent, Belgium July 9-13, 2012
A. Torokhti, S.J. Miklavcic (2012) Robust estimation of large data sets by piecewise-linear interpolating estimator. International Workshop on Statistical Modeling (IWSM 2012), Prague, July 16-20, 2012
C.J. Brien, (2011) Factor allocation in gene-expression microarray experiments, International Conference on Design of Experiments (ICODOE-2011), May 10-13, 2011, Memphis, TN, USA
J. Cai, M.R. Golzarian, S.J. Miklavcic (2011) Novel image segmentation based on machine learning and its application to plant analysis, Int. Journal of Information and Electronics Engineering, 1, 79-84.
J. Cai, M.R. Golzarian, S.J. Miklavcic (2011) Novel image segmentation using Gaussian mixture models - application to plant phenotypic analysis, 3rd International Conference on Signal Acquisition and Processing (ICSAP), 308-312.
J. Cai (2011) High Order LPC Smoothed Spectra for Speech Enhancement, 3rd International Conference on Signal Acquisition and Processing (ICSAP).
J. Cai (2011) Robust thinning algorithm and Its Applications in pattern recognition and 3D plant modelling, Proceedings of the International Conference on Multimedia Technology, 2011.
M.R. Golzarian, J. Cai, R.A. Frick, S.J. Miklavcic (2011) Segmentation of cereal plant images using level set methods. A comparative study, Int. Journal of Information and Electronics Engineering, 1, 72-78.
M.R. Golzarian, J. Cai, R.A. Frick, S.J. Miklavcic (2011) A comparative evaluation of level set algorithms with applications for the segmentation of narrow-leaf plants", 3rd International Conference on Signal Acquisition and Processing (ICSAP), pp282-286.
M.R. Golzarian, R.A. Frick, K. Rajendran, B. Berger, S. Roy, M. Tester, D.S. Lun (2011) Accurate estimation of plant biomass using information extracted from high-throughput plant images, Journal of Plant Methods, 7(2), DOI: 10.1186/1746-4811-7-2.
M.R. Golzarian, R.A. Frick (2011) Classification of wheat, ryegrass and brome grass species at early growth stages using principal component analysis, Journal of Plant Methods, 7(28), Published Sept 2011.
M.R. Golzarian (2011) Adaptive Segmentation of Plant Images, an Integration of Colour Space Features and Self-Organizing Maps, in Proceedings of International Conference on Multimedia Technology, July 2011, Hangzhou, China.
K. Ip, C. Colijn, and D. S. Lun (2011) Analysis of complex metabolic behavior through pathway decomposition. BMC Syst. Biol., 5:91.
J. Aarao, B.H. Bradshaw-Hajek, S.J. Miklavcic, D.A. Ward (2011) Numerical implementation of the EDEM for modified Helmholtz BVPs on annular domains, Journal of Computational and Applied Mathematics, 235, 1342-1353.
A. Eryilmaz, D. S. Lun, and B. T. Swapna (2011) Control of multi-hop communication networks for inter-session network coding, IEEE Trans. Inform. Theory, 57(2):1092-1110
C. Jungreuthmayer, G.M. Birnbaumer, J. Zanghellini, P. Ertl (2011) 3D numerical simulation of a Lab-on-a-Chip - Increasing measurement sensitivity of interdigitated capacitors by passivation optimization, Lab On A Chip, 11(7), 1318-1325.
V.L. Nguyen, B.L. Huynh, H. Wallwork and J. Stangoulis (2011) Identification of Quantitative Trait Loci for Grain Arabinoxylan Concentration in Bread Wheat, Crop Science, Vol. 51 No. 3, p. 1143-1150
A. Torokhti and S.J. Miklavcic (2011) Filtering of infinite sets of stochastic signals: an approach based on interpolation techniques, Journal of Signal Processing, 91, pp2556-2566.
B.H. Bradshaw-Hajek, S.J. Miklavcic, L.R. White (2010) The actual dielectric response function for a colloidal suspension of spherical particles, Langmuir, 26(11), pp 7875-7884
B.H. Bradshaw-Hajek, S.J. Miklavcic, L.R. White(2010) High-frequency behaviour of the dynamic mobility and dielectric response of concentrated colloidal dispersions, Langmuir, volume 26(3), pages 1656-1665.
C.J. Brien, R.A. Bailey (2010) Decomposition tables for experiments, 2.Two-one randomizations, The Annals of Statistics, Vol 38 (5), pp 3164-3190
C.J. Brien, S.B. Abreu, W. Skinner (2010) ToF-SIMS as a New Method to Determine the Contact Angle of Mineral Surfaces, Langmuir vol 26(11), pp 8122-8130
J. Cai (2010) Integration of Optical Flow and Dynamic Programming for Stereo Matching, IET Image Processing.
J. Zanghellini, F. Wodlei, H.H. von Gruenberg (2010) Phospholipid demixing and the birth of a lipid drop, J. Theoretical Biology, 264, 952-961.
J. Aarao, B.H. Bradshaw-Hajek, S.J. Miklavcic, D.A. Ward (2010) The extended-domain-eigenfunction method for soliving elliptic boundary value problems with annular domains, Journal of Physics A: Mathematical & Theoretical, volume 43 (18)
H.I.M. Boshoff, D. S. Lun (2010) Systems biology approaches to understanding microbacterial survival mechanisms", Drug Discov. Today: Dis. Mech., 7(1):e75-e82, Invited paper.
X. Shi, D.S. Lun, M. Médard, R. Kötter, J.C. Meldrim; A.J. Barry (2010) Joint base-calling of two DNA sequences with factor graphs, IEEE Trans. Inform. Theory, 56(2):724-733.
A. Torokhti; S.J. Miklavcic (2010) Data compression under constraints of causality and variable finite memory, Signal Processing, 90(10), 2822-2834