### 2017

**Algama, M.**, Tasker, E., Williams, C., Parslow, A.C., Bryson-Richardson, R.J. & **Keith, J.M.** (2017) Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach. *BMC Genomics* 18(1), 259, 14 pages.

**Azad, A.K.M.**, Lawen, A. & **Keith, J.M. **(2017) Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer. * PLoS ONE* 12(3), e0173331.

Fan, T.H., **Sun, S.** & He, P.A. (2017) The time required for allele frequency change. *ANZIAM Journal* 58(3-4), 464-473.

Jiang, F., Yang, H. & **Tian, T.** (2107) Property and numerical simulation of the Ait-Sahalia-Rho model with nonlinear growth conditions. *Discrete and Continuous Dynamical Systems - Series B*, 22(1), 101-113.

Li, L., **Tian, T. **& Zhang, X. (2017) The impact of radiation on the development of lung cancer. *Journal of Theoretical Biology* 428, 147-152.

**Sun, S.**, **Klebaner, F.** & **Tian, T.** (2017) Mathematical modelling for variations of inbreeding populations fitness with single and polygenic traits. *BMC Genomics* 18(2), 196, 11 pages.

Tasker, E. & **Keith, J.** (2017) Sequence segmentation with changeptGUI. *Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution. ***Keith, J.** (eds.). Humana Press, pp. 293-312. (Methods in Molecular Biology; vol. 1525)

**Tian, T.** & Song, J. (2017) Inference method for developing mathematical models of cell signaling pathways using proteomic datasets. *Bioinformatics: Volume II: Structure, Function, and Applications. ***Keith, J.** (eds.). Humana Press, pp. 329-344.

### 2016

**Alyami, S.A.**, **Azad, A.K.M.** & **Keith, J.M.** (2016) The neighbourhood MCMC sampler for learning Bayesian networks. *First International Workshop on Pattern Recognition.* Jiang, X., Chen, G., Capi, G. & Ishii, C. (eds.). Bellingham WA: SPIE, 100111K. (Proceedings of SPIE; vol. 10011)

**Alyami, S.A.**, **Azad, A.K.M.** & **Keith, J.M.** (2016) Uniform sampling of directed and undirected graphs conditional on vertex connectivity. *International Conference on Graph Theory and its Applications.* Hinz, A., Arumugam, S., Balakrishnan, R., Raj, F., Karthick, T., Somasundaram, K. & Zhu, X. (eds.). Elsevier, pp. 43-55. (Electronic Notes in Discrete Mathematics; vol. 53)

Barbour, A., Chiganski, P. & **Klebaner, F.C.** (2016) On the emergence of random initial conditions in fluid limits. *Journal of Applied Probability* 53(4), pp. 1193-1205.

**Collevecchio, A.**, **Garoni, T.M.**, Hyndman, T. & **Tokarev, D.** (2016) The worm process for the Ising model is rapidly mixing. *Journal of Statistical Physics* 164, pp. 1082-1102.

**Collevecchio, A.**, **Hamza, K.** & **Shi, M.** (2016) Boostrap random walk. *Stochastic Processes and their Applications* 126(6), pp. 1744-1760.

**Collevecchio, A.**, Mehrabian, A. & Wormald, N.C. (2016) Longest paths in random Apollonian networks and largest *r*-ary subtrees of random *d*-ary recursive trees. *Journal of Applied Probability* 53(3), pp. 846-856.

**Hamza, K.**, Jagers, P. & **Klebaner, F.C**. (2016) On the establishment, persistence, and inevitable extinction of populations. *Journal of Mathematical Biology* 72(4), pp. 797-820.

Jagers, P. & **Klebaner, F.C.** (2016) From size to age and type structure dependent branching: A first step to sexual reproduction in general population processes. *Branching Processes and Their Applications.* Lecture Notes in Statistics 219, Springer, pp. 137-148.

Jiang, F., Yang, H. & **Tian, T.** (2016) Stability analysis for second-order stochastic neutral partial functional systems subject to infinite delays and impulses. *Advances in Difference Equation* 2016: 224.

**Klebaner, F.C.**, Landsman, Z., Makov, U. & Yao, J. (2016) Optiomal portfolios with downside risk. *Quantitative Finance*: 11 pages.

Koolen, J. & **Markowsky, G.** (2016) A collection of results concerning simple random walk on distance-regular graphs. *Discrete Mathematics* 339(2), pp. 737-744.

Kutadinata, R., Moase, W., Manzie, C., **Zhang, L.** & **Garoni, T.M.** (2016) Enhancing the performance of existing urban traffic light control through extremum-seeking. *Transportation Research Part C: Emerging Technologies* 62, pp. 1-20.

Li, X. & **Tian, T.** (2016) A new cost-profit model for measuring the optimal scale of China’s foreign exchange reserve. *Mathematical Problems in Engineering*, 2016, Article ID 9261279.

**Tian, T.** (2016) Bayesian computation methods for inferring regulatory network models using biomedical data. *Translational Biomedical Informatics: A Precision Medicine Perspective.* Shen, B., Tang, H. & Jiang, X. (eds.). Singapore: Springer, pp. 289-307. (Advances in Experimental Medicine and Biology; vol. 939)

Truong, L., Sarvi, M. Currie, G. & **Garoni, T.M.** (2016) Required traffic micro-simulation runs for reliable multivariate performance estimates. *Journal of Advanced Transportation* 50(3), pp. 296-314.

Wang, J., **Wu, Q.**, Hu, X.T. & **Tian, T**. (2016) An integrated approach to infer dynamic protein-gene interactions - A case study of the human P53 protein. *Methods* 110, pp. 3-13.

Wu, F., **Tian, T.**, Rowlings, J.B. & Yin, G. (2016) Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations. *Journal of Chemical Physics* 144: 174112.

**Wu, Q.** & **Tian, T.** (2016) Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay. *Scientific Reports*, 6: 31909.

Yen, J.D.L., Thomson, J.R., **Keith, J.M.**, Paganin, D.M., Fleishman, E., Dobkin, D.S., Bennett, J.M. & Mac Nally, R. (2016) Balancing generality and specificity in ecological gradient analysis with species abundance distributions and individual size distributions. *Global Ecology and Biogeography*: 15 pages. DOI: 10.1111/geb.12537.

Yen, J.D.L., Thomson, J.R., **Keith, J.M.**, Paganin, D.M., & Mac Nally, R. (2016) How do different aspects of biodiversity change through time? A case study on an Australian bird community. *Ecography*: 9 pages. DOI: 10.1111/ecog.02306.

### 2015

Acan, H., **Collevecchio, A.**, Mehrabian, A. & Wormald, N. On the push&pull protocol for rumour spreading. *Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing (PODC'15).* Spirakis, P. G. (ed.). New York NY USA: Association for Computing Machinery (ACM), pp. 405-412. (Submitted SIAM Discrete Mathematics, first review received.)

Azad, A.K.M., Lawen, A. & **Keith, J.M.** (2015) “Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling. *BMC Systems Biology *9(2). DOI: 10.1186/s12918-014-0135-x.

Barbour, A.D., **Hamza, K.**, Kaspi, H. & **Klebaner, F.C.** (2015) Escape from the boundary in Markov Population Processes. *Advances in Applied Probability* 47(4), pp. 1190-1211.

Bowman, D., Flek, R. & **Markowsky, G.T.** (2015) Rotation numbers and symbolic dynamics. *Annales Academiæ Scientiarum Fennicaæ Mathematica *40, pp. 227-234.

Dong, T., Yang, B. & **Tian, T**. (2015) Volatility analysis of Chinese stock market using high-frequency financial big data. *2015 IEEE International Conference on Smart City.* Cerin, C., Zhang, W. & Wang, H. (eds.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 769-774.

**Fan, J.Y.**, **Hamza, K.** & **Klebaner, F.C.** (2015) Mimicking self-similar processes, *Bernoulli* 21(3), pp. 1341–1360. DOI: 10.3150/13-BEJ588.

**Hamza, K.**, **Klebaner, F.C.**, Landsman, Z. & **Tan, Y.O.** (2015) Option pricing for symmetric Levy returns with applications. *Asia-Pacific Financial Markets* 22(1), pp. 27-52.

Joosten, S.A., Sands, S., Edwards, B.A., **Hamza, K.**, Turton, A.R., Lau, K.K-P., Crossett, M., Berger, P.J. & Hamilton, G.S. (2015) Evaluation of the role of lung volume and airway size and shape in supine-predominant obstructive sleep apnoea patients. *Respirology* 20(5), pp. 819 - 827.

Jung, P. & **Markowsky, G.T.** (2015) Hölder continuity and occupation-time formulas for fBm self-intersection local time and its derivative. *Journal of Theoretical Probability* 28(1), pp. 299-312.

**Keith, J.M.** (2015) Sampling phylogenetic tree space with the generalized Gibbs sampler. *Cladistics* 31(4), 438-440.

**Keith, J.M.** & Spring, D.A. (2015) Agent-based Bayesian spread model applied to red imported fire ants in Brisbane. *Biosecurity Surveillance: Quantitative Approaches.* Jarrad, F., Low-Choy, S. & Mengersen, K. (eds.). Wallingford UK: CABI, pp. 334-347.

**Klebaner, F.C.**, Logachov, A.V. & Mogulskii, A.A. (2015) Large deviations for processes on half-line. *Electronic Communications in Probability* 20, pp. 1-14.

**Markowsky, G.T.** (2015) The exit time of planar Brownian motion and the Phragmén-Lindelöf principle. *Journal of Mathematical Analysis and Applications* 422(1), pp. 638-645.

Schreider, S. Plummer, J., **McInnes, D.** & **Miller, B.** (2015) Sensitivity analysis of gas supply optimization models. *Annals of Operations Research* 226(1), pp. 565-588.

**Sun, S.**, **Klebaner, F.** & **Tian, T.** (2015) A new approach for estimating probability of metastasis at diagnosis. *Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine.* Huan, J. . L., Miyano, S., Shehu, A., Hu, X., Ma, B., Rajasekaran, S., Gombar, V. K., Matthieu, I., Yoo, I., Zhou, J., Chen, B., Pai, V. & Pierce, B. (eds.). New York NY USA: Institute of Electrical and Electronics Engineers, p. 653-656.

**Tian, Y.**, Zhu, Z., Lee, G.M., **Klebaner, F.C.** & **Hamza, K.** (2015) Calibrating and pricing with a stochastic-local volatility model. *Journal Of Derivatives* 22(3), pp. 21-39.

Truong, L.T., Sarvi, M., Currie, G. & **Garoni, T.M.** (2015) How many simulation runs are required to achieve statistically confident results: A case study of simulation-based surrogate safety measures. *2015 IEEE 18th International Conference on Intelligent Transportation Systems (ITSC 2015).* Vazquez, M. A. S. (ed.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 274 - 278.

Wang, J., **Wu, Q.** & **Tian, T.** (2015) Integrated study to infer dynamic protein-gene interactions in human P53 regulatory networks. *Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine.* Huan, J.L., Miyano, S., Shehu, A., Hu, X., Ma, B., Rajasekaran, S., Gombar, V. K., Matthieu, I., Yoo, I., Zhou, J., Chen, B., Pai, V. & Pierce, B. (eds.). New York NY USA: Institute of Electrical and Electronics Engineers, pp. 273-276.

Woolfit, M., **Algama, M.**, **Keith, J.M.**, McGraw, E.A. & Popovici, J. (2015) Discovery of putative small non-coding RNAs from the obligate intracellular bacterium *Wolbachia pipientis*. *PLoS ONE* 10(3), e0118595.

**Wu, Q.**, Jiang, F. & **Tian, T**. (2015) Sensitivity and robustness analysis for stochastic model of nanog gene regulatory network. *International Journal of Bifurcation and Chaos in Applied Sciences and Engineering* 25(7), 1540009.

Yen, J.D.L., Thomson, J.R., Paganin, D.M., **Keith, J.M.** & Mac Nally, R. (2015) Function regression in ecology and evolution: FREE. *Methods in Ecology and Evolution *6(1), pp. 17-26.

Zhang, W., **Tian, T.**, & Zou, X. (2015) Negative feedback contributes to the stochastic expression of the interferon-β gene in virus-triggered type I interferon signaling pathways. *Mathematical Biosciences* 265, pp. 12-27.

**Zhou, Z.**, Xu, X., **Garoni, T.M.** & Deng, Y., Leaf-excluded percolation in two and three dimensions. *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics* 91(2), 022140.

### 2014

**Aharon, R.**, Janes, P.W., Burgess, A., **Hamza, K.**, **Klebaner, F.C.** & Lackmann, M. (2014) A mathematical model for eph/ephrin-directed segregation of intermingled cells. *PLoS ONE* 9(12): e111803.

**Algama, M. **& **Keith, J.M.** (2014) Investigating genomic structure using changept: A Bayesian segmentation model. *Computational and Structural Biotechnology Journal* 10(17), pp. 107-115.

**Algama, M.**, Oldmeadow, C., Tasker, E.C., Mengersen, K.L. & **Keith, J.M.** (2014) Drosophila 3’ UTRs are more complex than protein-coding sequences. *PLoS ONE *9(5): e97336.

Baxter, M., Uddin, A.K.M.N., Raghav, S., Leong, P., Low, K., **Hamza, K.**, Holmes, P., Hamilton, G.S., Thyagarajan, D., Lau, K.K-P. & Bardin, P.G. (2014) Abnormal vocal cord movement treated with botulinum toxin in patients with asthma resistant to optimised management. *Respirology* 19(4), pp. 531-537.

Deng, Z. & **Tian, T.** (2014) A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. *BMC Bioinformatics* 15: 256.

Gramatikoff, K., Boyd, S.E., Smith, J.W. & **Keith, J.M. **(2014) Genomic taxonomy boost by lexical clustering. *Journal of Investigative Genomics* 1(1): 00004.

**Hamza, K.**, **Klebaner, F.C. **(2014) How did we get here? *Journal of Applied Probability *51A, pp. 63-72.

**Hamza, K.**, **Klebaner, F.C.** & **Mah, O.** (2014) Volatility in options formulae for general stochastic dynamics. *Discrete and Continuous Dynamical Systems - Series B* 19(2), pp. 435-446.

Joosten, S.A., O'Donoghue, F., Rochford, P.D., Barnes, M., **Hamza, K.**, Churchward, T., Berger, P.J. & Hamilton, G.S. (2014) Night-to-night repeatability of supine-related obstructive sleep apnea. *Annals of the American Thoracic Society* 11(5), pp. 761-769.

Jung, P. & **Markowsky, G.T.** (2014) On the Tanaka formula for the derivative of self-intersection local time for fractional Brownian motion. *Stochastic Processes and their Applications* 124(11), pp. 3846-3868.

**Klebaner, F.C.** & Liptser, R. (2014) When a stochastic exponential is a true martingale. Extension of the Benes method. *Theory of Probability and its Applications* 58(1), pp. 38-62.

Kutadinata, R., Moase, W., Manzie, C., **Zhang, L.** & **Garoni, T.** (2014) Extremum-seeking for adaptation of urban traffic signal control. *Proceedings of the 19th IFAC World Congress, 2014.* Boje, E. & Xia, X. (eds.). Oxford UK: International Federation of Automatic Control 19, pp. 5067-5072.

Lee, G.M., **Tian, Y.** & Zhu, Z. (2014) Monte Carlo pricing scheme for a stochastic-local volatility model. *Proceedings Book of World Congress on Engineering 2014.* Ao, S.I., Gelman, L. & Korsunsky, A.M. (eds.). Hong Kong: Newswood Limited, Vol. 2, pp. 1-6.

Li, X., Naidoo, P., Guy, P., Finlay, P., Foo, S-W., **Hamza, K.**, & Bardin, P.G. (2014). Lung-volume controlled computerised tomography in real-life acute severe asthma. *Journal of Asthma*, 51(3), pp. 282-287.

**Markowsky, G.T.** (2014) A probabilistic proof of the open mapping theorem for analytic functions. *Bulletin of the Australian Mathematical Society* 90(1), pp. 74-76.

Miller, A.B. & **Miller, B.** (2014) Tracking of the UAV trajectory on the basis of bearing-only observations. *2014 IEEE 53rd Annual Conference on Decision and Control (CDC).* Astolf, A. (ed.). California USA: Institute of Electrical and Electronics Engineers, pp. 4178-4184.

Miller, A.B. & **Miller, B.** (2014) UAV control on the basis of bearing-only observations.* 2014 Australian Control Conference.* Canberra Australia: Engineers Australia, pp. 31-36.

**Miller, B.** (2014) Controllable systems with impacts. *Journal of Mathematical Sciences* 199(5), pp. 571-582.

**Sun, S.**, **Klebaner, F.C.** & **Tian, T.** (2014) A new approach for estimating the progression of pancreatic cancer. *8th International Conference on Systems Biology (ISB).* Chen, L., Zhang, X-S., Wu, L-Y. & Wang, Y. (eds.). New Jersey: Institute of Electrical and Electronics Engineers, pp. 118-123.

**Sun, S., Klebaner, F.C.** & **Tian, T. **(2014) A new mathematical model for inbreeding depression in large populations. *Bioinformatics Research and Applications.* Basu, M., Pan, Y. & Wang, J. (eds.). Switzerland: Springer, *Lecture Notes in Bioinformatics *8492, pp. 310-321.

**Sun, S., Klebaner, F.C. & Tian, T.** (2014) A new model of time scheme for progression process of colorectal cancer, *BMC Systems Biology* 8(S3): S2.

**Tian, T.** (2014) Simplified stochastic models with time delay for studying the degradation process of mRNA molecules. *International Journal of Data Mining and Bioinformatics* 10(1), pp. 18-32.

**Tian, T.** & Harding, A. (2014) How MAP kinase modules function as robust, yet adaptable, circuits. *Cell Cycle* 13(15), pp. 2379-2390.

**Tian, T.** & Smith-Miles, K. (2014) Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell. *BMC Systems Biology*, 8(S1): S8.

**Tian, T.**, Zhou, Y., Wu, Y. & Ge, X. (2014) Estimation of parameters in mean-reverting stochastic systems, *Mathematical Problems in Engineering*, ID 317059.

**Tian, Y.**, Zhu, Z., Lee, G.M., Lo, T., **Klebaner, F.C. **& **Hamza, K.** (2014) Pricing window barrier options with a hybrid stochastic-local volatility model. *Proceedings of the 2104 IEEE Conference on Computational Intelligence for Financial Engineering & Economics (CIFEr).* Serguieva, A., Maringer, D., Palade, V. & Almeida, R.J. (eds.). USA: Institute of Electrical and Electronics Engineers, pp. 370-377.

Xu, X., Wang, J., **Zhou, Z.**, **Garoni, T.** & Deng, Y. (2014) Geometric structure of percolation clusters. *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics* 89(1): 012120.

Wu, F., Yin, G.G. & **Tian, T.** (2014) Gene regulatory networks driven by intrinsic noise with two-time scales: A stochastic averaging approach. *Frontiers of Mathematics in China* 9(4), pp. 947-963.

**Wu, Q.**, Smith-Miles, K. & **Tian, T.** (2014) Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. *BMC Bioinformatics* 15(S12): S3.

**Wu, Q.**, Wong, E.S.W. & Zhu, Z. (2014) A data-processing approach for exploring water-use maneuver of high-rise building. *Building Services Engineering Research & Technology* 35(4), pp. 341-348.

**Zhang, L.**, de Gier, J. & **Garoni, T.** (2014) Traffic disruption and recovery in road networks. *Physica A: Statistical Mechanics and its Applications* 401, pp. 82-102.

**Zhang, L. **& **Garoni, T.** (2014) Modelling disruption and recovery of traffic in road networks. *Cellular Automata.* Was, J., Ch Sirakoulis, G. & Bandini, S. (eds.). Switzerland: Springer, Vol. 8751, pp. 640-649.

**Zhang, L.**, **Shiri, S.** & **Garoni, T.** (2014) A study of aggregated speed in road networks using cellular automata. *Cellular Automata.* Was, J., Ch Sirakoulis, G. & Bandini, S. (eds.). Switzerland: Springer, Vol. 8751, pp. 596-604.

### 2013

Chen, C., Mengersen, K., Ickstadt, K. & **Keith, J.M.** (2013) A Bayesian regression model with variable selection for genome-wide association studies. *Case Studies in Bayesian Modeling and Analysis*. Alston, C.L., Mengersen, K.L. & Pettitt, A.N. (eds.). Chichester WSX UK: Wiley-Blackwell, pp. 103-117.

**Collevecchio, A.**, Cotar, C. & LiCalzi, M. (2013) On a preferential attachment and generalized Polya's urn model. *Annals of Applied Probability* 23(3), pp. 1219-1253.

Gillies, D. & **Sudbury, A.W.** (2013) Should causal models always be Markovian? The case of multi-causal forks in medicine. *European Journal for Philosophy of Science* 3(3), pp. 275-308.

**Hamza, K.**, Jagers, P. & **Klebaner, F.C.** (2013) The age structure of population-dependent general branching processes in environments with a high carrying capacity. *Steklov Institute of Mathematics. Proceedings,* 282(1), Springer, New York USA, pp. 90-105.

Jagers, P. & **Klebaner, F.C.** (2013) Dependence and interaction in branching processes. *Prokhorov and Contemporary Probability Theory.* Shiryaev, A.N., Varadhan, S.R.S. & Presman, E.L. (eds.). Heidelberg Germany: Springer, pp. 325-333.

Jung, P. & **Markowsky, G.T.** (2013) Random walks at random times: Convergence to iterated Lévy motion, fractional stable motions, and other self-similar processes. *Annals of Probability* 41(4), pp. 2682-2708.

**Keith, J.M.** & Davey, C.M. (2013) Bayesian approaches to the design of Markov chain Monte Carlo samplers. *Springer Proceedings in Mathematics and Statistics - Monte Carlo and Quasi-Monte Carlo Methods 2012.* Dick, J., Kuo, F. Y., Peters, G. W. & Sloan, I. H. (eds.). Heidelberg Germany: Springer, Vol. 65, pp. 455-466.

**Keith, J.M.** & Spring, D.A. (2013) An agent-based Bayesian approach to monitoring the progress of invasive species eradication programs. *Proceedings of the National Academy of Science of the United States of America *110(33), pp. 13428-13433.

Koolen, J., **Markowsky, G.T.** & Park, J. (2013) On electrical resistances on distance-regular graphs. *European Journal of Combinatorics* 34(4), pp. 770-786*.*

Lv, J-P., **Garoni, T.** & Deng, Y. (2013) Phase transitions in XY antiferromagnets on plane triangulations, *Physical Review B: Covering condensed matter and materials physics* 87(2), 024108.

**Markowsky, G.T.** (2013) A method for deriving hypergeometric and related identities using the H^{2} Hardy norm of conformal maps. *Integral Transforms and Special Functions* 24(4), pp. 302-313.

Miller, A.B. & **Miller, B.** (2013) Application of stochastic control to analysis and optimization of TCP. *2013 3rd Australian Control Conference.* Liu, W. (ed.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 238-243.

**Miller, B.** & Rubinovich, E. (2013) Discontinuous solutions in the optimal control problems and their representation by singular space-time transformations. *Automation and Remote Control* 74(12), pp. 1969-2006.

MacDonald, M., Korman, T., King, P.T., **Hamza, K.** & Bardin, P.G. (2013). Exacerbation phenotyping in chronic obstructive pulmonary disease. *Respirology* 18(8), 1280 - 1281.

**McInnes, D.J.** & **Miller, B.** (2013) Optimal control of time-inhomogeneous Markov chains with application to dam management. *2013 3rd Australian Control Conference.* Liu, W. (ed.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 230-237.

Mode, C.J., Durrett, R., **Klebaner, F.** & Olofsson, P. (2013) Applications of stochastic processes in biology and medicine. *International Journal of Stochastic Analysis* 2013: 790625.

Nazin, A.V., Lygeros, J. (ed.) & **Miller, B.** (2013) Mirror decent algorithm for a multi-armed bandit governed by a stationary finite state Markov chain. *European Control Conference*, Piscataway NJ USA, pp. 371-375.

Nazin, A.V. & **Miller, B.** (2013) On effectiveness of the mirror decent algorithm for a stochastic multi-armed bandit governed by a stationary finite Markov chain. *2013 3rd Australian Control Conference.* Liu, W. (ed.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 244-250.

Nazin, A.V. & **Miller, B.** (2013) Robust mirror decent algorithm for a multi-armed bandit governed by a stationary finite Markov chain.* Preprints of the 2013 IFAC Conference on Manufacturing Modelling, Management, and Control.* Bakhtadze, N., Chernyshov, K., Dolgui, A. & Lotosky, V. (eds.). Oxford England: Elsevier, Vol. 7, pp. 939-943.

Park, J., Koolen, J. & **Markowsky, G.T.** (2013) There are only finitely many distance-regular graphs with valency k at least three, fixed ratio k_{2}/k, and large diameter. *Journal of Combinatorial Theory Series B *103(6), pp. 733-741*.*

**Phatarfod, R.M.** (2013) Some aspects of the Benford law of leading significant digits. *The Mathematical Scientist* 38(2), pp. 73-85.

**Rau, C.R.F.** (2013) Bayes classifiers of three-dimensional rotations and the sphere with symmetries. *Statistics and Probability Letters* 83(3), pp. 930-935.

**Sun, S., Klebaner, F.C. & Tian, T.** (2013) A new mathematical model for progression of colorectal cancer, *Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine. *Li, G., Hu, X., Kim, S., Ressom, H., Hughes, M., Liu, B., McLachlan, G., Liebman, M. & Sun, H. (eds.). Piscataway NJ USA: Institute of Electrical and Electronics Engineers, pp. 560-565.

**Tian, T.** (2013) Chemical memory reactions induced bursting dynamics in gene expression. *PLoS ONE* 8(1): e52029.

**Tian, T**. & Wu, F. (2013) Robustness Analysis of the PI3K/AKT cell signaling module. *Journal of Medical and Bioengineering* 2(2), pp.93-97.

**Tian, Y.** (2013) Efficient portfolio valuation incorporating liquidity risk. *Quantitative Finance* 13(10), pp. 1575-1586.

Wang, J., Davidson, B. & **Tian, T.** (2013) Systems biology studies of gene network and cell signalling pathway in cancer research. *Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases - Translational Bioinformatics*. Shen, B. (ed.). Dordrecht Netherlands: Springer, pp. 109-129.

Wang, J., **Zhou, Z.**, Liu, Q., **Garoni, T.** & Deng, Y. (2013) High-precision Monte Carlo study of directed percolation in (d+1) dimensions. *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics* 88(4): 042102.

Wang, J., **Zhou, Z.**, Zhang, W., **Garoni, T.** & Deng, Y. (2013) Bond and site percolation in three dimensions. *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics* 87(5): 052107.

**Wu, Q.**, Smith-Miles, K. & **Tian, T.** (2013) Approximate Bayesian computation for estimating rate constants in biochemical reaction systems. *Proceedings: 2013 IEEE International Conference on Bioinformatics and Biomedicine*. Li, G-Z., Hu, X., Kim, S., Ressom, H., Hughes, M., Liu, B., McLachlan, G., Liebman, M. & Sun, H. (eds.). New Jersey USA: Institute of Electrical and Electronics Engineers, pp. 416-421.

**Wu, Q.**, Smith-Miles, K., Zhou, T. & **Tian, T.** (2013) Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model. *BMC Systems Biology* 7(S4): S14.

**Zhang, L.**, **Garoni, T.** & de Gier, J. (2013) A comparative study of Macroscopic Fundamental Diagrams of arterial road networks governed by adaptive traffic signal systems. *Transportation Research, Series B: Methodological* 49, pp. 1-23.

Zong, X., Wu, F. & **Tian, T.** (2013) Stability and stochastic stabilization of numerical solutions of regime-switching jump diffusion systems. *Journal of Difference Equations and Applications* 19(11), pp. 1173-1757.

### 2012

Andreev, M., Miller, A., **Miller, B.** & Stepanyan, K. (2012) Path planning for unmanned aerial vehicle under complicated conditions and hazards. *Journal of Computer and Systems Sciences International* 51(2), pp. 328-338.

Beaton, N.R., Flajolet, P., **Garoni, T.M.** & Guttmann, A.J. (2012) Some new self-avoiding walk and polygon models. *Fundamenta Informaticae* 117, pp. 19-33.

Boyd, S.E., Nair, B., Ng, S.W., **Keith, J.M.** & Orian, J. (2012) Computational Characterization of 3’ Splice Variants in the GFAP Isoform Family. *PLoS ONE* 7(3): e33565.

Chigansky, P. & **Klebaner, F.C.** (2012) Compound Poisson approximation for triangular arrays with application to threshold estimation.* Electronic Communications in Probability* 17(29), pp. 1-10.

Chigansky, P. & **Klebaner, F.C.** (2012) The Euler-Maruyama approximation for the absorption time of the CEV diffusion. *Discrete and Continuous Dynamical Systems - Series B*, 17(5), pp. 1455-1471.

Duff, C., Smith-Miles, K., Lopes, L. & **Tian, T.** (2012) Mathematical models of stem cell differentiation: the PU.1-Gata-1 interaction. *Journal of Mathematical Biology* 64(3), pp. 449-468.

Elgindy, K.T.M.A., Smith-Miles, K.A. & **Miller, B.** (2012) Solving optimal control problems using a Gegenbauer transcription method. *Proceedings of the 2012 Australian Control Conference.* Savkin, A. (ed.). Barton ACT Australia: Engineers Australia, pp. 417-424.

**Fan, J.Y.**, **Hamza, K.** & **Klebaner, F.C.** (2012) On the Markov property of some Brownian martingales. *Stochastic Processes and their Applications* 122(10), pp. 3506-3512.

**Hamza, K.** & **Klebaner, F.C.** (2012) On the statistical independence of primes. *The Mathematical Scientist* 37(2), pp. 97-105.

Joosten, S., **Hamza, K.**, Sands, S., Turton, A., Berger, P., & Hamilton, G. (2012). Phenotypes of patients with mild to moderate obstructive sleep apnoea as confirmed by cluster analysis. *Respirology* 17(1), pp. 99-107.

**Keith, J.M.**, Davey, C.M. & Boyd, S.E. (2012) A Bayesian method for comparing and combining binary classiﬁers in the absence of a gold standard. *BMC Bioinformatics* 13: 179.

Kerr, J.B., Brogan, L., Myers, M., Hutt, K.J., Mladenovska, T., Ricardo, S.D., **Hamza, K.**, Scott, C.L., Strasser, A. & Findlay, J.K. (2012) The primordial follicle reserve is not renewed after chemical or gamma-irradiation mediated depletion. *Reproduction* 143(4), pp. 469-476.

**Klebaner, F.C.** (2012) *Introduction to Stochastic Calculus with Applications*. 3 ed. UK: Imperial College Press.

Lakic, N. & **Markowsky, G.T.** (2012) The rate of convergence of the hyperbolic density on sequences of domains. *Contemporary Mathematics - Conformal Dynamics and Hyperbolic Geometry*. Bonahon, F., Devaney, R.L., Gardiner, F.P. & Saric, D. (eds.). Rhode Island USA: American Mathematical Society, Vol. 573, pp. 147-157.

Liu, Q., Deng, Y., **Garoni, T.** & Blöte, H. (2012) The O(n) loop model on a three-dimensional lattice. *Nuclear Physics B* 859(2), pp. 107-128.

**Markowsky, G.T.** (2012) A rigidity theorem for special families of rational functions. *Annales Academiæ Scientiarum Fennicaæ Mathematica* 37(1), pp. 277-284.

**Markowsky, G.T.** (2012) Birth-death chains and the local time of Brownian motion. *Bulletin of the Australian Mathematical Society* 85(3), pp. 497-504.

**Markowsky, G.T.** (2012) The derivative of the intersection local time of Brownian motion through Wiener chaos. *Séminaire de Probabilités XLIV*, Lecture Notes in Mathematics, 2046, pp. 141-148.

Miller, A.B. & **Miller, B.** (2012) Towards the analysis of TCP with the aid of stochastic control. *Proceedings of the IX International Conference: Systems Identification and Control Problems.* Lototsky, V.A. (ed.). Moscow: MAIK Nauka, pp. 326-346.

**Miller, B.** & Rubinovich, E. (2012) Space-time singular transformations methodology in problems with controlled impact interactions. *Proceedings of the X International Chetaev Conference Analitical Mechanics, Stability and Control.* Vassillyev, S.N., Kozlov, V.V., Degtyarev, G.L., Sidorov, I.N. & Gubaidullin, D.A. (eds.). Kazan, Russia: Kazan National Research Technical University Press, pp. 346-357.

Mountford, T.S. & **Sudbury, A.W.** (2012) Deposition processes with hardcore behaviour. *Journal of Statistical Physics* 146(4), pp. 687-700.

**Phatarfod, R.M.** (2012) Kelly gambling with the stock market and banks. *The Mathematical Scientist* 37(2), pp. 132-140.

**Sudbury, A.W.** (2012) Means and variances in stochastic multistage cancer models. *Journal of Applied Probability* 49(2), pp. 590-594.

**Tian, T.** & Ge, X. (2012) Calibration of stochastic differential equation models using implicit numerical methods and particle swarm optimization. *Proceedings of the 4th International Conference on Modelling, Identification and Control*. Xia, L. & Winfield, A. F. T. (eds.). USA: Institute of Electrical and Electronics Engineers, pp. 1105-1110.

**Tian, T.** & Song, J. (2012) Mathematical modelling of the MAP kinase pathway based on proteomics dataset. *PLoS ONE* 7(8): e42230.

**Tian, Y.**, Zhu, Z., **Klebaner, F.C.**, & **Hamza, K.** (2012) A hybrid stochastic volatility model incorporating local volatility. *Proceedings of the Fourth International Conference on Computational and Information Sciences.* Shen, W., Wang, Y. & Geng, X. (eds.). New Jersey USA: Institute of Electrical and Electronics Engineers, pp. 333-336.

**Tian, Y.**, Zhu, Z., **Klebaner, F.C.**, & **Hamza, K.** (2012) Pricing barrier and American options under the SABR model on the graphics processing unit. *Concurrency and Computation-Practice & Experience* 24(8), pp. 867-879. (Online version published in 2011.)

Wang, J. & **Tian, T.** (2012) Effective non-linear method for inferring genetic regulation from time-series microarray gene expression data. *Next Generation Microarray Bioinformatics.* Wang, J., Tan, A.C. & Tian, T. (eds.). New York USA: Humana Press, pp. 235-246.

**Wu, Q.**, Smith-Miles, K. & **Tian, T.** (2012) A two-variable model for stochastic modelling of chemical events with multi-step reactions. *Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*. Gao, J., Dubitzky, W., Wu, C., Liebman, M., Alhail, R., Ungar, L., Christianson, A. & Hu, X. (eds.). Philadelphia USA: Institute of Electrical and Electronics Engineers, pp. 270-275.

**Zhang, L.** (2012) On-line scheduling of empty containers. *Asia-Pacific Journal of Operational Research* 29(4), pp. 1-19.

### 2011

**Abramov, V.** (2011) Statistical analysis of single-server loss queueing systems. *Methodology and Computing in Applied Probability* 13(4), pp. 763-781.

**Abramov, V.**, **Klebaner, F.** & Liptser, R. (2011) The Euler-Maruyama approximations for the CEV model. *Discrete and Continuous Dynamical Systems - Series B,* 16(1), pp. 1-14.

Boyd, S.E., **Keith, J.M.**, Traven, A. & Beilharz, T. (2011) Probing connectivity between transcriptional and post-transcriptional gene networks. *Microbiology Australia*, 32(4), pp. 166-168.

**Buchmann, B.** & Maller, R. (2011) The small-time Chung-Wichura law for Levy processes with non-vanishing Brownian component. *Probability Theory and Related Fields,* E, pp. 1-28.

Chen, C., Schwender, H., **Keith, J.M.**, Nunkesser, R., Mengersen, K. & Macrossan, P. (2011) Methods for identifying SNP interactions: A review on variations of logic regression, random forest and Bayesian logistic regression. *IEEE/ACM Transactions on Computational Biology and Bioinformatics* 8(6), pp. 1580-1591.

**Clark, R.M.** & Thompson, R. (2011) Estimation and comparison of flowering curves. *Plant Ecology and Diversity* 4(2-3), pp. 189-200.

**Clark, R.M.** & Thompson, R. (2011) Sampling bias in the determination of first and last occurrences. *Plant Ecology and Diversity* 4(2-3), pp. 201-211.

de Gier, J., **Garoni, T.M.** & Rojas, O. (2011) Traffic flow on realistic road networks with adaptive traffic lights. *Journal of Statistical Mechanics: Theory and Experiment* 2011, pp. 1-43, P04008.

Evans, G., Sofronov, G.Y., **Keith, J.M.** & Kroese, D.P. (2011) Estimating change-points in biological sequences via the cross-entropy method. *Annals of Operations Research*, 189(1), pp. 155-165.

**Garoni, T.M.**, Ossola, G., Polin, M. & Sokal, A.D. (2011) Dynamic Critical Behavior of the Chayes-Machta Algorithm for the Random-Cluster Model. I. Two Dimensions. *Journal of Statistical Physics* 144(3), pp. 459-518.

**Hamza, K.** & **Sudbury, A.** (2011) The mixing advantage for bounded random variables. *Statistics and Probability Letters* 81(8), pp. 1190-1195.

Jagers, P. & **Klebaner, F.** (2011) Population-size-dependent, age-structured branching processes linger around their carrying capacity. *New frontiers in applied probability*. Glynn, P., Mikosch, T. & Rolski, T. (eds.). Special Volume 48A ed. Sheffield UK: Applied Probability Trust, pp. 249-260.

**Klebaner, F.** & Liptser, R. (2011) Asymptotic analysis of ruin in the constant elasticity of variance model. *Theory of Probability and its Applications* 55(2), pp. 291-297.

**Klebaner, F.**, Sagitov, S., Vatutin, V., Haccou, P. & Jagers, P. (2011) Stochasticity in the adaptive dynamics of evolution: the bare bones. *Journal of Biological Dynamics* 5(2), pp. 147-162.

Li, W., Luo, X., Hill, N.A., Ogden, R.W., **Tian, T.**, Smythe, A., Majeed, A.W. & Bird, N. (2011) Cross-bridge apparent rate constants of human gallbladder smooth muscle. *Journal of Muscle Research and Cell Motility* 32(3), pp.209-220.

Liu, Q., Deng, Y. & **Garoni, T.** (2011) Worm Monte Carlo study of the honeycomb-lattice loop model. *Nuclear Physics B,* 846(2), pp. 283-315.

Low, K., Lau, K., Holmes, P., Crossett, M., Vallance, N., Phyland, D., **Hamza, K.**, Hamilton, G. & Bardin, P. (2011) Abnormal vocal cord function in difficult-to-treat asthma. *American Journal of Respiratory and Critical Care Medicine* 184(1), pp. 50-56.

**Markowsky, G.** (2011) A retelling of Newton's work on Kepler's Laws. *Expositiones Mathematicae* 29(3), pp. 253-282.

**Markowsky, G.** (2011) Applying Brownian motion to the study of birth-death chains. *Statistics and Probability Letters* 81(8), pp. 1173-1178.

**Markowsky, G.** (2011) On the expected exit time of planar Brownian motion from simply connected domains. *Electronic Communications in Probability* 16, pp. 652-663.

Miller, A. & **Miller, B.** (2011) Control of connected Markov chains. Application to congestion avoidance in the internet. *Proceedings of the 50th IEEE Conference on Decision and Control and European Control Conference (CDC-ECC).* Polycarpou, M. (ed.). USA: Institute of Electrical and Electronics Engineers, pp. 7242-7248.

**Miller, B.** & **McInnes, D.** (2011) Management of a large dam via optimal price control. *Proceedings of the 18th World Congress: The International Federation of Automatic Control.* Bittanti, S., Cenedese, A. & Zampieri, S. (eds.). Milan Italy: International Federation of Automatic Control, Vol. 18, pp. 12432-12438.

**Miller, B.** & **McInnes, D.** (2011) Management of a dam sytems via optimal price control. *Procedia Computer Science.* Sato, M., Matsuoka, S., Dick van Albada, G., Dongarra, J. & Sloot, P.M.A. (eds.). Netherlands: Elsevier, Vol. 4, pp. 1373-1382.

**Miller, B.** & **McInnes, D.** (2011) Optimal management of a two dam system via stochastic control: parallel computing approach. *Proceedings of the 50th IEEE Conference on Decision and Control and European Control Conference (CDC-ECC).* Polycarpou, M. (ed.). USA: Institute of Electrical and Electronics Engineers, pp. 1417-1423.

**Miller, B.**, Miller, G. & Semenikhin, K. (2011) Methods to design optimal control of Markov process with finite state set in the presence of constraints. *Automation and Remote Control* 72(2), pp. 323-341.

**Miller, B.**, Rabinovich, E. & Bentsman, J. (2011) Spatiotemporal singular transformation in dynamical systems with impacts and its use in obtaining generalized solution of painleve problem. *Proceedings of the 18th IFAC World Congress.* Bittani, S., Cenedese, A. & Zampieri, S. (eds.). United Kingdom: Elsevier, Vol. 8, pp. 3463-3473.

**Miller, B.**, Stepanyan, K., Miller, A. & Andreev, M. (2011) 3D path planning in a threat environment. *Proceedings of the 50th IEEE Conference on Decision and Control and European Control Conference (CDC-ECC).* Polycarpou, M. (ed.). USA: Institute of Electrical and Electronics Engineers, pp. 6864-6868.

**Miller, B.**, Stepanyan, K., Miller, A. & Andreev, M. (2011) Parallel implementation of the UAV path planning in a hazard environment. *Proceedings of the XVII International Conference on Computational Mechanics and Modern Applied Software Systems.* Goryacheva, I., Pizymov, U. & Chezny, G. (eds.). Moscow Russia: Moscow Aviation Institute, pp. 698-700.

Nazin, A. & **Miller, B.** (2011) Online mirror descent algorithm for controlled homogeneous finite Markoc chains with unknown mean losses. *Proceedings of the 18th IFAC World Congress.* Bittani, S., Cedenese, A. & Zampieri, S. (eds.). United Kingdom: Elsevier, Vol. 18, pp. 12421-12426.

Nazin, A. & **Miller, B.** (2011) The mirror descent control algorithm for weakly regular homogeneous finite Markov chains with unknown mean losses.

Oldmeadow, C. & **Keith, J.** (2011) Model Selection in Bayesian Segmentation of multiple DNA alignments. *Bioinformatics* 27, pp. 604-610.

**Phatarfod, R.M.** (2011) Further aspects of gambling with the Kelly criterion. *The Mathematical Scientist* 36(1), pp. 47-56.

Qiao, M., Qi, H., Liu, A. & **Tian, T.** (2011) Analysis of Stability and Permanence for a HBV Model with Impulsive Releasing Immune Factor, *Chinese Annals of Mathematics, Series A*, 32, pp. 173-184. (In Chinese.) English translation was published in *Chinese Journal of Contemporary Mathematics*, 31(2), 149-162.

**Rau, C.** & Chiu, S. (2011) Grain rotations and distortions in the asymptotic variance of vacancy of the Boolean model. *Journal of Mathematical Analysis and Applications* 384(2), pp. 647-657.

**Sudbury, A.** (2011) Vectors and the 9-point circle. *Mathematical Gazette* 95(534), pp. 540-542.

**Tian, T.** (2011) Stochastic dynamics of a Hepatitis B virus transmission model. *Proceedings of the 2011 IEEE International Symposium on IT in Medicine and Education*. Li, S. & Dai, Y. (eds.). Beijing China: Institute of Electrical and Electronics Engineers, Vol. 1, pp. 496-500.

**Tian, T.** (2011) Stochastic modelling of gene regulatory networks. *Applied statistics for network biology: Methods in systems biology.* Dehmer, M., Emmert-Streib, F., Graber, A. & Salvador, A. (eds.). 1 ed. Germany: Wiley-Blackwell, pp. 13-37.

**Tian T.** (2011) Stochastic models for studying the degradation of mRNA molecules. *Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2011).* Wu, F-X., Zaki, M., Morishita, S., Pan, Y., Wong, S., Christianson, A. & Hu, X. (eds.). Los Alimos USA: Institute of Electrical and Electronics Engineers, pp. 167-172.

**Tian, T.**, Olson, S., Whitacre, J.M. & Harding, A. (2011) The origins of cancer robustness and evolvability. *Integrative Biology* 3(1), pp. 17-30.

**Tokarev, D.V.** (2011) A generalisation of Descartes' rule of signs. *Journal of the Australian Mathematical Society* 91(3), pp. 415-420.

### 2010

**Abramov, V.M.** (2010) Takacs' asymptotic theorem and its applications: A survey. *Acta Applicandae Mathematicae* 109(2), pp. 609-651. *download*

**Clark, R.M.** & Thompson, R.E. (2010) Predicting the impact of global warming on the timing of spring flowering. *International Journal of Climatology* 30, pp. 1599-1613.

Graham, J.P., O'Donnell, C.J., Craig, P.J., Walker, J.L., Hill, A.J., Cirillo, J.N., **Clark, R.M.**, Gledhill, S.R. & Schneider-Kolsky, M.E. (2010) The application of computerised tomography to the dental adeing of children and adolescents. *Forensic Science International* 195, pp. 58-62. *download*.

**Klebaner, F.C.** (2010) Approximations in population-dependent branching processes. *Lecture Notes in Statistics - Proceedings.* Gonzalez, M.V., del Puerto, I.M., Martinez, R., Molina, M., Mota, M. & Ramos, A. (eds.). Germany: Springer Verlag, Vol. 197, pp. 71-78.

**Klebaner, F.C.** & Liptser, R.S. (2010) Asymptotics in Ruin Analysis in a diffusion model. *Teor. Veroyatn. Primenen.* (Russian), 55(2), 1-9. *download*.

**Klebaner, F.C.** & **Azmy, E.** (2010) Solutions and simulations of some one-dimensional stochastic differential equations. *Asia-Pacific Financial Markets* 17, pp. 365-372.

Miller, A. & **Miller, B.** (2010) Congestion avoidance with the aid of stochastic control. *Proceedings of the 49th IEEE Conference on Decision and Control.* Ghorbel, F. (ed.). USA: Institute of Electrical and Electronics Engineers, pp. 552-558.

**Miller, B.**, Miller, G. & Siemenikhin, K. (2010) Towards the optimal control of Markov chains with constraints. *Automatica* 46(9), pp. 1495-1502.

**Miller, B.**, Stepanyan, K.V. & Miller, A.B. (2010) Simulation of permissible UAV trajectories. *Proceedings of the VIII International Conference on Nonequilibrium Processes in Nozzles and Jets, NPNJ'2010.* Levin, V.A., Pirumov, U.G. & Chernyi, G.G. (eds.). Moscow Russia: Moscow Aviation Institute, pp. 321-323.

Oldmeadow, C., Mengersen, K., Mattick, J. & **Keith, J.** (2010) Multiple evolutionary rate classes in animal genome evolution. *Molecular Biology and Evolution* 27(4), pp. 942-953.

Qiao, M., Qi, H. & **Tian, T.** (2010) Steady state solution and stability of an age-structured MSIQR epidemic model. *Intelligent Information Management* 2(5), pp. 316-324.

Stepanyan, K.V., Miller, A.B. & **Miller, B.** (2010) Path planning of UAV in dangerous environment (in Russian). *Proceedings of Conference on Information Technologies and Systems.* Kuleshov, A. (ed.). Moscow Russia: Russian Academy of Sciences, pp. 263-268.

**Sudbury, A.** (2010) Two-stage testing using selection schemes. *Statistics in Medicine* 29(21), pp. 2194-2199. *download**.*

**Tian, T.** (2010) Stochastic models for inferring genetic regulation from microarray gene expression data. BioSystems 99(3), pp. 192-200. *download*.

**Tian, Y.**, Zhu, Z., **Klebaner, F.C.**, & **Hamza, K.** (2010) Option pricing with the SABR model on the GPU. *Proceedings of the 3rd Workshop on High Performance Computational Finance.* Dixon, M., Daly, D., Eleftheriou, M., Moreira, J. & Ryu, K. (eds.). Piscataway USA: Institute of Electrical and Electronics Engineers, pp. 1-8.

Tibby, J., Gell, P., Hancock, G. & **Clark, R.M.** (2010) Complex reservoir sedimentation revealed by an unusual combination of sediment records, Kangaroo Creek Reservoir, South Australia. *Journal of Paleolimintology*, 43, pp. 535-549. *download*.

Wang, J. & **Tian, T.** (2010) Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. *BMC Bioinformatics* 11(36), pp.1-12. *download*.

### 2009

**Abramov, V.M.** (2009) Queueing Systems, Networks and Telecommunication Systems: Asymptotic Methods for Queueing Systems and Networks with Application to Telecommunications. Saarbrucken, Germany: Lambert Academic Publishing. ISBN 978-3-8383-2416-6

Bentsman, J., **Miller, B.**, Rubinovich, E. & Mazumder, S. K. (2009) Optimal control of dynamical systems with active singularities under single- and multi-impact sequences: A ball/racket system example. *Joint 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference.* Bailleieul, J. & Guo, L. (eds.). USA: Institute of Electrical and Electronics Engineers, pp. 5033-5038.

**Buchmann, B.** (2009) Weighted empirical processes in the nonparametric inference for Levy Processes. *Mathematical Methods of Statistics* 18(4), pp. 281-309. *download*.

**Buchmann, B.** & Chan, N.H. (2009) Integrated functionals of normal and fractional processes. *The Annals of Applied Probability* 19(1), pp. 47-90. - *download*.

**Hamza, K.** (2009) An exact test for hazard similarity. *Australian and New Zealand Journal of Statistics* 51(2), pp. 143-159. *download*.

**Hamza, K.**, Jagers, P., **Sudbury, A.W.** & **Tokarev, D.V.** (2009) The mixing advantage is less than 2.** ***Extremes* 12, pp. 19-31. *download*.

**Hamza, K.** & Maaouia, F. (2009) On the identification of a supercritical branching process. [Sur l'identification d'un processus de branchement surcritique.] *Comptes Rendus Mathematique* 347(5-6), pp. 321-325. download

**Klebaner, F.C.** & Landsman, Z. (2009) Option pricing for log-symmetric distributions of returns. *Methodology and Computing in Applied Probability* 11, pp. 339-357. download.

**Miller, B.** (2009) Optimization of queueing system via stochastic control. *Automatica* 45(6), pp. 1423-1430. *download*.

**Miller, B.**, Miller, G. & Siemenikhin, K. (2009) Control of Markov chains with constraints. *Proceedings of the VIII International Conference on System Identification and Control Problems.* Lototsky, V. A. (ed.). Moscow Russia: MAIK Nauka, pp. 1-23.

**Miller, B.**, Miller, G. & Siemenikhin, K. (2009) Optimal control of Markov chains with constraints. *Joint 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference*. Bailleiieul, J. & Guo, L. (eds.). USA: Institute of Electrical and Electronics Engineers, pp. 512-518.

**Miller, B.** & Rabinovich, E. (2009) Impulsive control with impulsive actions of two types. *Automation and Remote Control* 70(11), pp. 1795-1813.

**Sudbury, A.** (2009) Random sequential absorption on random trees. *Journal of Statistical Physics* 136(1), pp. 51-58. *download*.

**Tian, T.** (2009) Estimation of kinetic rates of MAP kinase activation from experimental data. *Proceedings 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS).* Huang, H., Yenduri, S. & Zhao, Z. (eds.). USA: Institute of Electrical and Electronics Engineers, pp. 457-462.

**Tokarev, D.V.** & Borovkov, K.A. (2009) On expectations of maxima of sets of independent random variables. *Statistics and Probability Letters* 79(23), pp. 2381-2388.

### 2008

**Abramov, V.M.** (2008) The effective bandwidth problem revisited. *Stochastic Models* 24(4), pp. 527-557. *download*.

**Abramov, V.M.** (2008) Continuity theorems for the M/M/1/n queueing system. *Queueing Systems : theory and applications* 59(1), pp. 63-86. *download*.

**Abramov, V.M.** (2008) Further analysis of confidence intervals for large client/server computer networks. *Reliability and Risk Analysis: Theory and Applications* 1(1), pp. 22-28. *download*

**Abramov, V.M.** (2008) Large closed queueing networks in semi-Markov environment and their applications. *Acta Applicandae Mathematicae* 100(3), pp. 201-226. *download*.

**Abramov, V.M.** & **Klebaner, F.C.** (2008) Prediction of missing observations by a control method. *Advances and Applications in Statistics* 8, pp. 109-129. *download*.

Bentsman, J., **Miller, B.** & Rubinovich, E.Y. (2008) Dynamical systems with active singularities: Input/State/Output modelling and control. *Automatica* 44 (7), pp. 1741-1752. *download*.

Bentsman, J., **Miller, B.**, Rubinovich, E.Y. & Mazumder, S.K. (2008) Input/state/output modelling and control of dynamical systems with active singularities: Single- and multi-impact sequences. *Proceedings of the 47th IEEE Conference on Decision and Control.* Abdallah, C.T. & Parisini, T. (eds.). Cancun Mexico: Institute of Electrical and Electronics Engineers, pp. 2123-2128.

**Buchmann, B.**, Maller, R. & Szimayer, A. (2008) An almost sure functional limit theorem at zero for a class of Levy processes normed by the square root function, and applications. *Probability Theory and Related Fields* 142(1), pp. 219-247. - *download*.

Gouet, R. & **Sudbury, A.W.** (2008) Blocking and Dimer processes on the Cayley tree. J*ournal of Statistical Physics* 130(5), pp. 935-955.

Hall, P., Qiu, P. & **Rau, C.R.F.** (2008) Tracking edges, corners and vertices in an image. *Scandinavian Journal of Statistics* 35, pp. 1-17.

**Hamza, K.** (2008) A new mean with inequalities. *The Bulletin of the Australian Mathematical Society* 77(3), pp. 365-371. *download*.

**Hamza, K.** & **Klebaner, F.C.** (2008) On the implicit Black-Scholes formula.** ***Stochastics: An International Journal of Probability and Stochastic Processes* [Formerly known as Stochastics and Stochastics Reports], 80(1), pp. 97-102. *download*.

**Klebaner, F.C.** & Chiganski, P. (2008) Distribution of the Brownian motion on its way to hitting zero. *Electronic Communications in Probability* 13(1), pp. 641-648. *download*.

**Klebaner, F.C.** & Liptser, R. (2008) Cramer's theorem for nonnegative multivariate point processes with independent increments. *Topics in Stochastic Analysis and Nonparametric Estimation*. IMA Volumes in Mathematics and its Applications, Vol. 145, Springer New York, pp. 21-28. - *download*.

**Klebaner, F.C.** & Liptser, R. (2008) Large deviations analysis of extinction in branching models. *Mathematical Populations Studies* 15(1), pp. 55-69.

**Miller, B.** (2008) Access and service rate control in queueing system. *Proceedings of the 17th IFAC World Congress 2008.* Chung, M. J. & Misra, P. (eds.). Seoul Korea: International Federation of Automatic Control, Vol. 17, pp. 3683-3688. *download*.

**Miller, B.** (2008) Optimization of stochastic networks via stochastic control.* Proceedings of VII International Conference System Identification and Control Problems.* Vassilyev, S.N. (ed.). Moscow Russia: MAIK Nauka, pp. 385-397.

**Norton, P.** & **Phatarfod, R.** (2008) Optimal strategies in one-day cricket. *Asia-Pacific Journal of Operational Research* 25(4), pp. 495-511. download.

**Sudbury, A.** (2008) The expected duration of random sequential adsorption. *Annals of Applied Probability* 18(1), pp. 100-108. *download*.

**Sudbury, A.** (2008) Emptiness probabilities in random sequential adsorbtion on the Bethe lattice. Modern Physics Letters B, 22(30), pp. 2931-2936. *download*.

Thompson, R. & **Clark, R.M.** (2008) Is spring starting earlier? *Holocene* (special issue in honour of F. Oldfield), 18(1), pp. 95-104.

### 2007

**Abramov, V.M.** (2007) Confidence intervals associated with performance analysis of symmetric large closed client/server computer networks. *Reliability and Risk Analysis: Theory and Applications*, 2(2), pp. 34-42. - *download*

**Abramov, V.M.** (2007) Multiserver queueing systems with retrials and losses. *ANZIAM Journal* [Formerly known as Journal of the Australian Mathematical Society, Ser. B], 48(3), pp. 297-314. - *download*.

**Abramov, V.M.** (2007) Asymptotic analysis of loss probabilities in GI/M/m/n queueing systems as n increases to infinity. *Quality Technology and Quantitative Management* 4(3), pp. 379-393. - *download*.

**Abramov, V.M.** (2007) Optimal control of a large dam. *Journal of Applied Probability* 44(1), pp. 249-258. - *download*.

**Abramov, V.M.** & **Klebaner, F.C.** (2007) Estimation and prediction of a non-constant volatility. *Asia-Pacific Financial Markets*, 14(1), pp. 1-23. - *download*.

Bentsman, J. & **Miller, B.** (2007) Dynamical systems with active singularities of elastic type: A modelling and control synthesis framework. *IEEE Transaction on Automation Control* 52(1), pp. 39-55. - *download*.

Bentsman, J., **Miller, B.**, Rubinovich, E. & Zheng, K. (2007) Hybrid dynamical systems with controlled discrete transitions. *Nonlinear Analysis: Hybrid Systems* 1 (4), pp. 466-481. *download*.

Brand, M., Sanjayan, J.G. & **Sudbury, A.W.** (2007) Dynamic response of pedestrian bridges for random crowd-loading. *Australian Journal of Civil Engineering*, Engineers Australia 3(1), pp. 27-38. *download*.

**Buchmann, B. **& Chan, N.H. (2007) Asymptotic theory of least squares estimators for nearly unstable processes under strong dependence. *Annals of Statistics* 35(5), pp. 2001-2017.

Dufour, F. & **Miller, B.** (2007) Necessary conditions for optimal singular stochastic control problems. *Stochastics: An International Journal of Probability and Stochastic Processes* [Formerly known as Stochastics and Stochastics Reports], 79(5), pp. 469-504. - *download*.

Dufour, F. & **Miller, B.** (2007) Maximum principle in non-linear optimal stochastic singular control problems. *Proceedings of European Control Conference 2007.* Tzafestas, S.G. (ed.). Athens Greece: European Union Control Association, pp. 1284-1291. *download*.

Ehrmann, E.H., Messer, H.M. & **Clark, R.M.** (2007) Flare-ups in endodontics and their relationship to various medications. *Australian Endodontic Journal:* the journal of the Australian Society of Endodontology Inc. 33(3), pp. 119-130. *download*.

**Hamza, K.** & **Klebaner, F.C.** (2007) On one inverse problem in financial mathematics. *Journal of Uncertain Systems* 1(4), pp. 246-255. *download*.

**Hamza, K.** & **Klebaner, F.C.** (2007) A family of non-Gaussian martingales with Gaussian marginals. *Journal of Applied Mathematics and Stochastic Analysis* 2007, pp. 1-19, Article ID 92723. *download*.

Jagers, P., **Klebaner, F.C.** & Sagitov, D. (2007) On the path to extinction. *Proceedings of the National Academy of Sciences of the United States of America* 104(15), pp. 6107-6111. download.

Jagers, P., **Klebaner, F.C.** & Sagitov, D. (2007) Markovian paths to extinction. *Advances in Applied Probability* 39(2), pp. 569-587. download.

**Klebaner, F.C.**, **Lim, A.K.K.** & Liptser, R. (2007) Functional Central Limit Theorem and Moderate Deviation Principle for stochastic Lotka-Volterra model. *Acta Applicandae Mathematicae* 97, pp. 53-68. *download*.

**Klebaner, F.C.**, Roesler, U. & Sagitov, S. (2007) Transformations of Galton-Watson processes and linear fractional reproduction. *Advances in Applied Probability* 39(4), pp. 1036-1053. download.

**Miller, B.** & Bentsman, J. (2007) Generalized solutions in systems with active unilateral constraints. *Nonlinear Analysis: Hybrid Systems*, 1(4), pp. 510-526. - *download*.

**Miller, B.** & Dufour, F. (2007) Generalised solutions in nonlinear optimal stochastic control problems (impulsive and singular controls). *Proceedings of VI International Conference - System Identification and Control Problems.* Lototsky, V.A. (ed.). Moscow RUSSIA: V A Trapeznikov Institute of Control Sciences, pp. 847-868.

**Miller, B.** & Rubinovich, E. (2007) Image motion compensation at charge-coupled device photographing in delay-integration mode. *Automation and Remote Control* 68(3), pp. 564-571. - *download*.

**Phatarfod, R.M.** (2007) Some aspects of gambling with the Kelly criterion. *The Mathematical Scientist* 32, pp. 23-31. - *download*.

Risbey, J., **Hamza, K.** & Marsden, J. (2007) Use of climate scenarious to aid in decision analysis for interannual water supply planning. *Water Resources Management* 21(6), pp. 919-932. - *download*.

### 2006

**Abramov, V.M.** (2006) Analysis of multiserver retrial queueing system: A martingale approach and an algorithm of solution. *Annals of Operations Research* 141(1), pp. 19-50. - *download*.

**Abramov, V.M. **(2006) Stochastic inequalities for single-server loss queueing systems. *Stochastic Analysis and Applications* 24(6), pp. 1205-1221. - *download*.

**Buchmann, B.** & Kluppelberg, C. (2006) Fractional integral equations and state space transforms. *Bernoulli* 12(3), pp. 431-456.

Burrage, K., Mac, S. & **Tian, T.** (2006) Accelerated leap methods for simulationg discrete stochastic chemical kinetics. *2nd Multidisciplinary International Symposium on Positive Systems (POSTA 2006).* Berlin Germany: Springer Verlag, pp. 359-366.

Dufour, F & **Miller, B.** (2006) Maximum principle for singular stachastic control problems. *SIAM Journal of Control and Optimization* 45(2), pp. 668-698. - *download*.

Fielding, M., **Klebaner, F.C.** & Landsman, Z. (2006) Random volatility and option prices with the generalized Student t-distribution. *Advances and Applications in Statistics* 6(1), pp. 111-120.

**Hamza, K.** & **Klebaner, F.C.** (2006) Nonexistance of non-constant volatility in the Black-Scholes formula. Discrete and Continuous Dynamic Systems - Series B, 6(4), pp. 829-834. - *download*.

**Hamza, K.** & **Klebaner, F.C.** (2006) On solutions of first order stochastic partial differential equations. *Far East Journal of Theoretical Statistics* 20(1), pp. 13-25. - *download*.

**Klebaner, F.C.**, **Le, T.T.N.** & Liptser, R. On estimation of volatility surface and prediction of future spot volatility. *Applied Mathematical Finance* 13(3), pp. 245-263. - *download*.

**Klebaner, F.C.** & Liptser, R. (2006) Likely path to extinction in simple branching models with large initial population. *Journal of Applied Mathamatics and Stochastic Analysis* 2006: ID 60376. - *download*.

**Miller, B.** & Bentsman, J. (2006) Optimal control problems in hybrid systems with active singularities. *Nonlinear Analysis, Theory, Methods and Applications* 65(5), pp. 999-1017. - *download*.

**Miller, B.** & Bentsman, J. (2006) Representation of motion of controlled dynamic systems with unilateral constraints. *Proceedings of the 45th IEEE Conference on Decision and Control.* Misra, P. (ed.). USA: Institute of Electrical and Electronics Engineers, pp. 4787-4792.

Steif, J.E. & **Sudbury, A.W.** (2006) Some results for poisoning in catalytic model. *Electronic Communications in Probability* 11, pp. 168-177. *download*.

Thompson, R. & **Clark, R.M.** (2006) Spatio-temporal modelling and assessment of within-species phenological variability using thermal time methods. I*nternational Journal of Biometeorology* 50(5), pp. 312-322. *download*.

### 2005

Bentsman, J. & **Miller, B.** (2005) Modelling and control of dynamical systems with active singularities and sensing in a singular motion. *Proceedings of the 16th IFAC World Congress.* Piztek, P. (ed.). Oxford UK: Elsevier, pp. 1-6.

**Buchmann, B.** & Kluppelberg, C. (2005) Maxima of stochastic processes driven by fractional Brownian motion. *Advances in Applied Probability* 37(3), pp. 743-764.

Dufour, F & **Miller, B.** (2005) Singular stochastic maximum principle. *Proceedings of the 16th IFAC World Congress.* Piztek, P. (ed.). Oxford UK: Elsevier, pp. 1-6.

Emeliyanov, D., Rubinovich, E. & **Miller, B.** (2005) Information set-based guidance algorithm against a decelerating maneuvering target. *IEEE Transactions on Aerospace and Electronic Systems* 41, pp. 65-74.

Goldentayer, L., **Klebaner, F.C.** & Liptser, R. (2005) Tracking Volatility. *Problems of Information Transmission* 41(3), pp. 212-229. *download*.

**Hamza, K.**, Jacka, S. & **Klebaner, F.C.** (2005) The Equivalent Martingale Measure Conditions in a General Model for Interest Rates. *Advances in Applied Probability* 37(2), pp. 415-434. - *download*.

**Klebaner, F.C.** (2005) Behaviour of a dynamic system far from its equilibrium. *Complex Analysis and Dynamical Systems II.* Agranovsky, M., Karp, L. & Shoikhet, D. (eds.). Ramat-Gan Israel: American Mathematical Society, Vol. 382, pp. 229-231.

**Klebaner, F.C.** (2005) Discrete time dynamical systems as population models. *Branching processes: Variation, Growth, and Extinction of Populations.* Haccou, P., Jagers, P. & Vatutin, V.A. (eds.). Cambridge UK: Cambridge University Press, pp. 88-94.

**Klebaner, F.C.** (2005) *Introduction to Stochastic Calculus with Applications*. 2nd ed. London UK: Imperial College Press.

**Klebaner, F.C.** (2005) Population size dependent processes. *Branching processes: Variation, Growth, and Extinction of Populations.* Haccou, P., Jagers, P. & Vatutin, V.A. (eds.). Cambridge UK: Cambridge University Press, pp. 133-135.

**Klebaner, F.C.** (2005) Slowly growing populations. *Branching processes: Variation, Growth, and Extinction of Populations.* Haccou, P., Jagers, P. & Vatutin, V.A. (eds.). Cambridge UK: Cambridge University Press, pp. 174-176.

**Le, T.T.N.** (2005) Stochastic Market Volatility Models. *Applied Financial Economics Letters* 1, pp. 177-188. *download*.

**Miller, B.**, Avrachenkov, K., Stepanyan, K. & Miller, G. (2005) Flow control as a stochastic optimal control problem with incomplete information. *Problems of Information Transmission* 41(2), pp. 150-170.

**Miller, B.** & Bentsman, J. (2005) The singularity opening approach to control of mechanical systems with constraints. *Proceedings of the 2nd IFAC Workshop.* Astolfi, A., Gordillo, F. & van der Shaft, A.J. (eds.). Oxford UK: Elsevier, pp. 1-6.

**Miller, B.** & Rubinovich, E. (2005) *Optimization of Dynamic Systems with Impulse Control.* 1 ed. Moscow Russia: Nauka.

Penrose, M.D. & **Sudbury, A.W.** (2005) Exact and approximate results for deposition and annihilation processes on graphs. *Annals of Applied Probability* 15(1B), pp. 853-889. - *download*.

**Sudbury, A.W.** (2005) Rigorous lower bounds for extinction probabilities of the contact process. *Journal of Applied Probability* 42(3), pp. 902-904. - *download*.

### 2004

**Abramov, V.M.** (2004) A large closed queueing network containing two types of node and multiple customer classes: one bottleneck station. *Queueing Systems : theory and applications* 48(1-2), pp. 45-73.

**Abramov, V.M.** (2004) Asymptotically flat and scalar flat metrics on R3 admitting a horizon. *Proceedings of the American Mathematical Society* 132(1), pp. 217-222.

**Abramov, V.M. **& Liptser, R. (2004) On existence of limiting distribution for time-nonhomogeneous countable Markov process. *Queueing Systems : theory and applications* 46(3), pp. 353-361.

Burrage, K. & **Tian, T.** (2004) Implicit stochastic Runge-Kutta methods for stochastic differential equations. *BIT (Copenhagen)* 44(1), pp. 21-39.

**Clark, R.M.** and Thompson, R. (2004) Botanical records reveal changing seasons in a warning world. *Australian Science* 25(9), pp. 37-39.

Dufour, F & **Miller, B.** (2005) Singular stochastic control problems. *SIAM Journal on Control and Optimization* 43(2), pp. 708-730.

Fock, J., Galea, M.P., Stillman, B.C., Rawicki, B. & **Clark, R.M.** (2004) Functional outcome following Botulinum toxin A injection to reduce spastic equinus in adults with traumatic brain injury. *Brain Injury* 18(1), pp. 57-63. *download*.

**Klebaner, F.C.** & Jagers, P (2005) Branching processes in near critical random environment. *Journal of Applied Probability* 41A, pp. 17-23.

Katori, M., Konno, N., **Sudbury, A.W.** & Tanemura, H. (2004) Dualities for the Domany-Kinzel model. *Journal of Theoretical Probability* 17(1), pp. 131-144. *download*.

**Sudbury, A.W. **(2004) The annihilating process on random trees and the square lattice. *Journal of Applied Probability* 41, pp. 816-831.

**Tian, T.** & Burrage, K. (2004) Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda. *Journal of Theoretical Biology* 227(2), pp. 229-237.