Research Interests
- Computational Biology
- Development and analysis of simulation methods for biochemical systems
- Stochastic modelling and computation in Systems Biology
- Applications to gene regulatory networks
Research Opportunities
If you are interested in studying in any of these areas, please e-mail me. I am looking for postdocs, graduate and undergraduate students at Ryerson and Western University.
There is a growing demand for graduates in Computational Biology. For career opportunities in academia/industry please visit the link for
Computational Biology jobs.
Selected Publications
Refereed papers
- A. Sayyidmousavi, K. Rohlf, S. Ilie, A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems, Mathematical Biosciences, 312 (2019) 23-32. [journal]
- M. Morshed, B. Ingalls, S. Ilie, An effective implicit finite-difference method for sensitivity analysis of stiff stochastic discrete biochemical systems, IET Systems Biology, 12 (4) (2018) 123-130. [journal]
- A. Sayyidmousavi, S. Ilie, An efficient hybrid method for stochastic reaction-diffusion biochemical systems with delay, AIP Advances, 7 (2017) 125305. [journal]
- M. Morshed, B. Ingalls, S. Ilie, An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems, BioSystems, 151 (2017) 43-52. [journal]
- J.M.A. Padgett, S. Ilie, An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems, AIP Advances, 6(3) (2016) 035217. [journal]
- S. Ilie, A. Storjohann, Abstracts of the 2015 East Coast Computer Algebra Day, ACM Comm. Computer Algebra, 50(1) (2016), 35-39.
- R. Strehl, S. Ilie, Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics, Journal of Chemical Physics, 143 (23) (2015), 234108. [journal]
- S. Ilie, K.R. Jackson, W.H. Enright, Adaptive time-stepping for the strong numerical solution of stochastic differential equations, Numerical Algorithms, 68(4) (2015) 791-812. [journal]
- S. Ilie, M. Morshed, Adaptive time-stepping using control theory for the Chemical Langevin Equation, Journal of Applied Mathematics, Vol. 2015 (2015), Article ID 567275.
- S. Ilie, M. Morshed, Automatic simulation of the Chemical Langevin Equation, Applied Mathematics, 4(1A) (2013) 235-241. [journal]
- S. Ilie, S. Gholami, Simplifying stochastic mathematical models of biochemical systems, Applied Mathematics, 4(1A) (2013) 248-256, doi: 10.4236/am.2013.41A038. [journal]
- S. Ilie, Variable time-stepping in the pathwise numerical solution of the chemical Langevin equation, Journal of Chemical Physics, 137 (2012) 234110. [journal]
- S. Ilie, A. Teslya, An adaptive stepsize method for the chemical Langevin equation, Journal of Chemical Physics, 136 (2012) 184101. [journal]
- S. Ilie, Efficient computation of spaced seeds, BMC Research Notes, 5(123) (2012). [journal]
- S. Ilie, R. Savani, Noise and oscillations in chemically reacting systems, Proc. of the 2011 International Conference on Scientific Computing (CSC'11), CSREA Press, USA, 2011, 81--86.
- L. Ilie, F. Fazayeli, S. Ilie. HiTEC: accurate error correction in high-throughput sequencing data, Bioinformatics, 27(3) (2011) 295 -- 302. [journal]
- L. Ilie, S. Ilie, S. Khoshraftar, A. Mansouri Bigvand, Seeds for effective oligonucleotide design, BMC Genomics, 12:280 (2011). [journal]
- L. Ilie, S. Ilie, A. Mansouri Bigvand, Bioinformatics, 27(17) (2011) 2433--2434. [journal]
- S. Ilie, E. Kudashkina, A model reduction technique for stochastic biochemical kinetics, Proc. of the 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP'10), Vol. II, CSREA Press, Las Vegas, 2010, 448--453.
- S. Ilie, W.H. Enright, K.R. Jackson, Numerical solution of stochastic models of biochemical kinetics, Canadian Applied Mathematics Quarterly, 17(3)(2009) 523 -- 554.[PDF]
- W. Wu, G. Reid, S. Ilie, Implicit Riquier bases for PDAE and their semi-discretizations, Journal of Symbolic Computation, 44(7)(2009) 923--941.[PDF]
- S. Ilie, R.M. Corless, C. Essex, The computational complexity of extrapolation methods, Mathematics in Computer Science, 2(4)(2009) 557-566.
- L. Ilie, S. Ilie, Fast computation of neighbor seeds, Bioinformatics, 25(6)(2009) 822--823.[PDF]
- S. Ilie, G. Soederlind, R.M. Corless, Adaptivity and computational complexity in the numerical solution of ODEs, Journal of Complexity, 24(3)(2008) 341--361.[PDF]
- R.M. Corless, S. Ilie, Polynomial cost for solving IVP for high-index DAE, BIT, 48(1)(2008) 29--49. [PDF]
- L. Ilie, S. Ilie, Multiple spaced seeds for homology search, Bioinformatics, 23(22)(2007) 2969--2977. [PDF]
- L. Ilie and S. Ilie, Fast computation of multiple spaced seeds for homology search, in: R. Giancarlo, S. Hannenhalli, eds., Proc. of the 7th Workshop on Algorithms in Bioinformatics (WABI'07), Lecture Notes in Bioinformatics 4645, Springer, Berlin, 2007, 346--358.
- D.J. Jeffrey, S. Ilie, J.M. Gardiner, S.W. Campbell: A symbolic-numeric approach to an electric field problem, in: D. Wang, L. Zhi, eds., Symbolic-Numeric Computation, Trends in Mathematics, Birkhauser, 2007, 349--359.
- L. Ilie and S. Ilie, Long spaced seeds for homology search, Proc. of the 2007 International Conference on Bioinformatics and Computational Biology (BIOCOMP'07), Vol. I, CSREA Press, Las Vegas, 2007, 3--8. [PDF]
- C. Essex, S. Ilie, R.M. Corless, Broken symmetry and long-term forecasting, Journal of Geophysical Research, 112(D24)(2007) D24S17.
- S. Ilie, R.M. Corless, G. Reid, Numerical solutions of index-1 differential algebraic equations can be computed in polynomial time, Numerical Algorithms, 41(2)(2006) 161--171. [PDF]
- S. Ilie, D.J. Jeffrey, A note on Laplace's equation inside a cylinder, Applied Mathematics Letters , 18 (1)(2005) 55--59. [PDF]
- D.J. Jeffrey, S. Ilie, An inclusion in a microchannel of a porous medium, in: S.N. Bora, ed., Environmental Fluid Mechanics, Allied Publishers, 2005 (ISBN 81-7764-788-1), 112--116.
- D.J. Jeffrey, S. Ilie, J.M. Gardiner, A symbolic-numeric approach to potential problems in physics, in: D. Wang, L. Zhi, eds., Proc. of the International Workshop on Symbolic-Numeric Computation (SNC 2005) (satellite conference of ISSAC 2005), Xi'an, China, July 19-21, 2005, 355--364.
- F. Jabeen, S. Ilie, Stochastic simulation of well-stirred biochemical systems, Canadian Applied and Industrial Mathematics Society Meeting (CAIMS 2018), Toronto, 2018.
- M. Morshed, B. Ingalls, S. Ilie, SIAM Workshop on Parameter Space Dimension Reduction (DR17)}, Pittsburgh, USA, 2017.
- M. Morshed, S. Ilie, Efficient and accurate numerical methods for stochastic models of biochemical kinetics, Chemical Biophysics Symposium 2014, Toronto, 2014.
- J. Padgett, S. Ilie, Canadian Mathematics Society Meeting (CMS 2014), Hamilton, 2014.
- F. Gassoumov, S. Ilie, Canadian Mathematics Society Meeting (CMS 2014), Hamilton, 2014.
- F. Gassoumov, S. Ilie, Canadian Mathematics Society Meeting (CMS 2013), Ottawa, 2013.
- A.Teslya, S. Ilie, An adaptive tau-leaping method for the simulation of chemically reacting systems, 7th International Congress on Industrial and Applied Mathematics (ICIAM 2011), Vancouver, 2011.
- A.Teslya, G. Penner, S. Ilie, Improved models for in vitro selection of aptamers, 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'10), Boston, 2010.
- L. Ilie and S. Ilie, Efficient computation of good neighbor seeds, 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'09) and 8th European Conference for Computational Biology (ECCB'09), Stockholm, 2009.
- L. Ilie and S. Ilie, Improved algorithms for local alignment, 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'08), Toronto, 2008.
- R.M. Corless, S. Ilie, G. Reid, Computational complexity of numerical solution of polynomial systems, Transgressive Computing 2006, Granada, Spain, April 24-26, 2006, 405--410.
- S. Gholami, S. Ilie, Simplifying stochastic discrete models of biochemical networks, Canadian Mathematics Society Winter Meeting (CMS 2019), Toronto, 2019.
- S. Ilie, An effective hybrid strategy for stochastic reaction-diffusion biochemical systems with delay, Canadian Applied and Industrial Mathematics Society Annual Meeting (CAIMS'18), Toronto, 2018.
- S. Gholami, S. Ilie, Model reduction of stochastic models of biochemical systems, Canadian Applied and Industrial Mathematics Society Meeting (CAIMS 2018), Toronto, 2018.
- S. Ilie, University of Guelph, BioMS Seminar, Guelph, 2017.
- S. Ilie, Western University, Applied Mathematics Colloquium, London, 2015.
- S. Ilie, J.M. Padgett, Adaptive time-stepping in the numerical solution of the reaction-diffusion master equation, AMMCS-CAIMS Congress 2015, Waterloo, 2015.
- S. Ilie, Effective methods for stochastic biochemical kinetics, Canadian Mathematics Society Meeting (CMS 2014), Hamilton, 2014.
- R. Strehl, S. Ilie, K. Rohlf, Efficient stochastic simulation of multiscale reaction-diffusion models, Canadian Mathematics Society Meeting (CMS 2014), Hamilton, 2014.
- S. Ilie, University of Waterloo, Quantitative Biology Seminar, Waterloo, 2014.
- S. Ilie, Efficient methods for stochastic simulations of biochemical systems, Canadian Applied and Industrial Mathematics Society Meeting (CAIMS 2014), Saskatoon, 2014.
- S. Ilie, Adaptive time-stepping in the numerical solution of stochastic models of biochemical systems, Canadian Applied and Industrial Mathematics Society Meeting (CAIMS 2013), Quebec City, 2013.
- S. Ilie, University of Ontario Institute of Technology, SHARCNET Seminar, Oshawa, 2012.
- S. Ilie, S. Gholami, Simplifying mathematical models of biochemical systems, Canadian Mathematics Society Meeting (CMS 2011), Toronto, 2011.
- S. Ilie, A. Teslya, An adaptive stepsize method for the Chemical Langevin Equation, 7th International Congress on Industrial and Applied Mathematics (ICIAM 2011), Vancouver, 2011.
- S. Ilie, K.R. Jackson, W.H. Enright, Adaptive time-stepping for the strong numerical solution of stochastic differential equations, International Conference on Scientific Computation And Differential Equations (SciCADE 2011), Toronto, 2011.
- S. Ilie, S. Gholami, 5th Geoffrey J. Butler Memorial Conference on Differential Equations and Population Biology 2011, Edmonton, 2011.
- S. Ilie, Adaptivity for one-step numerical methods for differential equations, Banff International Research Station Workshop on New Geometric and Numeric Tools for the Analysis of Differential Equations 2010, Banff, 2010.
- S. Ilie, Numerical simulations of stochastic models of chemical kinetics, invited lecture, Canadian Applied and Industrial Mathematics Society Annual Meeting (CAIMS'09), London, 2009.
- S. Ilie, M. Patel, Low and high-order numerical methods for stochastic biochemical kinetics, Biomathematics and Biostatistics Symposium, a Fields Institute meeting, University of Guelph, September 3, 2009.
- S. Ilie, Adaptivity and computational complexity of numerical solutions of ODEs, Southern Ontario Numerical Analysis Day (SONAD'08), York University, Toronto, 2008.
- S. Ilie, Adaptivity and computational complexity in the numerical solution of ODEs, University of Toronto, 2007.
- S. Ilie, Adaptivity and complexity - why adaptivity is always better than non-adaptivity, Lund University, Sweden, 2007.
- G. Soederlind and S. Ilie, Adaptivity and computational cost in the numerical solution of ODEs, International Conference on Scientific Computation and Differential Equations (SciCADE'07), St. Malo, France, 2007.
- S. Ilie, Complexity of numerical methods for initial value differential-algebraic equations, Lund University, Sweden, 2006.
- S. Ilie, R.M. Corless, Polynomial-time algorithms for solving differential algebraic equations, CAIMS - MITACS 2006 Joint Annual Conference, Toronto, June 15-20, 2006.
- S. Ilie, Numerical solutions of index-1 differential algebraic equations can be computed in polynomial time, International Conference on Scientific Computation and Differential Equations (SciCADE'05), Nagoya, Japan, May 23-27, 2005.
- S. Ilie, Numerical solutions of differential algebraic equations can be computed in polynomial time, University of Toronto, 2005.
- D.J. Jeffrey and S. Ilie, Laplace's equation around a sphere in a cylinder, invited lecture, Canadian Applied and Industrial Mathematics Society Annual Meeting (CAIMS - SCMAI'02), Calgary, 2002.
- S. Ilie, Polynomial cost of numerical solutions of differential algebraic equations,Workshop on Formal Theory of Partial Differential Equations and Their Applications, Joensuu, Finland, April 2-9, 2006.
- S. Ilie, R.M. Corless, G. Reid, Error backward for DAE, East Coast Computer Algebra Day (ECCAD'04), Wilfrid Laurier University, Waterloo, 2004.
Funding
(2010-2015, 2015-2020, 2020-2025)
(2015-2017, 2020-2022)
The name of the student co-author is underlined and of the postdoc co-author is italics underlined.