2010	Khalili,A., Liu, Javadi, K.B. Morad, M. R., Matyka, M., Kindler, K., Stocker, R. and Koza, Z. (in press). Application of porous media theories in marine biological modeling. In: Porous Media: Applications in Biological Systems and Biotechnology Ed. K. Vafai,Taylor & Francis.
	Roskosch, A., Morad, M. R., Khalili, A., and Lewandowski, J. (2010). Bioirrigation by Chironomus plumosus: advective flow investigated by particle image velocimetry. Journal of the North American Benthological Society. 29(3): 789-802.
	Morad, M.R., Khalili, A., Roskosch A., and Lewandowski J. (2010). Quantification of pumping rate of Chironomus Plumosus larvae in natural burrows. Aquatic Ecology. 44 (1): 143-153.
2009	Javadi, K., and Khalili, A. (2009). On generating uniform bottom shear stress. Part II: shear stress inducing devices. Recent Patents on Chemical Engineering, 2(3): 223-229.
	Roskosch, A., Jordan, S., Hette, N., Buchert, R., Khalili, A., Morad, M. R., Nützmann, G., Hupfer, M., and Lewandowski, J. (2009). Die Wirkung von Chironomus plumosus (Diptera: Chironomidiae) auf Transportprozesse in limnischen Systemen. - Deutsche Gesellschaft für Limnologie (DGL) - Erweiterte Zusammenfassungen der Jahrestagung 2008 (Konstanz): 449-454.
	Koza, Z., Matyka, M., and Khalili, A. (2009). Finite-size anisotropy in statistically uniform porous media. Physical Review E. 79: 066306-1-- 066306-7.
	Liu, B. and Khalili, A. (2009). Lattice Boltzmann model for exterior flows with an annealing preconditioning method. Physical Review E. 79: 066701-1-- 066701-7.
	Stöhr, M., Schanze, J. and Khalili, A. (2009).Visualization of gas-liquid mass transfer and wake structure of rising bubbles using pH-sensitive PLIF. Experiments in Fluids, 47:135–143.
	Morad, M.R. and Khalili, A. (2009). Transition layer thickness in a fluid-porous medium of multi-sized spherical beads. Experiments in Fluids, 46 (2): 323-330.
2008	Alam, M. and Khalili, A. (2008). Instabilities and patterns in horizontally oscillating particulate suspension. Physical Review E, 77:041305-1--041305-1.
	Matyka, M., Khalili, A. and Koza, Z. (2008). Tortuosity-porosity relation in porous media flow. Physical Review E, 78: 026306-1--026306-8.
	Liu, B. and Khalili, A. (2008). Acceleration of steady-state lattice Boltzmann simulations for exterior flows. Physical Review E, 78: 056701-1--056701-9.
	Khalili, A., Javadi, K., Saidi, A., Goharzadeh, A., Huettel, M. and Jørgensen, B.B. (2008). On Generating Uniform Bottom Shear Stress, Part I: A Quantitative Study of Microcosm Chambers. Recent Patents on Chemical Engineering, 1(3): 174-191.
2007	Bera, P. and Khalili, A. (2007). Stability of buoyancy opposed mixed convection in a vertical channel and its dependence on permeability. Adv. Water Res.30(11), 2296-2308.
2006	Bera, P. and Khalili, A. (2006). Influence of Prandtl number on the stability of mixed convective flow in a vertical channel filled with a porous medium. Phys. Fluids, 18. 124103-1 - 124103-10.
	Bhattacharyya, S., Dhinakaran, S. and Khalili, A. (2006). Fluid motion around and through a porous cylinder.Chem. Eng. Sci. 61, 4451-4461.
	Stoehr, M. and Khalili, A. (2006). Dynamic regimes of buoyancy-affected two-phase flow in unconsolidated porous media. Phys. Rev. E, 73, 036301-1 -- 036301-8
2005	Goharzadeh, A., Khalili, A. and Jørgensen, B. B. (2005). Transition layer thickness at a fluid-porous interface. Phys. Fluids, 17. 057102-1 - 057102-10.
	Khalili, A. (2005). Modelling seawater-pore water exchange near seabeds. In Oil pollution and its environmental impact in the Arabic Gulf region. M. Al-Azhab, W. E-Shorbagy and S. Al-Ghais (eds) 147-156. Elsevier
	Goharzadeh, A., Saidi, A., Wang, D., Merzkirch, W. and Khalili, A. (2005). An experimental investigation of the Brinkman layer thickness at a fluid-porous interface. In One Hundred Years Boundary Layer Research. G. E. A. Meier and K. R. Sreenivasan (eds) . 445-454, Springer Verlag.
2003	Khalili, A. and Shivakumara, I. S. (2003).Non-Darcian effects on the onset of convection in a porous layer with throughflow.Transport in Porous Media, 53, 245-263.
	Forster, S., Khalili, A. and Kitlara, J. (2003).Variation of non-local irrigation in a subtidal benthic community. J. Mar. Res.61, 335-357.
	Khalili, A., Shivakumara, I. S. and Suma, S. P. (2003). Convective instability in superposed fluid and porous layers with throughflow. Transport in Porous Media, 51, 1-18.
2002	Khalili, A., Shivakumara, I. S. and Huettel, M. (2002). Effects of throughflow and internal heat generation on convective instabilities in an anisotropic porous layer. J. Porous Media, 5, 187-198.
	Bera, P. and Khalili, A. (2002). Stability of mixed convection in an anisotropic vertical porous channel. Phys. Fluids, 14, 1617-1630.
	Bera, P. and Khalili, A. (2002). Double-diffusive natural convection in an anisotropic porous cavity with opposing buoyancy forces: multi-solutions and oscillations. Int. J. Heat Mass, 45, 3205-3222.
2001	Khalili, A., Huettel, M. and Merzkirch, W. (2001). Techniques for fine-scale boundary layer measurements. In `The benthic boundary layer: transport processes and biogeochemistry', B. P. Boudreau and B. B. Jørgensen (eds.), Oxford University Press.
2000	Chakraborty, B. B., Khattar, D. and Khalili, A. (2000). Effect of rotation on stability of suspended sediments. Phys. Fluids, 12, 3074-3077.
1999	Khalili, A., Basu, A. J., Pietrzyk, U. and Raffel, M. (1999). An experimental study of recirculating flow through fluid-sediment interfaces. J. Fluid Mech., 383, 229-247.
	Pringault O, Epping E, Guyoneaud R, Khalili A, and Kuhl, M. (1999). Dynamics of anoxygenic photosynthesis in an experimental green sulphur bacteria biofilm. Environ. Microbiol., 1, 295-305.
	Epping, E., Khalili, A. and Thar, R. (1999). Photosynthesis and the dynamics of oxygen consumption in a microbial mat as calculated from transient oxygen microprofiles. Limnol. Oceanogr., 44, 1936-1948.
	Khalili and A. J. Basu and U. Pietrzyk and Jørgensen, B. B. (1999). Advective transport through permeable sediments: a new numerical and experimental approach. Acta Mechanica, 132, 221-227.
	Basu, A. J. and Khalili, A. (1999). Computation of flow through fluid-sediment interfaces in a benthic chamber. Phys. Fluids, 12, 3074-3077.
1998	Khalili, A. and Shivakumara, I. S. (1998). Onset of convection in a porous layer with net through-flow and internal heat generation. Phys. Fluids,10, 315-317.
	Khalili, A., Basu, A. J. and Pietrzyk, U. (1998). Flow visualization in porous media via positron emission tomography. Phys. Fluids, 10, 1031-1033.