Dr. Khaled Khairy
EMBL Heidelberg

Meyerhofstraße 1, 69117 Heidelberg, Germany

khairy@embl.de

Research interests / Publications / Scientific software

Publications

Peer-reviewed Articles:

R. Tomer, Khairy K., Keller P., , "Shedding light on the system: Studying embryonic development with light sheet microscopy.", Curr Opin Genet Dev. 2011 Aug 19. [Epub ahead of print]

K. Khairy and Howard J., , "Minimum-energy vesicle and cell shapes calculated using spherical harmonics parameterization", Soft Matter 7(5):2138-2143 (2011).

K. Khairy and Keller P., , "Reconstructing embryonic development", Genesis, 49(7):488-513 (2011).

Keller P., A. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, E. Stelzer , "Fast high-contrast imaging of fish and fly development with scanned light sheet-based structured illumination microscopy", Nature Methods, 7(8):637-642 (2010).

Redemann S., J. Pecreaux, N. Goehring, K. Khairy, E. Stelzer, A. Hyman, J.Howard , "Membrane invaginations reveal cortical sites that pull on mitotic spindles in one-cell C.elegans embryos", PLoS One, 5(8):e12301 (2010).

Mayer J., K. Khairy, J. Howard, "Drawing an elephant with 4 parameters", American Journal of Physics, 78(6):648-649 (2010).

Khairy K., J. Foo, J. Howard, "Shapes of Red Blood Cells: Comparison of 3D Confocal Images with the Bilayer-couple Model", Cellular and Molecular Bioengineering, 1:173-181 (2008).

Khairy K., E. Reynaud, E. Stelzer, "Detection of Deformable Objects in 3D Images using Markov Chain Monte Carlo and Spherical Harmonics", (peer-reviewed) Conference Proceedings MICCAI, NY 2008.

Khairy K., J. Howard, “Spherical Harmonics-Based Parametric Deconvolution of 3D Surface Images using Bending Energy Minimization” Medical Image Analysis, 12(2): 217-227, (2008).

Khairy K., D. Budil, P. Fajer, “Nonlinear-Least-Squares Analysis of Slow Motional Regime EPR Spectra”, Journal of Magnetic Resonance,183:152-159 (2006).

Budil D., K. Sale, K. Khairy, P. Fajer, “Calculating Slow-Motional Electron Paramagnetic Resonance Spectra from Molecular Dynamics Using a Diffusion Operator Approach”, Journal of Physical Chemistry A, 110(10):3703-13, (2006).

Poole K., K. Khairy, J.Friedrichs, D. Cisneros, J. Howard, D. Mueller, “Molecular-scale Topographic Cues Induce the Orientation and Directional Movement of Fibroblasts onTwo-dimensional Collagen Surfaces”,Journal of Molecular Biology, 349:380-386, (2005). (Note: the first three authors contributed equally to this work).

Jiang, F., K. Khairy, K. Poole, J. Howard, and D. Mueller, “Creating nanoscopic collagen matrices using atomic force microscopy”, Microscopy Research and Technique, 64:435-440, (2004).

PhD Thesis:

“Molecular Modeling Assisted Simulation and Analysis of Magnetic Resonance Spectra Using the Stochastic Liouville Equation: an Object Oriented Approach”, Chemistry Department, Northeastern University, March 2002.

Patents:

K. Khairy, J. Howard, “Method and Device for Reconstructing an Object Surface" ,patent pending.

K. Khairy, J. Pecreaux, J. Howard, “Spherical Harmonics 3D Active contours for Membrane Bilayer-Bound Surfaces.", patent pending.

Books:

Davies G., E. Ghabbour, K. Khairy,“Humic substances : structures, properties and uses”, published by:Royal Society of Chemistry, 1999.

Conference contributions:

Khairy K., J. Pecreaux, J. Howard, (2007), "Spherical Harmonics 3D Active contours for Membrane Bilayer-Bound Surfaces", MICCAI Society Meeting, Brisbane, Australia.

Khairy K., J. Foo, J. Howard, (2007), "What is the Basis for Erythrocyte Morphology", Biophysical Society Meeting, Baltimore , MD, USA.

Khairy K., J. Foo, J. Howard, (2005), "Explaining Cell Shapes using Spherical Harmonic Functions: An Implementation in Matlab", Forum "Matlab for Pharmaceutical and Biotechnology Projects", Heidelberg, Germany.

Khairy K., J.Friedrichs, K.Poole, J.Howard and D.Müller, (2003),”Directed Motility of Mouse Dermal Fibroblasts on Collagen-coated Mica Surfaces”, Motion, sensation and self-organization in living cells workshop, Dresden, Germany.

Khairy K. and J. Howard,(2003),”Simulation of Collagen Deformation due to Fibroblast Traction Forces using the Immersed Boundary Method”, Society of Experimental Biology, annual meeting, Southampton, UK.

Khairy K., P. Fajer and D.Budil,(2002), Simulation of Spin Label Motion in EPR Spectra of Muscle Fibers, Biophysical Journal, 82 (1), 479.

Sale K., P.Fajer, K.Khairy and D.Budil,(2002), Parameterization of Slow-motional EPR Spectra Using Molecular Dynamics, Biophysical Journal, 82 (1), 479.