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Khaled Khairy, PhD
Khaled Khairy, PhD

Khaled Khairy, PhD

Associate Member, St. Jude Faculty

  • Director, Center for Bioimage Informatics



Fellowship – MaxPlack Institute of Molecular Cell Biology and Genetics, Dresden, Germany
PhD – Northeastern University, Boston, Massachusetts

Research Interests

  • Applications of biophysical/biomechanical priors in image reconstruction, machine learning and computer vision
  • Biomechanical basis for the morphology of membrane-bound biological structures
  • Computational approaches for efficient biological shape and morphodynamics representation

Selected Publications

Khairy K, Lemon W, Amat F, Keller P. A preferred curvature-based continuum mechanics framework for modeling embryogenesis. Biophysical Journal 114(2):267-277, 2018. 

Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, Bogovic J, Hanslovsky P, Jefferis GSXE, Kazhdan M, Khairy K, Saalfeld S, Fetter RD, Bock DD. A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster. Cell 174(3):730-743, 2018.

Burns R, Perlman E, Baden A, Roncal WG, Falk B, Chandrashekhar V, Collman F, Seshamani S, Patsolic J, Lillaney K, Kazhdan M, Hider Jr R, Pryor D, Matelsky J, Gion T, Manavalan P, Wester B, Chevillet M, Trautman ET, Khairy K, Bridgeford E, Kleissas DM, Tward DJ, Crow AK, Wright MA, Miller MI, Smith SJ, Vogelstein RJ, Deisseroth K, Vogelstein JT. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods 2018 (in press).

Tomer R, Khairy K, Amat F, Keller P. Quantitative High-Speed Imaging of Entire Developing Embryos with Simultaneous Multi-View Light Sheet Microscopy. Nature Methods 9(7):755-63, 2012.

Tomer R, Khairy K, Keller P. Shedding light on the system: Studying embryonic development with light sheet microscopy. Curr Opin Genet Dev 21(5):558-565, 2011.

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

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

Keller P, Schmidt A, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer E. 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, Pecreaux J, Goehring N, Khairy K, Stelzer E, Hyman A, Howard J. Membrane invaginations reveal cortical sites that pull on mitotic spindles in one-cell C.elegans embryos. PLoS One 5(8):e12301, 2010.

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

Khairy K, Foo J, Howard J. 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, Reynaud E, Stelzer E. Detection of Deformable Objects in 3D Images using Markov Chain Monte Carlo and Spherical Harmonics. Peer-reviewed Conference Proceedings MICCAI New York 2008.

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

Khairy K, Budil D, Fajer P, Nonlinear-Least-Squares Analysis of Slow Motional Regime EPR Spectra. Journal of Magnetic Resonance 183(1):152-159, 2006.

Budil D, Sale K, Khairy K, Fajer P. 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, Khairy K, Friedrichs J, Cisneros D, Howard J, Mueller D. Molecular- scale Topographic Cues Induce the Orientation and Directional Movement of Fibroblasts on Two-dimensional Collagen Surfaces. Journal of Molecular Biology 349:380-386, 2005.

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

Last update: October 2018