Selected Publications
Schmitt JE, DeBevits JJ, Roalf DR, Ruparel K, Gallagher RS, Gur RC, Alexander-Bloch A, Eom TY, Alam S, Steinberg J, Akers W, Khairy K, Crowley TB, Emanuel B, Zakharenko SS, McDonald-McGinn DM, Gur RE. A Comprehensive Analysis of Cerebellar Volumes in the 22q11.2 Deletion Syndrome. Biol Psychiatry Cogn Neurosci Neuroimaging Jan;8(1):79-90, 2023. doi:10.1016/j.bpsc.2021.11.008.
Alam S, Eom T-Y, Steinberg J, Ackerman D, Schmitt JE, Akers WJ, Zakharenko SS, Khairy K. An end-to-end pipeline for fully automatic morphological quantification of mouse brain structures from MRI imagery. Front Bioinform Jun 8;2:865443, 2022. doi:10.3389/fbinf.2022.865443.
Baggett DW, Medyukhina A, Tripathi S, Shirnekhi HK, Wu H, Pounds SB, Khairy K, Kriwacki R. An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells. Front Bioinform Jun 6;2:897238, 2022. doi:10.3389/fbinf.2022.897238
Chandra B, Michmerhuizen NL, Shirnekhi HK, Tripathi S, Pioso BJ, Baggett DW, Mitrea DM, Iacobucci I, White MR, Chen J, Park CG, Wu H, Pounds S, Medyukhina A, Khairy K, Gao Q, Qu C, Abdelhamed S, Gorman SD, Bawa S, Maslanka C, Kinger S, Dogra P, Ferrolino MC, Di Giacomo D, Mecucci C, Klco JM, Mullighan CG, Kriwacki RW. Phase Separation Mediates NUP98 Fusion Oncoprotein Leukemic Transformation. Cancer Discov Apr 1;12(4):1152-1169, 2022. doi:10.1158/2159-8290.CD-21-0674
Mahalingam G, Torres R, Kapner D, Trautman ET, Fliss T, Seshamani S, Perlman E, Young R, Kinn S, Buchanan J, Takeno MM, Yin W, Bumbarger DJ, Gwinn RP, Nyhus J, Lein E, Smith SJ, Reid RC, Khairy KA, Saalfeld S, Collman F, Macarico da Costa N. A scalable and modular automated pipeline for stitching of large electron microscopy datasets. Elife Jul 26;11:e76534, 2022. doi:10.7554/eLife.76534
Scheffer LK, Xu CS, Januszewski M, Lu Z, Takemura SY, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S, Clements J, Hubbard PM, Katz WT, Umayam L, Zhao T, Ackerman D, Blakely T, Bogovic J, Dolafi T, Kainmueller D, Kawase T, Khairy KA, Leavitt L, Li PH, Lindsey L, Neubarth N, Olbris DJ, Otsuna H, Trautman ET, Ito M, Bates AS, Goldammer J, Wolff T, Svirskas R, Schlegel P, Neace E, Knecht CJ, Alvarado CX, Bailey DA, Ballinger S, Borycz JA, Canino BS, Cheatham N, Cook M, Dreher M, Duclos O, Eubanks B, Fairbanks K, Finley S, Forknall N, Francis A, Hopkins GP, Joyce EM, Kim S, Kirk NA, Kovalyak J, Lauchie SA, Lohff A, Maldonado C, Manley EA, McLin S, Mooney C, Ndama M, Ogundeyi O, Okeoma N, Ordish C, Padilla N, Patrick CM, Paterson T, Phillips EE, Phillips EM, Rampally N, Ribeiro C, Robertson MK, Rymer JT, Ryan SM, Sammons M, Scott AK, Scott AL, Shinomiya A, Smith C, Smith K, Smith NL, Sobeski MA, Suleiman A, Swift J, Takemura S, Talebi I, Tarnogorska D, Tenshaw E, Tokhi T, Walsh JJ, Yang T, Horne JA, Li F, Parekh R, Rivlin PK, Jayaraman V, Costa M, Jefferis GS, Ito K, Saalfeld S, George R, Meinertzhagen IA, Rubin GM, Hess HF, Jain V, Plaza SM. A connectome and analysis of the adult Drosophila central brain. Elife Sep 7;9:e57443. doi:10.7554/eLife.57443, 2020.
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: August 2023