Publications

Gamm UA, Huang BK, Mis EK, Khokha MK, Choma MA: Visualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography. Sci Rep. 2017 Nov 8; 2017 Nov 8. PMID: 29118359

Pierce RW, Merola J, Lavik JP, Kluger MS, Huttner A, Khokha MK, Pober JS: A p190BRhoGAP mutation and prolonged RhoB activation in fatal systemic capillary leak syndrome. J Exp Med. 2017 Nov 2; 2017 Nov 2. PMID: 29097442

Forouzmand E, Owens NDL, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KWY: Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Dev Biol. 2017 Jun 15; 2016 Jul 12. PMID: 27418388

Garfinkel AM, Khokha MK: An interspecies heart-to-heart: Using Xenopus to uncover the genetic basis of congenital heart disease. Curr Pathobiol Rep. 2017 Jun; 2017 May 6. PMID: 29082114

Deniz E, Jonas S, Hooper M, N Griffin J, Choma MA, Khokha MK: Analysis of Craniocardiac Malformations in Xenopus using Optical Coherence Tomography. Sci Rep. 2017 Feb 14; 2017 Feb 14. PMID: 28195132

Khokha MK, Mitchell LE, Wallingford JB: An opportunity to address the genetic causes of birth defects. Pediatr Res. 2017 Feb; 2016 Nov 3. PMID: 27925620

Khokha MK, Mitchell LE, Wallingford JB: White paper on the study of birth defects. Birth Defects Res. 2017 Jan 30; 2017 Jan 27. PMID: 28398650

Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN: Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Dev Biol. 2016 Oct 26; 2016 Oct 26. PMID: 27784267

Sencan I, Huang BK, Bian Y, Mis E, Khokha MK, Cao H, Choma M: Ultrahigh-speed, phase-sensitive full-field interferometric confocal microscopy for quantitative microscale physiology. Biomed Opt Express. 2016 Nov 1; 2016 Oct 20. PMID: 27896006

Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J. 2016 Oct 4; 2016 Jul 19. PMID: 27436874

Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK: Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell. 2016 Sep 12; 2016 Sep 1. PMID: 27593162

Zhou KC, Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA: Erratum: Particle streak velocimetry-optical coherence tomography: a novel method for multidimensional imaging of microscale fluid flows: erratum. Biomed Opt Express. 2016 Jun 1; 2016 May 23. PMID: 27375950

Zhou KC, Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA: Particle streak velocimetry-optical coherence tomography: a novel method for multidimensional imaging of microscale fluid flows. Biomed Opt Express. 2016 Apr 1; 2016 Mar 30. PMID: 27375926

Duncan AR, Khokha MK: Xenopus as a model organism for birth defects-Congenital heart disease and heterotaxy. Semin Cell Dev Biol. 2016 Mar; 2016 Feb 22. PMID: 26910255

Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK: Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep. 2016 Jan 26; 2016 Jan 7. PMID: 26774488

Reza N, Khokha MK, Del Viso F: Nucleoporin gene expression in Xenopus tropicalis embryonic development. Int J Dev Biol. 2016. PMID: 27389988

Bhattacharya D, Marfo CA, Li D, Lane M, Khokha MK: CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. Dev Biol. 2015 Dec 15; 2015 Nov 4. PMID: 26546975

Endicott SJ, Basu B, Khokha M, Brueckner M: The NIMA-like kinase Nek2 is a key switch balancing cilia biogenesis and resorption in the development of left-right asymmetry. Development. 2015 Dec 1; 2015 Oct 22. PMID: 26493400

Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ: CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015 Oct; 2015 Aug 31. PMID: 26322839

Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA: Three-dimensional, three-vector-component velocimetry of cilia-driven fluid flow using correlation-based approaches in optical coherence tomography. Biomed Opt Express. 2015 Sep 1; 2015 Aug 24. PMID: 26417520

Griffin JN, Sondalle SB, Del Viso F, Baserga SJ, Khokha MK: The ribosome biogenesis factor Nol11 is required for optimal rDNA transcription and craniofacial development in Xenopus. PLoS Genet. 2015 Mar; 2015 Mar 10. PMID: 25756904

Huang BK, Gamm UA, Jonas S, Khokha MK, Choma MA: Quantitative optical coherence tomography imaging of intermediate flow defect phenotypes in ciliary physiology and pathophysiology. J Biomed Opt. 2015 Mar. PMID: 25751026

Romberg N, Al Moussawi K, Nelson-Williams C, Stiegler AL, Loring E, Choi M, Overton J, Meffre E, Khokha MK, Huttner AJ, West B, Podoltsev NA, Boggon TJ, Kazmierczak BI, Lifton RP: Mutation of NLRC4 causes a syndrome of enterocolitis and autoinflammation. Nat Genet. 2014 Oct; 2014 Sep 14. PMID: 25217960

Boskovski MT, Yuan S, Pedersen NB, Goth CK, Makova S, Clausen H, Brueckner M, Khokha MK: The heterotaxy gene GALNT11 glycosylates Notch to orchestrate cilia type and laterality. Nature. 2013 Dec 19; 2013 Nov 13. PMID: 24226769

Jonas S, Zhou E, Deniz E, Huang B, Chandrasekera K, Bhattacharya D, Wu Y, Fan R, Deserno TM, Khokha MK, Choma MA: A novel approach to quantifying ciliary physiology: microfluidic mixing driven by a ciliated biological surface. Lab Chip. 2013 Nov 7. PMID: 23970350

Lane MA, Kimber M, Khokha MK: Breeding based remobilization of Tol2 transposon in Xenopus tropicalis. PLoS One. 2013; 2013 Oct 8. PMID: 24116167

van Veenendaal NR, Ulmer B, Boskovski MT, Fang X, Khokha MK, Wendler CC, Blum M, Rivkees SA: Embryonic exposure to propylthiouracil disrupts left-right patterning in Xenopus embryos. FASEB J. 2013 Feb; 2012 Nov 12. PMID: 23150524

del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK: Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics. 2012 Nov 21; 2012 Nov 21. PMID: 23171430

Deniz E, Jonas S, Khokha M, Choma MA: Endogenous contrast blood flow imaging in embryonic hearts using hemoglobin contrast subtraction angiography. Opt Lett. 2012 Jul 15. PMID: 22825198

Abu-Daya A, Khokha MK, Zimmerman LB: The hitchhiker's guide to Xenopus genetics. Genesis. 2012 Mar; 2012 Feb 16. PMID: 22344745

Khokha MK: Xenopus white papers and resources: folding functional genomics and genetics into the frog. Genesis. 2012 Mar; 2012 Feb 20. PMID: 22287484

del Viso F, Khokha M: Generating diploid embryos from Xenopus tropicalis. Methods Mol Biol. 2012. PMID: 22956081

Jonas S, Bhattacharya D, Khokha MK, Choma MA: Microfluidic characterization of cilia-driven fluid flow using optical coherence tomography-based particle tracking velocimetry. Biomed Opt Express. 2011 Jul 1; 2011 Jun 22. PMID: 21750777

Stafford DA, Brunet LJ, Khokha MK, Economides AN, Harland RM: Cooperative activity of noggin and gremlin 1 in axial skeleton development. Development. 2011 Mar. PMID: 21303853

Fakhro KA, Choi M, Ware SM, Belmont JW, Towbin JA, Lifton RP, Khokha MK, Brueckner M: Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning. Proc Natl Acad Sci U S A. 2011 Feb 15; 2011 Jan 31. PMID: 21282601

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS: The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30. PMID: 20431018

Wills AE, Choi VM, Bennett MJ, Khokha MK, Harland RM: BMP antagonists and FGF signaling contribute to different domains of the neural plate in Xenopus. Dev Biol. 2010 Jan 15; 2009 Nov 10. PMID: 19913009

Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CY, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB: Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn. 2009 Jun. PMID: 19441086

Wills A, Dickinson K, Khokha M, Baker JC: Bmp signaling is necessary and sufficient for ventrolateral endoderm specification in Xenopus. Dev Dyn. 2008 Aug. PMID: 18651654

Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS: Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. BMC Biol. 2007 Jul 25; 2007 Jul 25. PMID: 17651506

Choi VM, Harland RM, Khokha MK: Developmental expression of FoxJ1.2, FoxJ2, and FoxQ1 in Xenopus tropicalis. Gene Expr Patterns. 2006 Jun; 2006 Feb 7. PMID: 16461016

Wills A, Harland RM, Khokha MK: Twisted gastrulation is required for forebrain specification and cooperates with Chordin to inhibit BMP signaling during X. tropicalis gastrulation. Dev Biol. 2006 Jan 1. PMID: 16321373

Khokha MK, Loots GG: Strategies for characterising cis-regulatory elements in Xenopus. Brief Funct Genomic Proteomic. 2005 May. PMID: 15975265

Khokha MK, Yeh J, Grammer TC, Harland RM: Depletion of three BMP antagonists from Spemann's organizer leads to a catastrophic loss of dorsal structures. Dev Cell. 2005 Mar. PMID: 15737935

Grammer TC, Khokha MK, Lane MA, Lam K, Harland RM: Identification of mutants in inbred Xenopus tropicalis. Mech Dev. 2005 Mar. PMID: 15763207

Trott KA, Stacy BA, Lifland BD, Diggs HE, Harland RM, Khokha MK, Grammer TC, Parker JM: Characterization of a Mycobacterium ulcerans-like infection in a colony of African tropical clawed frogs (Xenopus tropicalis). Comp Med. 2004 Jun. PMID: 15253278

Khokha MK, Hsu D, Brunet LJ, Dionne MS, Harland RM: Gremlin is the BMP antagonist required for maintenance of Shh and Fgf signals during limb patterning. Nat Genet. 2003 Jul. PMID: 12808456

Khokha MK, Chung C, Bustamante EL, Gaw LW, Trott KA, Yeh J, Lim N, Lin JC, Taverner N, Amaya E, Papalopulu N, Smith JC, Zorn AM, Harland RM, Grammer TC: Techniques and probes for the study of Xenopus tropicalis development. Dev Dyn. 2002 Dec. PMID: 12454926

Highlighted Publication

florsCoverDevelopments
Cover image by George Takahashi and Fang Huang. At the base of the cilium, localization of the nucleoporin Nup188 (colored spheres) is organized to form cylinders, as determined by W-4PiSMSN super-resolution microscopy. To learn more about the requirement for Nup188 at cilia and its organization there, as well as to access the QR code for visualizing and manipulating the 3D nanoscopy data, see del Viso et al., Developmental Cell, Volume 38 , Issue 5 , 478 - 492, 2016.
The Precision Paradigm: Mustafa Kezar Khokha, MD

The Precision Paradigm: Mustafa Kezar Khokha, MD

PICU and Sequencing Efforts