Publications
2023
- Mink1 regulates spemann organizer cell fate in the xenopus gastrula via Hmga2.Colleluori V, Khokha MK. Dev Biol. 2023 Mar; 2022 Dec 23. PMID: 36572140.
2022
- Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR.Sempou E, Kostiuk V, Zhu J, Cecilia Guerra M, Tyan L, Hwang W, Camacho-Aguilar E, Caplan MJ, Zenisek D, Warmflash A, Owens NDL, Khokha MK. Nat Commun. 2022 Nov 5; 2022 Nov 5. PMID: 36335122.
- Kap-β2/Transportin mediates β-catenin nuclear transport in Wnt signaling.Hwang WY, Kostiuk V, González DP, Lusk CP, Khokha MK. Elife. 2022 Oct 27; 2022 Oct 27. PMID: 36300792.
- A retrospective cohort analysis of the Yale pediatric genomics discovery program.Al-Ali S, Jeffries L, Faustino EVS, Ji W, Mis E, Konstantino M, Zerillo C, Jiang YH, Spencer-Manzon M, Bale A, Zhang H, McGlynn J, McGrath JM, Tremblay T, Brodsky NN, Lucas CL, Pierce R, Deniz E, Khokha MK, Lakhani SA. Am J Med Genet A. 2022 Oct; 2022 Jul 28. PMID: 35899841.
- Xenopus Tadpole Craniocardiac Imaging Using Optical Coherence Tomography.Deniz E, Mis EK, Lane M, Khokha MK. Cold Spring Harb Protoc. 2022 Jun 7; 2022 Jun 7. PMID: 34031211.
- Microinjection of Xenopus tropicalis Embryos.Lane M, Mis EK, Khokha MK. Cold Spring Harb Protoc. 2022 Apr 1; 2022 Apr 1. PMID: 34244348.
- Obtaining Xenopus tropicalis Embryos by Natural Mating.Lane M, Khokha MK. Cold Spring Harb Protoc. 2022 Apr 1; 2022 Apr 1. PMID: 34031213.
- Obtaining Xenopus tropicalis Embryos by In Vitro Fertilization.Lane M, Khokha MK. Cold Spring Harb Protoc. 2022 Apr 1; 2022 Apr 1. PMID: 34031212.
- Raising and Maintaining Xenopus tropicalis from Tadpole to Adult.Lane M, Slocum M, Khokha MK. Cold Spring Harb Protoc. 2022 Apr 1; 2022 Apr 1. PMID: 34031210.
- Obtaining Xenopus tropicalis Eggs.Lane M, Mis EK, Khokha MK. Cold Spring Harb Protoc. 2022 Apr 1; 2022 Apr 1. PMID: 34031209.
2021
- PPIL4 is essential for brain angiogenesis and implicated in intracranial aneurysms in humans.Barak T, Ristori E, Ercan-Sencicek AG, Miyagishima DF, Nelson-Williams C, Dong W, Jin SC, Prendergast A, Armero W, Henegariu O, Erson-Omay EZ, Harmancı AS, Guy M, Gültekin B, Kilic D, Rai DK, Goc N, Aguilera SM, Gülez B, Altinok S, Ozcan K, Yarman Y, Coskun S, Sempou E, Deniz E, Hintzen J, Cox A, Fomchenko E, Jung SW, Ozturk AK, Louvi A, Bilgüvar K, Connolly ES Jr, Khokha MK, Kahle KT, Yasuno K, Lifton RP, Mishra-Gorur K, Nicoli S, Günel M. Nat Med. 2021 Dec; 2021 Dec 9. PMID: 34887573.
- A convergent molecular network underlying autism and congenital heart disease.Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. Cell Syst. 2021 Nov 17; 2021 Aug 18. PMID: 34411509.
- Functional testing for variant prioritization in a family with long QT syndrome.Najari Beidokhti M, Bertalovitz AC, Ji W, McCormack J, Jeffries L, Sempou E, Khokha MK, McDonald TV, Lakhani SA. Mol Genet Genomics. 2021 Jul; 2021 Apr 19. PMID: 33876311.
- DLG5 variants are associated with multiple congenital anomalies including ciliopathy phenotypes.Marquez J, Mann N, Arana K, Deniz E, Ji W, Konstantino M, Mis EK, Deshpande C, Jeffries L, McGlynn J, Hugo H, Widmeier E, Konrad M, Tasic V, Morotti R, Baptista J, Ellard S, Lakhani SA, Hildebrandt F, Khokha MK. J Med Genet. 2021 Jul; 2020 Jul 6. PMID: 32631816.
- Mechanical stretch scales centriole number to apical area via Piezo1 in multiciliated cells.Kulkarni S, Marquez J, Date P, Ventrella R, Mitchell BJ, Khokha MK. Elife. 2021 Jun 29; 2021 Jun 29. PMID: 34184636.
- Expansion of NEUROD2 phenotypes to include developmental delay without seizures.Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez-Agosto JA, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Am J Med Genet A. 2021 Apr; 2021 Jan 13. PMID: 33438828.
- Recessive Mutations in SYNPO2 as a Candidate of Monogenic Nephrotic Syndrome.Mao Y, Schneider R, van der Ven PFM, Assent M, Lohanadan K, Klämbt V, Buerger F, Kitzler TM, Deutsch K, Nakayama M, Majmundar AJ, Mann N, Hermle T, Onuchic-Whitford AC, Zhou W, Margam NN, Duncan R, Marquez J, Khokha M, Fathy HM, Kari JA, El Desoky S, Eid LA, Awad HS, Al-Saffar M, Mane S, Lifton RP, Fürst DO, Shril S, Hildebrandt F. Kidney Int Rep. 2021 Feb; 2020 Nov 10. PMID: 33615072.
- Xenopus as a platform for discovery of genes relevant to human disease.Kostiuk V, Khokha MK. Curr Top Dev Biol. 2021; 2021 Apr 23. PMID: 34074532.
- Nucleoporin NUP205 plays a critical role in cilia and congenital disease.Marquez J, Bhattacharya D, Lusk CP, Khokha MK. Dev Biol. 2021 Jan 1; 2020 Oct 13. PMID: 33065118.
2020
- DAAM2 Variants Cause Nephrotic Syndrome via Actin Dysregulation.Schneider R, Deutsch K, Hoeprich GJ, Marquez J, Hermle T, Braun DA, Seltzsam S, Kitzler TM, Mao Y, Buerger F, Majmundar AJ, Onuchic-Whitford AC, Kolvenbach CM, Schierbaum L, Schneider S, Halawi AA, Nakayama M, Mann N, Connaughton DM, Klämbt V, Wagner M, Riedhammer KM, Renders L, Katsura Y, Thumkeo D, Soliman NA, Mane S, Lifton RP, Shril S, Khokha MK, Hoefele J, Goode BL, Hildebrandt F. Am J Hum Genet. 2020 Dec 3; 2020 Nov 23. PMID: 33232676.
- Challenges and opportunities at the interface of birth defects, human genetics and developmental biology.Khokha MK, Liu KJ, Wallingford JB. Development. 2020 Nov 9; 2020 Nov 9. PMID: 33168578.
- Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations.Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, Onuchic-Whitford AC, Youying M, Kolb A, Salmanullah D, Chen E, van der Ven AT, Rao J, Ityel H, Seltzsam S, Rieke JM, Chen J, Vivante A, Hwang DY, Kohl S, Dworschak GC, Hermle T, Alders M, Bartolomaeus T, Bauer SB, Baum MA, Brilstra EH, Challman TD, Zyskind J, Costin CE, Dipple KM, Duijkers FA, Ferguson M, Fitzpatrick DR, Fick R, Glass IA, Hulick PJ, Kline AD, Krey I, Kumar S, Lu W, Marco EJ, Wentzensen IM, Mefford HC, Platzer K, Povolotskaya IS, Savatt JM, Shcherbakova NV, Senguttuvan P, Squire AE, Stein DR, Thiffault I, Voinova VY, Somers MJG, Ferguson MA, Traum AZ, Daouk GH, Daga A, Rodig NM, Terhal PA, van Binsbergen E, Eid LA, Tasic V, Rasouly HM, Lim TY, Ahram DF, Gharavi AG, Reutter HM, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Lifton RP, Xu H, Mane SM, Sanna-Cherchi S, Sharrocks AD, Raught B, Fisher SE, Bouchard M, Khokha MK, Shril S, Hildebrandt F. Am J Hum Genet. 2020 Oct 1; 2020 Sep 4. PMID: 32891193.
- The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN-associated AMC as a type of viable fetal akinesia deformation sequence.Mis EK, Al-Ali S, Ji W, Spencer-Manzon M, Konstantino M, Khokha MK, Jeffries L, Lakhani SA. Am J Med Genet A. 2020 Oct; 2020 Aug 19. PMID: 32812332.
- Novel compound heterozygous variants in NHLRC2 in a patient with FINCA syndrome.Brodsky NN, Boyarchuk O, Kovalchuk T, Hariyan T, Rice A, Ji W, Khokha M, Lakhani S, Lucas CL. J Hum Genet. 2020 Oct; 2020 May 21. PMID: 32435055.
- A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred foals.Rivas VN, Magdesian KG, Fagan S, Slovis NM, Luethy D, Javsicas LH, Caserto BG, Miller AD, Dahlgren AR, Peterson J, Hales EN, Peng S, Watson KD, Khokha MK, Finno CJ. PLoS Genet. 2020 Sep; 2020 Sep 28. PMID: 32986719.
- Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development.Farley-Barnes KI, Deniz E, Overton MM, Khokha MK, Baserga SJ. PLoS Genet. 2020 Aug; 2020 Aug 19. PMID: 32813698.
- Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome.Alharatani R, Ververi A, Beleza-Meireles A, Ji W, Mis E, Patterson QT, Griffin JN, Bhujel N, Chang CA, Dixit A, Konstantino M, Healy C, Hannan S, Neo N, Cash A, Li D, Bhoj E, Zackai EH, Cleaver R, Baralle D, McEntagart M, Newbury-Ecob R, Scott R, Hurst JA, Au PYB, Hosey MT, Khokha M, Marciano DK, Lakhani SA, Liu KJ. Hum Mol Genet. 2020 Jul 21. PMID: 32196547.
- De novo damaging variants associated with congenital heart diseases contribute to the connectome.Ji W, Ferdman D, Copel J, Scheinost D, Shabanova V, Brueckner M, Khokha MK, Ment LR. Sci Rep. 2020 Apr 27; 2020 Apr 27. PMID: 32341405.
- Differential turnover of Nup188 controls its levels at centrosomes and role in centriole duplication.Vishnoi N, Dhanasekeran K, Chalfant M, Surovstev I, Khokha MK, Lusk CP. J Cell Biol. 2020 Mar 2. PMID: 32211895.
- Author Correction: Visualizing flow in an intact CSF network using optical coherence tomography: implications for human congenital hydrocephalus.Date P, Ackermann P, Furey C, Fink IB, Jonas S, Khokha MK, Kahle KT, Deniz E. Sci Rep. 2020 Feb 12; 2020 Feb 12. PMID: 32047215.
- Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects.Marquez J, Criscione J, Charney RM, Prasad MS, Hwang WY, Mis EK, García-Castro MI, Khokha MK. J Clin Invest. 2020 Feb 3. PMID: 31904590.
2019
- Familial Dilated Cardiomyopathy Associated With a Novel Combination of Compound Heterozygous TNNC1 Variants.Landim-Vieira M, Johnston JR, Ji W, Mis EK, Tijerino J, Spencer-Manzon M, Jeffries L, Hall EK, Panisello-Manterola D, Khokha MK, Deniz E, Chase PB, Lakhani SA, Pinto JR. Front Physiol. 2019; 2020 Jan 22. PMID: 32038292.
- Alkylglycerol monooxygenase, a heterotaxy candidate gene, regulates left-right patterning via Wnt signaling.Duncan AR, González DP, Del Viso F, Robson A, Khokha MK, Griffin JN. Dev Biol. 2019 Dec 1; 2019 Aug 6. PMID: 31398317.
- Quantitative Phenotyping of Xenopus Embryonic Heart Pathophysiology Using Hemoglobin Contrast Subtraction Angiography to Screen Human Cardiomyopathies.Deniz E, Jonas S, Khokha MK, Choma MA. Front Physiol. 2019; 2019 Sep 20. PMID: 31620018.
- A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.Mitros T, Lyons JB, Session AM, Jenkins J, Shu S, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS. Dev Biol. 2019 Aug 1; 2019 Apr 10. PMID: 30980799.
- Whole-Exome Sequencing of Adult and Pediatric Cohorts of the Rare Vascular Disorder Systemic Capillary Leak Syndrome.Pierce R, Ji W, Chan EC, Xie Z, Long LM, Khokha M, Lakhani S, Druey KM. Shock. 2019 Aug. PMID: 30289850.
- Xenopus: Driving the Discovery of Novel Genes in Patient Disease and Their Underlying Pathological Mechanisms Relevant for Organogenesis.Hwang WY, Marquez J, Khokha MK. Front Physiol. 2019; 2019 Jul 30. PMID: 31417417.
- Identification of novel mutations and phenotype in the steroid resistant nephrotic syndrome gene NUP93: a case report.Sandokji I, Marquez J, Ji W, Zerillo CA, Konstantino M, Lakhani SA, Khokha MK, Warejko JK. BMC Nephrol. 2019 Jul 17; 2019 Jul 17. PMID: 31315584.
- Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility.Robson A, Makova SZ, Barish S, Zaidi S, Mehta S, Drozd J, Jin SC, Gelb BD, Seidman CE, Chung WK, Lifton RP, Khokha MK, Brueckner M. Proc Natl Acad Sci U S A. 2019 Jul 9; 2019 Jun 24. PMID: 31235600.
- Gaussian process post-processing for particle tracking velocimetry.Tang T, Deniz E, Khokha MK, Tagare HD. Biomed Opt Express. 2019 Jul 1; 2019 Jun 7. PMID: 31360598.
- Genes and mechanisms of heterotaxy: patients drive the search.Sempou E, Khokha MK. Curr Opin Genet Dev. 2019 Jun; 2019 Jun 21. PMID: 31234044.
- Visualizing flow in an intact CSF network using optical coherence tomography: implications for human congenital hydrocephalus.Date P, Ackermann P, Furey C, Fink IB, Jonas S, Khokha MK, Kahle KT, Deniz E. Sci Rep. 2019 Apr 17; 2019 Apr 17. PMID: 30996265.
- De novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy.Sega AG, Mis EK, Lindstrom K, Mercimek-Andrews S, Ji W, Cho MT, Juusola J, Konstantino M, Jeffries L, Khokha MK, Lakhani SA. J Med Genet. 2019 Feb; 2018 Oct 15. PMID: 30323019.
- Patients with common variable immunodeficiency with autoimmune cytopenias exhibit hyperplastic yet inefficient germinal center responses.Romberg N, Le Coz C, Glauzy S, Schickel JN, Trofa M, Nolan BE, Paessler M, Xu ML, Lambert MP, Lakhani SA, Khokha MK, Jyonouchi S, Heimall J, Takach P, Maglione PJ, Catanzaro J, Hsu FI, Sullivan KE, Cunningham-Rundles C, Meffre E. J Allergy Clin Immunol. 2019 Jan; 2018 Jun 20. PMID: 29935219.
2018
- Candidate Heterotaxy Gene FGFR4 Is Essential for Patterning of the Left-Right Organizer in Xenopus.Sempou E, Lakhani OA, Amalraj S, Khokha MK. Front Physiol. 2018; 2018 Dec 4. PMID: 30564136.
- WDR5 regulates left-right patterning via chromatin-dependent and -independent functions.Kulkarni SS, Khokha MK. Development. 2018 Nov 28; 2018 Nov 28. PMID: 30377171.
- RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus.Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. Development. 2018 Oct 18; 2018 Oct 18. PMID: 30337486.
- Mutations in multiple components of the nuclear pore complex cause nephrotic syndrome.Braun DA, Lovric S, Schapiro D, Schneider R, Marquez J, Asif M, Hussain MS, Daga A, Widmeier E, Rao J, Ashraf S, Tan W, Lusk CP, Kolb A, Jobst-Schwan T, Schmidt JM, Hoogstraten CA, Eddy K, Kitzler TM, Shril S, Moawia A, Schrage K, Khayyat AIA, Lawson JA, Gee HY, Warejko JK, Hermle T, Majmundar AJ, Hugo H, Budde B, Motameny S, Altmüller J, Noegel AA, Fathy HM, Gale DP, Waseem SS, Khan A, Kerecuk L, Hashmi S, Mohebbi N, Ettenger R, Serdaroğlu E, Alhasan KA, Hashem M, Goncalves S, Ariceta G, Ubetagoyena M, Antonin W, Baig SM, Alkuraya FS, Shen Q, Xu H, Antignac C, Lifton RP, Mane S, Nürnberg P, Khokha MK, Hildebrandt F. J Clin Invest. 2018 Oct 1; 2018 Sep 4. PMID: 30179222.
- WDR5 Stabilizes Actin Architecture to Promote Multiciliated Cell Formation.Kulkarni SS, Griffin JN, Date PP, Liem KF Jr, Khokha MK. Dev Cell. 2018 Sep 10. PMID: 30205038.
- The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. Cell. 2018 Jul 26. PMID: 30053424.
- Cytotoxic T-Lymphocyte-Associated Protein 4 Haploinsufficiency-Associated Inflammation Can Occur Independently of T-Cell Hyperproliferation.Le Coz C, Nolan BE, Trofa M, Kamsheh AM, Khokha MK, Lakhani SA, Novelli A, Zackai EH, Sullivan KE, Briuglia S, Bhatti TR, Romberg N. Front Immunol. 2018; 2018 Jul 24. PMID: 30087679.
- Functional Assays to Screen and Dissect Genomic Hits: Doubling Down on the National Investment in Genomic Research.Musunuru K, Bernstein D, Cole FS, Khokha MK, Lee FS, Lin S, McDonald TV, Moskowitz IP, Quertermous T, Sankaran VG, Schwartz DA, Silverman EK, Zhou X, Hasan AAK, Luo XJ. Circ Genom Precis Med. 2018 Apr. PMID: 29654098.
- RAPGEF5 Regulates Nuclear Translocation of β-Catenin.Griffin JN, Del Viso F, Duncan AR, Robson A, Hwang W, Kulkarni S, Liu KJ, Khokha MK. Dev Cell. 2018 Jan 22; 2017 Dec 28. PMID: 29290587.
- CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis.Deniz E, Mis EK, Lane M, Khokha MK. Methods Mol Biol. 2018. PMID: 30151766.
2017
- CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ. Nat Commun. 2017 Dec 8; 2017 Dec 8. PMID: 29222508.
- A p190BRhoGAP mutation and prolonged RhoB activation in fatal systemic capillary leak syndrome.Pierce RW, Merola J, Lavik JP, Kluger MS, Huttner A, Khokha MK, Pober JS. J Exp Med. 2017 Dec 4; 2017 Nov 2. PMID: 29097442.
- Visualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography.Gamm UA, Huang BK, Mis EK, Khokha MK, Choma MA. Sci Rep. 2017 Nov 8; 2017 Nov 8. PMID: 29118359.
- Developmentally regulated long non-coding RNAs in Xenopus tropicalis.Forouzmand E, Owens NDL, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KWY. Dev Biol. 2017 Jun 15; 2016 Jul 12. PMID: 27418388.
- An interspecies heart-to-heart: Using Xenopus to uncover the genetic basis of congenital heart disease.Garfinkel AM, Khokha MK. Curr Pathobiol Rep. 2017 Jun; 2017 May 6. PMID: 29082114.
- Analysis of Craniocardiac Malformations in Xenopus using Optical Coherence Tomography.Deniz E, Jonas S, Hooper M, N Griffin J, Choma MA, Khokha MK. Sci Rep. 2017 Feb 14; 2017 Feb 14. PMID: 28195132.
- An opportunity to address the genetic causes of birth defects.Khokha MK, Mitchell LE, Wallingford JB. Pediatr Res. 2017 Feb; 2016 Nov 3. PMID: 27925620.
- White paper on the study of birth defects.Khokha MK, Mitchell LE, Wallingford JB. Birth Defects Res. 2017 Jan 30; 2017 Jan 27. PMID: 28398650.
2016
- Ultrahigh-speed, phase-sensitive full-field interferometric confocal microscopy for quantitative microscale physiology.Sencan I, Huang BK, Bian Y, Mis E, Khokha MK, Cao H, Choma M. Biomed Opt Express. 2016 Nov 1; 2016 Oct 20. PMID: 27896006.
- Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis.Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. BMC Dev Biol. 2016 Oct 26; 2016 Oct 26. PMID: 27784267.
- Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. EMBO J. 2016 Oct 4; 2016 Jul 19. PMID: 27436874.
- Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia.Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK. Dev Cell. 2016 Sep 12; 2016 Sep 1. PMID: 27593162.
- Erratum: Particle streak velocimetry-optical coherence tomography: a novel method for multidimensional imaging of microscale fluid flows: erratum.Zhou KC, Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA. Biomed Opt Express. 2016 Jun 1; 2016 May 23. PMID: 27375950.
- Particle streak velocimetry-optical coherence tomography: a novel method for multidimensional imaging of microscale fluid flows.Zhou KC, Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA. Biomed Opt Express. 2016 Apr 1; 2016 Mar 30. PMID: 27375926.
- Xenopus as a model organism for birth defects-Congenital heart disease and heterotaxy.Duncan AR, Khokha MK. Semin Cell Dev Biol. 2016 Mar; 2016 Feb 22. PMID: 26910255.
- Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK. Cell Rep. 2016 Jan 26; 2016 Jan 7. PMID: 26774488.
- Nucleoporin gene expression in Xenopus tropicalis embryonic development.Reza N, Khokha MK, Del Viso F. Int J Dev Biol. 2016. PMID: 27389988.
2015
- CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus.Bhattacharya D, Marfo CA, Li D, Lane M, Khokha MK. Dev Biol. 2015 Dec 15; 2015 Nov 4. PMID: 26546975.
- The NIMA-like kinase Nek2 is a key switch balancing cilia biogenesis and resorption in the development of left-right asymmetry.Endicott SJ, Basu B, Khokha M, Brueckner M. Development. 2015 Dec 1; 2015 Oct 22. PMID: 26493400.
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. Nat Methods. 2015 Oct; 2015 Aug 31. PMID: 26322839.
- Three-dimensional, three-vector-component velocimetry of cilia-driven fluid flow using correlation-based approaches in optical coherence tomography.Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA. Biomed Opt Express. 2015 Sep 1; 2015 Aug 24. PMID: 26417520.
- The ribosome biogenesis factor Nol11 is required for optimal rDNA transcription and craniofacial development in Xenopus.Griffin JN, Sondalle SB, Del Viso F, Baserga SJ, Khokha MK. PLoS Genet. 2015 Mar; 2015 Mar 10. PMID: 25756904.
- Quantitative optical coherence tomography imaging of intermediate flow defect phenotypes in ciliary physiology and pathophysiology.Huang BK, Gamm UA, Jonas S, Khokha MK, Choma MA. J Biomed Opt. 2015 Mar. PMID: 25751026.
2014
- Mutation of NLRC4 causes a syndrome of enterocolitis and autoinflammation.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. Nat Genet. 2014 Oct; 2014 Sep 14. PMID: 25217960.
2013
- The heterotaxy gene GALNT11 glycosylates Notch to orchestrate cilia type and laterality.Boskovski MT, Yuan S, Pedersen NB, Goth CK, Makova S, Clausen H, Brueckner M, Khokha MK. Nature. 2013 Dec 19; 2013 Nov 13. PMID: 24226769.
- A novel approach to quantifying ciliary physiology: microfluidic mixing driven by a ciliated biological surface.Jonas S, Zhou E, Deniz E, Huang B, Chandrasekera K, Bhattacharya D, Wu Y, Fan R, Deserno TM, Khokha MK, Choma MA. Lab Chip. 2013 Nov 7. PMID: 23970350.
- Breeding based remobilization of Tol2 transposon in Xenopus tropicalis.Lane MA, Kimber M, Khokha MK. PLoS One. 2013; 2013 Oct 8. PMID: 24116167.
- Embryonic exposure to propylthiouracil disrupts left-right patterning in Xenopus embryos.van Veenendaal NR, Ulmer B, Boskovski MT, Fang X, Khokha MK, Wendler CC, Blum M, Rivkees SA. FASEB J. 2013 Feb; 2012 Nov 12. PMID: 23150524.
2012
- Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing.del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. BMC Genomics. 2012 Nov 21; 2012 Nov 21. PMID: 23171430.
- Endogenous contrast blood flow imaging in embryonic hearts using hemoglobin contrast subtraction angiography.Deniz E, Jonas S, Khokha M, Choma MA. Opt Lett. 2012 Jul 15. PMID: 22825198.
- The hitchhiker's guide to Xenopus genetics.Abu-Daya A, Khokha MK, Zimmerman LB. Genesis. 2012 Mar; 2012 Feb 16. PMID: 22344745.
- Xenopus white papers and resources: folding functional genomics and genetics into the frog.Khokha MK. Genesis. 2012 Mar; 2012 Feb 20. PMID: 22287484.
- Generating diploid embryos from Xenopus tropicalis.del Viso F, Khokha M. Methods Mol Biol. 2012. PMID: 22956081.
2011
- Microfluidic characterization of cilia-driven fluid flow using optical coherence tomography-based particle tracking velocimetry.Jonas S, Bhattacharya D, Khokha MK, Choma MA. Biomed Opt Express. 2011 Jul 1; 2011 Jun 22. PMID: 21750777.
- Cooperative activity of noggin and gremlin 1 in axial skeleton development.Stafford DA, Brunet LJ, Khokha MK, Economides AN, Harland RM. Development. 2011 Mar. PMID: 21303853.
- Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning.Fakhro KA, Choi M, Ware SM, Belmont JW, Towbin JA, Lifton RP, Khokha MK, Brueckner M. Proc Natl Acad Sci U S A. 2011 Feb 15; 2011 Jan 31. PMID: 21282601.
2010
- The genome of the Western clawed frog Xenopus tropicalis.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. Science. 2010 Apr 30. PMID: 20431018.
- BMP antagonists and FGF signaling contribute to different domains of the neural plate in Xenopus.Wills AE, Choi VM, Bennett MJ, Khokha MK, Harland RM. Dev Biol. 2010 Jan 15; 2009 Nov 10. PMID: 19913009.
2009
- Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes.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. Dev Dyn. 2009 Jun. PMID: 19441086.
2008
- Bmp signaling is necessary and sufficient for ventrolateral endoderm specification in Xenopus.Wills A, Dickinson K, Khokha M, Baker JC. Dev Dyn. 2008 Aug. PMID: 18651654.
2007
- Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis.Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS. BMC Biol. 2007 Jul 25; 2007 Jul 25. PMID: 17651506.
2006
- Developmental expression of FoxJ1.2, FoxJ2, and FoxQ1 in Xenopus tropicalis.Choi VM, Harland RM, Khokha MK. Gene Expr Patterns. 2006 Jun; 2006 Feb 7. PMID: 16461016.
- Twisted gastrulation is required for forebrain specification and cooperates with Chordin to inhibit BMP signaling during X. tropicalis gastrulation.Wills A, Harland RM, Khokha MK. Dev Biol. 2006 Jan 1. PMID: 16321373.
2005
- Strategies for characterising cis-regulatory elements in Xenopus.Khokha MK, Loots GG. Brief Funct Genomic Proteomic. 2005 May. PMID: 15975265.
- Identification of mutants in inbred Xenopus tropicalis.Grammer TC, Khokha MK, Lane MA, Lam K, Harland RM. Mech Dev. 2005 Mar. PMID: 15763207.
- Depletion of three BMP antagonists from Spemann's organizer leads to a catastrophic loss of dorsal structures.Khokha MK, Yeh J, Grammer TC, Harland RM. Dev Cell. 2005 Mar. PMID: 15737935.
The Precision Paradigm: Mustafa Kezar Khokha, MD
PICU and Sequencing Efforts
Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell. 2016 Sep 12;38(5):478-92. doi: 10.1016/j.devcel.2016.08.002. Epub 2016 Sep 1.