ZFIN ID: ZDB-LAB-970908-70
Stephen C. Ekker Laboratory
PI/Director: Ekker, Stephen C.
Contact Person: Ekker, Stephen C.
Email: stephen.ekker@austin.utexas.edu
URL: http://zfishbook.org
Country: United States
Phone: 507-284-5530
Fax: 507-284-9349; 507-284-1767
Line Designation: au

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My laboratory is studying and helping further the zebrafish (Danio rerio) as a model vertebrate to address major issues in human health and biology since training. This system has the potential for diverse genetic and behavioral studies typically restricted to the world of the fly or worm but conducted within the biological framework of a vertebrate. One arm of my laboratory has focused on technology development for the zebrafish for more than a decade, including the establishment of morpholino sequence-specific knockdown technology for this fish. In parallel, we engineered transposon tools for the zebrafish including protein trap gene-breaking vectors to generate a collection of molecularly characterized and revertible mutant zebrafish lines, an ongoing effort in the laboratory. Custom restriction endonucleases offer a third leg, targeted genetic modification. The successful HDR system for zebrafish we recently described offers the potential for a deeper level of genetic manipulation for both making knockout/knock-in animals as well as in vivo tracking of proteins such as receptors.

The Ekker lab is deeply committed to the broad vision that quality science education is imperative for generating qualified scientists, engineers and health care workers to address major concerns in the world. I also believe that a science-literate citizenry will also be essential for our future. To that end, I am committed to serving as a mentor for post-docs, graduate students, MD/PhD students, post-bacs, undergraduates and related scientists within my laboratory. I serve on NIH study panels to review training grants, and I’ve served as Associate Director of a T32 while I was a full-time faculty member at the University of Minnesota. I have also had the privilege of working alongside some amazing, similar-minded individuals who helped launch the Integrated Science Education Outreach (InSciEd Out) program to achieve science excellence in K-12 schools.

Blackburn, Patrick Graduate Student Campbell, Jarryd Graduate Student Cousin, Margot Graduate Student
Westcot, Stephanie Graduate Student Bedell, Victoria Technical Staff Greenwood, Tammy Technical Staff
Harm, Rhianna Technical Staff McNulty, Melissa Technical Staff Predmore-Rogers, Kelly Technical Staff
Urban, Mark Technical Staff

Wilson, M.H., Ekker, S.C., Farber, S.A. (2023) Correction: Imaging cytoplasmic lipid droplets in vivo with fluorescent perilipin 2 and perilipin 3 knock-in zebrafish. eLIFE. 12
Sabharwal, A., Wishman, M.D., Cervera, R.L., Serres, M.R., Anderson, J.L., Holmberg, S.R., Kar, B., Treichel, A.J., Ichino, N., Liu, W., Yang, J., Ding, Y., Deng, Y., Lacey, J.M., Laxen, W.J., Loken, P.R., Oglesbee, D., Farber, S.A., Clark, K.J., Xu, X., Ekker, S.C. (2022) Genetic therapy in a mitochondrial disease model suggests a critical role for liver dysfunction in mortality. eLIFE. 11:
Ding, Y., Lang, D., Yan, J., Bu, H., Li, H., Jiao, K., Yang, J., Ni, H., Morotti, S., Le, T., Clark, K.J., Port, J., Ekker, S.C., Cao, H., Zhang, Y., Wang, J., Grandi, E., Li, Z., Shi, Y., Li, Y., Glukhov, A.V., Xu, X. (2022) A phenotype-based forward genetic screen identifies Dnajb6 as a sick sinus syndrome gene. eLIFE. 11:
Sabharwal, A., Campbell, J.M., Schwab, T.L., WareJoncas, Z., Wishman, M.D., Ata, H., Liu, W., Ichino, N., Hunter, D.E., Bergren, J.D., Urban, M.D., Urban, R.M., Holmberg, S.R., Kar, B., Cook, A., Ding, Y., Xu, X., Clark, K.J., Ekker, S.C. (2022) A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Genes. 13(8):
Liu, F., Kambakam, S., Almeida, M.P., Ming, Z., Welker, J.M., Wierson, W.A., Schultz-Rogers, L.E., Ekker, S.C., Clark, K.J., Essner, J.J., McGrail, M. (2022) Cre/lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration. eLIFE. 11:
Schultz-Rogers, L.E., Thayer, M.L., Kambakam, S., Wierson, W.A., Helmer, J.A., Wishman, M.D., Wall, K.A., Greig, J.L., Forsman, J.L., Puchhalapalli, K., Nair, S., Weiss, T.J., Luiken, J.M., Blackburn, P.R., Ekker, S.C., Kool, M., McGrail, M. (2022) Rbbp4 loss disrupts neural progenitor cell cycle regulation independent of Rb and leads to Tp53 acetylation and apoptosis. Developmental Dynamics : an official publication of the American Association of Anatomists. 251(8):1267-1290
Sabharwal, A., Kar, B., Restrepo-Castillo, S., Holmberg, S.R., Mathew, N.D., Kendall, B.L., Cotter, R.P., WareJoncas, Z., Seiler, C., Nakamaru-Ogiso, E., Clark, K.J., Ekker, S.C. (2021) The FusX TALE Base Editor (FusXTBE) for Rapid Mitochondrial DNA Programming of Human Cells In Vitro and Zebrafish Disease Models In Vivo. The CRISPR journal. 4(6):799-821
Wilson, M.H., Ekker, S.C., Farber, S.A. (2021) Imaging cytoplasmic lipid droplets in vivo with fluorescent perilipin 2 and perilipin 3 knock-in zebrafish. eLIFE. 10
Welker, J.M., Wierson, W.A., Almeida, M.P., Mann, C.M., Torrie, M.E., Ming, Z., Ekker, S.C., Clark, K.J., Dobbs, D.L., Essner, J.J., McGrail, M. (2021) GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish. Bio-protocol. 11:e4100
Almeida, M.P., Welker, J.M., Siddiqui, S., Luiken, J., Ekker, S.C., Clark, K.J., Essner, J.J., McGrail, M. (2021) Endogenous zebrafish proneural Cre drivers generated by CRISPR/Cas9 short homology directed targeted integration. Scientific Reports. 11:1732
Martínez-Gálvez, G., Joshi, P., Friedberg, I., Manduca, A., Ekker, S.C. (2021) Deploying MMEJ using MENdel in precision gene editing applications for gene therapy and functional genomics. Nucleic acids research. 49:67-78
Koleilat, A., Dugdale, J.A., Christenson, T.A., Bellah, J.L., Lambert, A.M., Masino, M.A., Ekker, S.C., Schimmenti, L.A. (2020) L-type voltage-gated calcium channel agonists mitigate hearing loss and modify ribbon synapse morphology in the zebrafish model of Usher syndrome type 1. Disease models & mechanisms. 13(11):
Bedell, V.M., Meng, Q.C., Pack, M.A., Eckenhoff, R.G. (2020) A vertebrate model to reveal neural substrates underlying the transitions between conscious and unconscious states. Scientific Reports. 10:15789
Ichino, N., Serres, M.R., Urban, R.M., Urban, M.D., Treichel, A.J., Schaefbauer, K.J., Greif, L.E., Varshney, G.K., Skuster, K.J., McNulty, M.S., Daby, C.L., Wang, Y., Liao, H.K., El-Rass, S., Ding, Y., Liu, W., Anderson, J.L., Wishman, M.D., Sabharwal, A., Schimmenti, L.A., Sivasubbu, S., Balciunas, D., Hammerschmidt, M., Farber, S.A., Wen, X.Y., Xu, X., McGrail, M., Essner, J.J., Burgess, S.M., Clark, K.J., Ekker, S.C. (2020) Building the vertebrate codex using the gene breaking protein trap library. eLIFE. 9:
Thierer, J.H., Ekker, S.C., Farber, S.A. (2020) Author Correction: The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 11:3707
Wierson, W.A., Welker, J.M., Almeida, M.P., Mann, C.M., Webster, D.A., Torrie, M.E., Weiss, T.J., Kambakam, S., Vollbrecht, M.K., Lan, M., McKeighan, K.C., Levey, J., Ming, Z., Wehmeier, A., Mikelson, C.S., Haltom, J.A., Kwan, K.M., Chien, C.B., Balciunas, D., Ekker, S.C., Clark, K.J., Webber, B.R., Moriarity, B.S., Solin, S.L., Carlson, D.F., Dobbs, D.L., McGrail, M., Essner, J. (2020) Efficient targeted integration directed by short homology in zebrafish and mammalian cells. eLIFE. 9:
Ma, X., Zhu, P., Ding, Y., Zhang, H., Qiu, Q., Dvornikov, A.V., Wang, Z., Kim, M., Wang, Y., Lowerison, M., Yu, Y., Norton, N., Herrmann, J., Ekker, S.C., Hsiai, T.K., Lin, X., Xu, X. (2020) Retinoid X receptor alpha is a spatiotemporally predominant therapeutic target for anthracycline-induced cardiotoxicity. Science advances. 6:eaay2939
McKinstry-Wu, A.R., Wasilczuk, A.Z., Harrison, B.A., Bedell, V.M., Sridharan, M.J., Breig, J.J., Pack, M., Kelz, M.B., Proekt, A. (2019) Analysis of stochastic fluctuations in responsiveness is a critical step toward personalized anesthesia. eLIFE. 8:
Wierson, W.A., Simone, B.W., WareJoncas, Z., Mann, C., Welker, J.M., Kar, B., Emch, M.J., Friedberg, I., Gendron, W.A.C., Barry, M.A., Clark, K.J., Dobbs, D.L., McGrail, M.A., Ekker, S.C., Essner, J.J. (2019) Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. The CRISPR journal. 2(6):417-433
Thierer, J.H., Ekker, S.C., Farber, S.A. (2019) The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 10:3426
Ichino, N., Ekker, S.C. (2019) Taking a closer look at whole organisms. eLIFE. 8
Varga, Z.M., Ekker, S.C., Lawrence, C. (2018) Workshop Report: Zebrafish and Other Fish Models-Description of Extrinsic Environmental Factors for Rigorous Experiments and Reproducible Results. Zebrafish. 15:533-535
Ata, H., Ekstrom, T.L., Martínez-Gálvez, G., Mann, C.M., Dvornikov, A.V., Schaefbauer, K.J., Ma, A.C., Dobbs, D., Clark, K.J., Ekker, S.C. (2018) Robust Activation of Microhomology-mediated End Joining for Precision Gene Editing Applications. PLoS Genetics. 14:e1007652
Ignatius, M.S., Hayes, M.N., Moore, F.E., Tang, Q., Garcia, S.P., Blackburn, P.R., Baxi, K., Wang, L., Jin, A., Ramakrishnan, A., Reeder, S., Chen, Y., Nielsen, G.P., Chen, E.Y., Hasserjian, R.P., Tirode, F., Ekker, S.C., Langenau, D.M. (2018) tp53 deficiency causes a wide tumor spectrum and increases embryonal rhabdomyosarcoma metastasis in zebrafish.. eLIFE. 7:
Simone, B.W., Martínez-Gálvez, G., WareJoncas, Z., Ekker, S.C. (2018) Fishing for understanding: Unlocking the zebrafish gene editor's toolbox. Methods (San Diego, Calif.). 150:3-10
Hoeppner, L.H., Sinha, S., Wang, Y., Bhattacharya, R., Dutta, S., Gong, X., Bedell, V.M., Suresh, S., Chun, C., Ramchandran, R., Ekker, S.C., Mukhopadhyay, D. (2018) Correction: RhoC maintains vascular homeostasis by regulating VEGF-induced signaling in endothelial cells (doi:10.1242/jcs.167601). Journal of Cell Science. 131(6)
Bedell, V., Buglo, E., Marcato, D., Pylatiuk, C., Mikut, R., Stegmaier, J., Scudder, W., Wray, M., Züchner, S., Strähle, U., Peravali, R., Dallman, J.E. (2018) Zebrafish: A Pharmacogenetic Model for Anesthesia. Methods in enzymology. 602:189-209
Stainier, D.Y.R., Raz, E., Lawson, N.D., Ekker, S.C., Burdine, R.D., Eisen, J.S., Ingham, P.W., Schulte-Merker, S., Yelon, D., Weinstein, B.M., Mullins, M.C., Wilson, S.W., Ramakrishnan, L., Amacher, S.L., Neuhauss, S.C.F., Meng, A., Mochizuki, N., Panula, P., Moens, C.B. (2017) Guidelines for morpholino use in zebrafish. PLoS Genetics. 13:e1007000
El-Rass, S., Eisa-Beygi, S., Khong, E., Brand-Arzamendi, K., Mauro, A., Zhang, H., Clark, K.J., Ekker, S.C., Wen, X.Y. (2017) Disruption of pdgfra alters endocardial and myocardial fusion during zebrafish cardiac assembly.. Biology Open. 6(3):348-357
Gerlai, R., Poshusta, T.L., Rampersad, M., Fernandes, Y., Greenwood, T.M., Cousin, M.A., Klee, E.W., Clark, K.J. (2017) Forward Genetic Screening Using Behavioral Tests in Zebrafish: A Proof of Concept Analysis of Mutants. Behavior Genetics. 47(1):125-139
Ding, Y., Long, P.A., Bos, J.M., Shih, Y.H., Ma, X., Sundsbak, R.S., Chen, J., Jiang, Y., Zhao, L., Hu, X., Wang, J., Shi, Y., Ackerman, M.J., Lin, X., Ekker, S.C., Redfield, M.M., Olson, T.M., Xu, X. (2016) A modifier screen identifies DNAJB6 as a cardiomyopathy susceptibility gene.. JCI insight. 1(14)
Leveque, R.E., Clark, K.J., Ekker, S.C. (2016) Mayo Clinic Zebrafish Facility Overview. Zebrafish. 13 Suppl 1:S44-6
Varga, Z.M., Lawrence, C., Ekker, S.C., Eisen, J.S. (2016) Universal Healthcare for Zebrafish. Zebrafish. 13 Suppl 1:S1-4
Lee, H.B., Schwab, T.L., Koleilat, A., Ata, H., Daby, C.L., Cervera, R.L., McNulty, M.S., Bostwick, H.S., Clark, K.J. (2016) Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping. Human gene therapy. 27:425-35
Ma, A.C., McNulty, M.S., Tanya, P.L., Jarryd, C.M., Martínez-Gálvez, G., Argue, D.P., Lee, H.B., Urban, M.D., Bullard, C.E., Blackburn, P.R., Man, T.K., Clark, K.J., Ekker, S.C. (2016) FusX: A rapid one-step TALE assembly system for genome science. Human gene therapy. 27(6):451-63
Welker, J.M., Wierson, W.A., Wang, Y., Poshusta, T.L., McNulty, M.S., Tisdale, E.E., Solin, S.L., Ekker, S.C., Clark, K.J., McGrail, M., Essner, J.J. (2016) GoldyTALEN Vectors with Improved Efficiency for Golden Gate TALEN Assembly. Human gene therapy. 27:423-4
Ni, J., Wangensteen, K.J., Nelsen, D., Balciunas, D., Skuster, K.J., Urban, M.D., Ekker, S.C. (2016) Active recombinant Tol2 transposase for gene transfer and gene discovery applications. Mobile DNA. 7:6
Ata, H., Clark, K.J., Ekker, S.C. (2016) The zebrafish genome editing toolkit. Methods in cell biology. 135:149-70
Ma, A.C., Chen, Y., Blackburn, P.R., Ekker, S.C. (2016) TALEN-Mediated Mutagenesis and Genome Editing. Methods in molecular biology (Clifton, N.J.). 1451:17-30
Hoeppner, L.H., Sinha, S., Wang, Y., Bhattacharya, R., Dutta, S., Gong, X., Bedell, V.M., Suresh, S., Chun, C.Z., Ramchandran, R., Ekker, S.C., Mukhopadhyay, D. (2015) RhoC maintains vascular homeostasis by regulating VEGF-induced signaling in endothelial cells. Journal of Cell Science. 128(19):3556-68
Westcot, S.E., Hatzold, J., Urban, M.D., Richetti, S.K., Skuster, K.J., Harm, R.M., Lopez Cervera, R., Umemoto, N., McNulty, M.S., Clark, K.J., Hammerschmidt, M., Ekker, S.C. (2015) Protein-Trap Insertional Mutagenesis Uncovers New Genes Involved in Zebrafish Skin Development, Including a Neuregulin 2a-Based ErbB Signaling Pathway Required during Median Fin Fold Morphogenesis. PLoS One. 10:e0130688
Bedell, V.M., Ekker, S.C. (2015) Using Engineered Endonucleases to Create Knockout and Knockin Zebrafish Models. Methods in molecular biology (Clifton, N.J.). 1239:291-305
Sun, X., Ekker, S.C., Shelden, E.A., Takubo, N., Wang, Y., Burghardt, T.P. (2014) In Vivo Orientation of Single Myosin Lever Arms in Zebrafish Skeletal Muscle. Biophysical journal. 107:1403-1414
Craig, T.A., Zhang, Y., Magis, A.T., Funk, C.C., Price, N.D., Ekker, S.C., Kumar, R. (2014) Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing. Zebrafish. 11(3):207-18
He, B.L., Shi, X., Man, C.H., Ma, A.C., Ekker, S.C., Chow, H.C., So, C.W., Choi, W.W., Zhang, W., Zhang, Y., and Leung, A.Y. (2014) Functions of FMS-like tyrosine kinase 3 (flt3) in zebrafish hematopoiesis and its relevance to human acute myeloid leukemia. Blood. 123(16):2518-29
Cousin, M.A., Ebbert, J.O., Wiinamaki, A.R., Urban, M.D., Argue, D.P., Ekker, S.C., Klee, E.W. (2014) Larval zebrafish model for FDA-approved drug repositioning for tobacco dependence treatment. PLoS One. 9:e90467
Singh, M., Bhartiya, D., Maini, J., Sharma, M., Singh, A.R., Kadarkaraisamy, S., Rana, R., Sabharwal, A., Nanda, S., Ramachandran, A., Mittal, A., Kapoor, S., Sehgal, P., Asad, Z., Kaushik, K., Vellarikkal, S.K., Jagga, D., Muthuswami, M., Chauhan, R.K., Leonard, E., Priyadarshini, R., Halimani, M., Malhotra, S., Patowary, A., Vishwakarma, H., Joshi, P., Bhardwaj, V., Bhaumik, A., Bhatt, B., Jha, A., Kumar, A., Budakoti, P., Lalwani, M.K., Meli, R., Jalali, S., Joshi, K., Pal, K., Dhiman, H., Laddha, S.V., Jadhav, V., Singh, N., Pandey, V., Sachidanandan, C., Ekker, S.C., Klee, E.W., Scaria, V., Sivasubbu, S. (2014) The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. Database : the journal of biological databases and curation. 2014:bau011
Campbell, J.M., Hartjes, K.A., Nelson, T.J., Xu, X., and Ekker, S.C. (2013) New and TALENted Genome Engineering Toolbox. Circulation research. 113(5):571-587
Tietz Bogert, P.S., Huang, B.Q., Gradilone, S.A., Masyuk, T.V., Moulder, G.L., Ekker, S.C., and Larusso, N.F. (2013) The zebrafish as a model to study polycystic liver disease. Zebrafish. 10(2):211-217
Ma, A.C., Lee, H.B., Clark, K.J., and Ekker, S.C. (2013) High Efficiency In Vivo Genome Engineering with a Simplified 15-RVD GoldyTALEN Design. PLoS One. 8(5):e65259
Blackburn, P.R., Campbell, J.M., Clark, K.J., and Ekker, S.C. (2013) The CRISPR System-Keeping Zebrafish Gene Targeting Fresh. Zebrafish. 10(1):116-8
Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A.R., Swarnkar, M., Singh, N., Pandey, V., Torroja, C., Clark, M.D., Kocher, J.P., Clark, K.J., Stemple, D.L., Klee, E.W., Ekker, S.C., Scaria, V., and Sivasubbu, S. (2013) A sequence-based variation map of zebrafish. Zebrafish. 10(1):15-20
Ding, Y., Liu, W., Deng, Y., Jomok, B., Yang, J., Huang, W., Clark, K.J., Zhong, T., Lin, X., Ekker, S.C., and Xu, X. (2013) Trapping Cardiac Recessive Mutants via Expression-based Insertional Mutagenesis Screening. Circulation research. 112(4):606-617
Chen, Z., Lee, H., Henle, S.J., Cheever, T.R., Ekker, S.C., and Henley, J.R. (2013) Primary Neuron Culture for Nerve Growth and Axon Guidance Studies in Zebrafish (Danio rerio). PLoS One. 8(3):e57539
Philpott, C., Donack, C.J., Cousin, M.A., and Pierret, C. (2012) Reducing the noise in behavioral assays: sex and age in adult zebrafish locomotion. Zebrafish. 9(4):191-194
Bedell, V.M., Wang, Y., Campbell, J.M., Poshusta, T.L., Starker, C.G., Krug, R.G., Tan, W., Penheiter, S.G., Ma, A.C., Leung, A.Y., Fahrenkrug, S.C., Carlson, D.F., Voytas, D.F., Clark, K.J., Essner, J.J., and Ekker, S.C. (2012) In vivo genome editing using a high-efficiency TALEN system. Nature. 491(7422):114-118
Hoeppner, L.H., Phoenix, K.N., Clark, K.J., Bhattacharya, R., Gong, X., Sciuto, T.E., Vohra, P., Suresh, S., Bhattacharya, S., Dvorak, A.M., Ekker, S.C., Dvorak, H.F., Claffey, K.P., and Mukhopadhyay, D. (2012) Revealing the role of phospholipase Cβ3 in the regulation of VEGF-induced vascular permeability. Blood. 120(11):2167-2173
Craig, T.A., Zhang, Y., McNulty, M.S., Middha, S., Ketha, H., Singh, R.J., Magis, A.T., Funk, C., Price, N.D., Ekker, S.C., and Kumar, R. (2012) Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1α,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Developing Zebrafish. Molecular endocrinology (Baltimore, Md.). 26(9):1630-1642
McNulty, M.S., Bedell, V.M., Greenwood, T.M., Craig, T.A., Ekker, S.C., and Kumar, R. (2012) Expression of sclerostin in the developing zebrafish (Danio rerio) brain and skeleton. Gene expression patterns : GEP. 12(7-8):228-235
Klee, E.W., Schneider, H., Clark, K.J., Cousin, M.A., Ebbert, J.O., Hooten, W.M., Karpyak, V.M., Warner, D.O., and Ekker, S.C. (2012) Zebrafish: a model for the study of addiction genetics. Human genetics. 131(6):977-1008
Bedell, V.M., Person, A.D., Larson, J.D., McLoon, A., Balciunas, D., Clark, K.J., Neff, K.I., Nelson, K.E., Bill, B.R., Schimmenti, L.A., Beiraghi, S., and Ekker, S.C. (2012) The lineage-specific gene ponzr1 is essential for zebrafish pronephric and pharyngeal arch development. Development (Cambridge, England). 139(4):793-804
Liao, H.K., Wang, Y., Watt, K.E., Wen, Q., Breitback, J., Kemmet, C.K., Clark, K.J., Ekker, S.C., Essner, J.J., and McGrail, M. (2012) Tol2 gene trap integrations in the zebrafish amyloid precursor protein genes appa and aplp2 reveal accumulation of secreted APP at the embryonic veins. Developmental Dynamics : an official publication of the American Association of Anatomists. 241(2):415-425
Xu, J., Gao, J., Li, J., Xue, L., Clark, K.J., Ekker, S.C., and Du, S.J. (2012) Functional analysis of slow Myosin heavy chain 1 and myomesin-3 in sarcomere organization in zebrafish embryonic slow muscles. Journal of genetics and genomics = Yi chuan xue bao. 39(2):69-80
Clark, K.J., Argue, D.P., Petzold, A.M., Ekker, S.C. (2012) zfishbook: connecting you to a world of zebrafish revertible mutants.. Nucleic acids research. 40(Database issue):D907-11
Ekker, S., Clark, K., ZFIN Staff (2012) Curation of zfishbook links. ZFIN Direct Data Submission.
Hoffman, S.J., Psaltis, P.J., Clark, K.J., Spoon, D.B., Chue, C.D., Ekker, S.C, and Simari, R.D. (2012) An in vivo method to quantify lymphangiogenesis in zebrafish. PLoS One. 7(9):e45240
Ma, A.C., Fung, T.K., Lin, R.H., Chung, M.I., Yang, D., Ekker, S.C., and Leung, A.Y. (2011) Methionine aminopeptidase 2 is required for HSC initiation and proliferation. Blood. 118(20):5448-57
Ding, Y., Sun, X., Huang, W., Hoage, T., Redfield, M., Kushwaha, S., Sivasubbu, S., Lin, X., Ekker, S., and Xu, X. (2011) Haploinsufficiency of Target of Rapamycin Attenuates Cardiomyopathies in Adult Zebrafish. Circulation research. 109(6):658-69
Clark, K.J., Voytas, D.F., and Ekker, S.C. (2011) A TALE of Two Nucleases: Gene Targeting for the Masses. Zebrafish. 8(3):147-149
Bedell, V.M., Westcot, S.E., and Ekker, S.C. (2011) Lessons from morpholino-based screening in zebrafish. Briefings in functional genomics & proteomics. 10(4):181-8
Clark, K.J., Balciunas, D., Pogoda, H.M., Ding, Y., Westcot, S.E., Bedell, V.M., Greenwood, T.M., Urban, M.D., Skuster, K.J., Petzold, A.M., Ni, J., Nielsen, A.L., Patowary, A., Scaria, V., Sivasubbu, S., Xu, X., Hammerschmidt, M., and Ekker, S.C. (2011) In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Nature Methods. 8(6):506-512
Klee, E.W., Ebbert, J.O., Schneider, H., Hurt, R.D., and Ekker, S.C. (2011) Zebrafish for the Study of the Biological Effects of Nicotine. Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco. 13(5):301-312
Alexandre, D., Alonzeau, J., Bill, B.R., Ekker, S.C., and Waschek, J.A. (2011) Expression Analysis of PAC1-R and PACAP Genes in Zebrafish Embryos. Journal of molecular neuroscience : MN. 43(1):94-100
Clark, K.J., Boczek, N.J., and Ekker, S.C. (2011) Stressing zebrafish for behavioral genetics. Reviews in the Neurosciences. 22(1):49-62
Clark, K.J., Urban, M.D., Skuster, K.J., and Ekker, S.C. (2011) Transgenic zebrafish using transposable elements. Methods in cell biology. 104:137-149
Wang, Y., Kaiser, M.S., Larson, J.D., Nasevicius, A., Clark, K.J., Wadman, S.A., Roberg-Perez, S.E., Ekker, S.C., Hackett, P.B., McGrail, M., and Essner, J.J. (2010) Moesin1 and Ve-cadherin are required in endothelial cells during in vivo tubulogenesis. Development (Cambridge, England). 137(18):3119-3128
Petzold, A.M., Bedell, V.M., Boczek, N.J., Essner, J.J., Balciunas, D., Clark, K.J., and Ekker, S.C. (2010) SCORE imaging: specimen in a corrected optical rotational enclosure. Zebrafish. 7(2):149-154
Person, A.D., Beiraghi, S., Sieben, C.M., Hermanson, S., Neumann, A.N., Robu, M.E., Schleiffarth, J.R., Billington, C.J. Jr, van Bokhoven, H., Hoogeboom, J.M., Mazzeu, J.F., Petryk, A., Schimmenti, L.A., Brunner, H.G., Ekker, S.C., and Lohr, J.L. (2010) WNT5A mutations in patients with autosomal dominant Robinow syndrome. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(1):327-337
Petzold, A.M., Balciunas, D., Sivasubbu, S., Clark, K.J., Bedell, V.M., Westcot, S.E., Myers, S.R., Moulder, G.L., Thomas, M.J., and Ekker, S.C. (2009) Nicotine response genetics in the zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 106(44):18662-18667
Bill, B.R., Petzold, A.M., Clark, K.J., Schimmenti, L.A., and Ekker, S.C. (2009) A primer for morpholino use in zebrafish. Zebrafish. 6(1):69-77
Shibasaki, Y., Kim, B.S., Young, A.J., McLoon, A.L., Ekker, S.C., Taton, T.A. (2009) Crosslinked, Glassy Styrenic Surfactants Stabilize Quantum Dots Against Environmental Extremes. Journal of Materials Chemistry. 19:6324-6327
Ekker, S.C., Parichy, D.M., and Cheng, K.C. (2008) Research implications of pigment biology in zebrafish. Zebrafish. 5(4):233-235
Bill, B.R., Balciunas, D., McCarra, J.A., Young, E.D., Xiong, T., Spahn, A.M., Garcia-Lecea, M., Korzh, V., Ekker, S.C., and Schimmenti, L.A. (2008) Development and notch signaling requirements of the zebrafish choroid plexus. PLoS One. 3(9):e3114
Ekker, S.C. (2008) All eyes on zebrafish. Zebrafish. 5(3):153
Knowlton, M.N., Li, T., Ren, Y., Bill, B.R., Ellis, L.B., and Ekker, S.C. (2008) A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information. BMC Bioinformatics. 9(1):7
Aleström, P., Begemann, G., Carvan, M.J. 3rd, Cheng, K.C., Crosier, K., Crosier, P., Ekker, S., Huttenlocher, A., Kawakami, K., Kelly, G., Korzh, V., Lieschke, G., Mione, M., Neely, M.N., Neuhauss, S., and Trede, N.S. (2008) Views on four key questions about zebrafish research. Zebrafish. 5(1):9-24
Ekker, S.C. (2008) Zinc finger-based knockout punches for zebrafish genes. Zebrafish. 5(2):121-123
Wang, L., Dutta, S.K., Kojima, T., Xu, X., Khosravi-Far, R., Ekker, S.C., and Mukhopadhyay, D. (2007) Neuropilin-1 Modulates p53/Caspases Axis to Promote Endothelial Cell Survival. PLoS One. 2(11):e1161
Ekker, S., and ZFIN staff (2007) Curation of Morpholino Database Links. ZFIN Direct Data Submission.
Alvarez, Y., Cederlund, M.L., Cottell, D.C., Bill, B.R., Ekker, S.C., Torres-Vazquez, J., Weinstein, B.M., Hyde, D.R., Vihtelic, T.S., and Kennedy, B.N. (2007) Genetic determinants of hyaloid and retinal vasculature in zebrafish. BMC Developmental Biology. 7(1):114
Robu, M.E., Larson, J.D., Nasevicius, A., Beiraghi, S., Brenner, C., Farber, S.A., and Ekker, S.C. (2007) p53 activation by knockdown technologies. PLoS Genetics. 3(5):e78
Patterson, L.J., Gering, M., Eckfeldt, C.E., Green, A.R., Verfaillie, C.M., Ekker, S.C., and Patient, R. (2007) The transcription factors, Scl and Lmo2, act together during development of the hemangioblast in zebrafish. Blood. 109(6):2389-2398
Ekker, S.C., Stemple, D.L., Clark, M., Chien, C.B., Rasooly, R.S., and Javois, L.C. (2007) Zebrafish genome project: bringing new biology to the vertebrate genome field. Zebrafish. 4(4):239-251
Sivasubbu, S., Balciunas, D., Amsterdam, A.,and Ekker, S.C. (2007) Insertional mutagenesis strategies in zebrafish. Genome biology. 8(1):S9
Pickart, M.A., Klee, E.W., Nielsen, A.L., Sivasubbu, S., Mendenhall, E.M., Bill B.R., Chen, E., Eckfeldt, C.E., Knowlton, M., Robu, M.E., Larson, J.D., Deng, Y., Schimmenti, L.A., Ellis, L.B., Verfaillie, C.M., Hammerschmidt, M., Farber, S.A., and Ekker, S.C. (2006) Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One. 1(1):e104
Balciunas, D., Wangensteen, K.J., Wilber, A., Bell, J., Geurts, A., Sivasubbu, S., Wang, X., Hackett, P.B., Largaespada, D.A., McIvor, R.S., and Ekker, S.C. (2006) Harnessing a High Cargo-Capacity Transposon for Genetic Applications in Vertebrates. PLoS Genetics. 2(11):e169
Sivasubbu, S., Balciunas, D., Davidson, A.E., Pickart, M.A., Hermanson, S.B., Wangensteen, K.J., Wolbrink, D.C., and Ekker, S.C. (2006) Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development. Mechanisms of Development. 123(7):513-529
Chen, E., Larson, J.D., and Ekker, S.C. (2006) Functional analysis of zebrafish Microfibril-Associated Glycoprotein-1 (MAGP-1) in vivo reveals roles for microfibrils in both vascular development and function. Blood. 107(11):4364-4374
Kwan, T.T., Liang, R., Verfaillie, C.M., Ekker, S.C., Chan, L.C., Lin, S., and Leung, A.Y. (2006) Regulation of primitive hematopoiesis in zebrafish embryos by the death receptor gene. Experimental hematology. 34(1):27-34
Kim, H.J., Schleiffarth, J.R., Jessurun, J., Sumanas, S., Petryk, A., Lin, S., and Ekker, S.C. (2005) Wnt5 signaling in vertebrate pancreas development. BMC Biology. 3:23
Chen, E., Stringer, S.E., Rusch, M.A., Selleck, S.B., and Ekker, S.C. (2005) A unique role for 6-O sulfation modification in zebrafish vascular development. Developmental Biology. 284(2):364-376
Eckfeldt, C.E., Mendenhall, E.M., Flynn, C.M., Wang, T.F., Pickart, M.A., Grindle, S.M., Ekker, S.C., and Verfaillie, C.M. (2005) Functional analysis of human hematopoietic stem cell gene expression using zebrafish. PLoS Biology. 3(8):e254
Klee, E.W., Shim, K.J., Pickart, M.A., Ekker, S.C., and Ellis, L.B. (2005) AMOD: a morpholino oligonucleotide selection tool. Nucleic acids research. 33(Web Server issue):W506-511
Balciunas, D., and Ekker, S.C. (2005) Trapping Fish Genes with Transposons. Zebrafish. 1(4):335-341
Leung, A.Y., Mendenhall, E.M., Kwan, T.T., Liang, R., Eckfeldt, C., Chen, E., Hammerschmidt, M., Grindley, S., Ekker, S.C., and Verfaillie, C.M. (2005) Characterization of expanded intermediate cell mass in zebrafish chordin morphant embryos. Developmental Biology. 277(1):235-254
Chen, E., and Ekker, S.C. (2004) Zebrafish as a genomics research model. Current pharmaceutical biotechnology. 5(5):409-413
Pickart, M.A., Sivasubbu, S., Nielsen, A.L., Shriram, S., King, R.A., and Ekker, S.C. (2004) Functional genomics tools for the analysis of zebrafish pigment. Pigment cell research. 17(5):461-470
Balciunas, D., Davidson, A.E., Sivasubbu, S., Hermanson, S.B., Welle, Z., and Ekker, S.C. (2004) Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics. 5(1):62
Larson, J.D., Wadman, S.A., Chen, E., Kerley, L., Clark, K.J., Eide, M., Lippert, S., Nasevicius, A., Ekker, S.C., Hackett, P.B., and Essner, J.J. (2004) Expression of VE-cadherin in zebrafish embryos: A new tool to evaluate vascular development. Developmental Dynamics : an official publication of the American Association of Anatomists. 231(1):204-213
Pickart, M., King, R., and Ekker, S.C. (2004) Molecular genetics of pigmentation in the zebrafish. Pigment cell research. 17(4):436-437
Chen, E., Hermanson, S., and Ekker, S.C. (2004) Syndecan-2 is essential for angiogenic sprouting during zebrafish development. Blood. 103(5):1710-1719
Ekker, S.C. (2004) Nonconventional antisense in zebrafish for functional genomics applications. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:121-136
Hermanson, S., Davidson, A.E., Sivasubbu, S., Balciunas, D., and Ekker, S.C. (2004) Sleeping Beauty transposon for efficient gene delivery. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:349-362
Davidson, A.E., Balciunas, D., Mohn, D., Shaffer, J., Hermanson, S., Sivasubbu, S., Cliff, M.P., Hackett, P.B., and Ekker, S.C. (2003) Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Developmental Biology. 263(2):191-202
Beiraghi, S., Beckman, E., Shiroma, D., and Ekker, S.C. (2002) Nicotine and embryonic development in zebrafish. American journal of human genetics. 71(4):318
Sumanas, S., Kim, H.J., Hermanson, S.B., and Ekker, S.C. (2002) Lateral line, nervous system, and maternal expression of Frizzled 7a during zebrafish embryogenesis. Mechanisms of Development. 115(1-2):107-111
Dupuy, A.J., Clark, K., Carlson, C.M., Fritz, S., Davidson, A.E., Markley, K.M., Finley, K., Fletcher, C.F., Ekker, S.C., Hackett, P.B., Horn, S., and Largaespada, D.A. (2002) Mammalian germ-line transgenesis by transposition. Proceedings of the National Academy of Sciences of the United States of America. 99(7):4495-4499
Beckman, E., Ekker, S.C., and Beiraghi, S. (2002) Effect of nicotine on embryonic development of zebrafish. Journal of dental research. 81:1619
Bingham, S., Nasevicius, A., Ekker, S.C., and Chandrasekhar, A. (2001) Sonic hedgehog and tiggy-winkle hedgehog cooperatively induce zebrafish branchiomotor neurons. Genesis (New York, N.Y. : 2000). 30(3):170-174
Etheridge, L.A., Wu, T., Liang, J.O., Ekker, S.C., and Halpern, M.E. (2001) Floor plate develops upon depletion of tiggy-winkle and sonic hedgehog. Genesis (New York, N.Y. : 2000). 30(3):164-169
Finley, K.R., Davidson, A.E., and Ekker, S.C. (2001) Three-color imaging using fluorescent proteins in living zebrafish embryos. Biotechniques. 31(1):66-68
Klee, E.W., Ekker, S.C., and Ellis, L.B.M. (2001) Target selection for Danio rerio functional genomics. Genesis (New York, N.Y. : 2000). 30(3):123-125
Sumanas, S., Kim, H.J., Hermanson, S., and Ekker, S.C. (2001) Zebrafish frizzled-2 morphant displays defects in body axis elongation. Genesis (New York, N.Y. : 2000). 30(3):114-118
Ekker, S.C., and Larson, J.D. (2001) Morphant Technology in Model Developmental Systems. Genesis (New York, N.Y. : 2000). 30:89-93
Nasevicius, A. and Ekker, S.C. (2001) The zebrafish as a novel system for functional genomics and therapeutic development applications. Current opinion in molecular therapeutics. 3(3):224-228
Ross, J.J., Shimmi, O., Vilmos, P., Petryk, A., Kim, H., Gaudenz, K., Hermanson, S., Ekker, S.C., O'Connor, M.B., and Marsh, J.L. (2001) Twisted gastrulation is a conserved extracellular BMP antagonist. Nature. 410(6827):479-483
Ekker, S.C. (2000) Morphants: a new systematic vertebrate functional genomics approach. Yeast (Chichester, England). 17(4):302-306
Nasevicius, A., Larson, J., and Ekker, S.C. (2000) Distinct requirements for zebrafish angiogenesis revealed by a VEGF-A morphant. Yeast (Chichester, England). 17(4):294-301
Nasevicius, A. and Ekker, S.C. (2000) Effective targeted gene 'knockdown' in zebrafish. Nature Genetics. 26(2):216-220
Nasevicius, A., Hyatt, T.M., Hermanson, S.B., and Ekker, S.C. (2000) Sequence, expression, and location of zebrafish frizzled 10. Mechanisms of Development. 92(2):311-314
Hyatt, T.M. and Ekker, S.C. (1999) Vectors and techniques for ectopic gene expression in zebrafish. In The Zebrafish: Biology. H.W. Detrich, L.I. Zon, and M. Westerfield, eds. Methods Cell Biol.. 59:117-126
Nasevicius, A., Hyatt, T., Kim, H., Guttman, J., Walsh, E., Sumanas, S., Wang, Y.S., and Ekker, S.C. (1998) Evidence for a fizzled-mediated wnt pathway required for zebrafish dorsal mesoderm formation. Development (Cambridge, England). 125:4283-4292
Ekker, S.C., Ungar, A.R., Greenstein, P., vonKessler, D.P., Porter, J.A., Moon, R.T., and Beachy, P.A. (1995) Patterning activities of vertebrate hedgehog proteins in the developing eye and brain. Current biology : CB. 5:944-955