Stephen Ekker

Summary

Affiliation: Mayo Clinic
Country: USA

Publications

  1. pmc Lessons from morpholino-based screening in zebrafish
    Victoria M Bedell
    Mayo Clinic, Guggenheim, Rochester, MN 55905, USA
    Brief Funct Genomics 10:181-8. 2011
  2. pmc Development and Notch signaling requirements of the zebrafish choroid plexus
    Brent R Bill
    Department of Genetics, Cell and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS ONE 3:e3114. 2008
  3. pmc High efficiency In Vivo genome engineering with a simplified 15-RVD GoldyTALEN design
    Alvin C Ma
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
    PLoS ONE 8:e65259. 2013
  4. pmc In vivo protein trapping produces a functional expression codex of the vertebrate proteome
    Karl J Clark
    Mayo Clinic, Rochester, Minnesota, USA
    Nat Methods 8:506-15. 2011
  5. pmc zfishbook: connecting you to a world of zebrafish revertible mutants
    Karl J Clark
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
    Nucleic Acids Res 40:D907-11. 2012
  6. ncbi request reprint New and TALENted genome engineering toolbox
    Jarryd M Campbell
    Center for Translational Science Activities, Mayo Clinic, Rochester, MN 55905, USA
    Circ Res 113:571-87. 2013
  7. pmc Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools
    Tyler H Koep
    Clinical and Translational Sciences, Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA
    BMC Infect Dis 13:71. 2013
  8. pmc Mojo Hand, a TALEN design tool for genome editing applications
    Kevin L Neff
    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
    BMC Bioinformatics 14:1. 2013
  9. pmc Insertional mutagenesis strategies in zebrafish
    Sridhar Sivasubbu
    Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, Mall Road, Delhi 110007, India
    Genome Biol 8:S9. 2007
  10. pmc A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information
    Michelle N Knowlton
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 9:7. 2008

Research Grants

  1. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2006
  2. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2003
  3. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2004
  4. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2005
  5. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2005
  6. Intron-based Mutagenic Transposons for Zebrafish
    Stephen Ekker; Fiscal Year: 2009
  7. Intron-based Mutagenic Transposons for Zebrafish
    Stephen Ekker; Fiscal Year: 2009
  8. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2004
  9. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2003
  10. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2003

Collaborators

Detail Information

Publications40

  1. pmc Lessons from morpholino-based screening in zebrafish
    Victoria M Bedell
    Mayo Clinic, Guggenheim, Rochester, MN 55905, USA
    Brief Funct Genomics 10:181-8. 2011
    ..Therefore, with careful management, MOs remain a valuable tool for discovery screening as well as individual gene knockdown analysis...
  2. pmc Development and Notch signaling requirements of the zebrafish choroid plexus
    Brent R Bill
    Department of Genetics, Cell and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS ONE 3:e3114. 2008
    ..Despite its importance in neurobiology, little is known about how this structure forms...
  3. pmc High efficiency In Vivo genome engineering with a simplified 15-RVD GoldyTALEN design
    Alvin C Ma
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
    PLoS ONE 8:e65259. 2013
    ..In conclusion, these high efficiency 15-RVD GoldyTALENs are useful for high-throughput mutagenesis in diverse application including hypothesis testing from basic science to precision medicine...
  4. pmc In vivo protein trapping produces a functional expression codex of the vertebrate proteome
    Karl J Clark
    Mayo Clinic, Rochester, Minnesota, USA
    Nat Methods 8:506-15. 2011
    ..The RP2 mutagenesis system is a step toward a unified 'codex' of protein expression and direct functional annotation of the vertebrate genome...
  5. pmc zfishbook: connecting you to a world of zebrafish revertible mutants
    Karl J Clark
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
    Nucleic Acids Res 40:D907-11. 2012
    ....
  6. ncbi request reprint New and TALENted genome engineering toolbox
    Jarryd M Campbell
    Center for Translational Science Activities, Mayo Clinic, Rochester, MN 55905, USA
    Circ Res 113:571-87. 2013
    ..Herein, this review emphasizes the latest developments in genome engineering and how applications within the field are transforming our understanding of personalized medicine with an emphasis on cardiovascular diseases. ..
  7. pmc Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools
    Tyler H Koep
    Clinical and Translational Sciences, Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA
    BMC Infect Dis 13:71. 2013
    ..However, the variability and predictors of AH in the indoor school environment and the feasibility of classroom humidification to levels that could decrease viral survival have not been studied...
  8. pmc Mojo Hand, a TALEN design tool for genome editing applications
    Kevin L Neff
    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
    BMC Bioinformatics 14:1. 2013
    ....
  9. pmc Insertional mutagenesis strategies in zebrafish
    Sridhar Sivasubbu
    Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, Mall Road, Delhi 110007, India
    Genome Biol 8:S9. 2007
    ....
  10. pmc A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information
    Michelle N Knowlton
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 9:7. 2008
    ..We have created a database to facilitate web-based distribution of data from such genetic studies...
  11. doi request reprint Zebrafish genome project: bringing new biology to the vertebrate genome field
    Stephen C Ekker
    Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Rochester, Minnesota 55905, USA
    Zebrafish 4:239-51. 2007
  12. pmc Zinc finger-based knockout punches for zebrafish genes
    Stephen C Ekker
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
    Zebrafish 5:121-3. 2008
    ..This ZFN-based technology to generate targeted knockouts in this aquatic animal opens the door to an array of new biological models of human disease and genetic testing...
  13. pmc Haploinsufficiency of target of rapamycin attenuates cardiomyopathies in adult zebrafish
    Yonghe Ding
    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
    Circ Res 109:658-69. 2011
    ..We explored adult zebrafish as a novel vertebrate model for dissecting signaling pathways in cardiomyopathy...
  14. pmc Zebrafish for the study of the biological effects of nicotine
    Eric W Klee
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    Nicotine Tob Res 13:301-12. 2011
    ..When combined with a battery of molecular-genetic tools and behavioral assays, these attributes enable studies to be conducted that are not practical using traditional animal models...
  15. pmc Transposon tools hopping in vertebrates
    Jun Ni
    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
    Brief Funct Genomic Proteomic 7:444-53. 2008
    ..We have summarized the major transposon vector systems active in vertebrates, comparing and contrasting known critical biochemical and in vivo properties, for future tool design and new genetic applications...
  16. pmc Genetic determinants of hyaloid and retinal vasculature in zebrafish
    Yolanda Alvarez
    UCD School of Biomolecular, and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    BMC Dev Biol 7:114. 2007
    ..To exploit the advantages of zebrafish for genetic, developmental and pharmacological studies of retinal vasculature, we characterised the intraocular vasculature in zebrafish...
  17. doi request reprint Looking to the future
    Stephen C Ekker
    Zebrafish 5:1-2. 2008
  18. doi request reprint A facile method for somatic, lifelong manipulation of multiple genes in the mouse liver
    Kirk J Wangensteen
    The Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
    Hepatology 47:1714-24. 2008
    ..Conclusion: Coexpression with FAH is an effective technique for lifelong expression of transgenes in adult hepatocytes with applicability to a wide variety of genetic studies in the liver...
  19. doi request reprint Down on the (fish) farm
    Stephen C Ekker
    Zebrafish 5:139-40. 2008
  20. pmc p53 activation by knockdown technologies
    Mara E Robu
    University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS Genet 3:e78. 2007
    ..p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies...
  21. ncbi request reprint Messenger RNA as a source of transposase for sleeping beauty transposon-mediated correction of hereditary tyrosinemia type I
    Andrew Wilber
    The Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, USA
    Mol Ther 15:1280-7. 2007
    ....
  22. ncbi request reprint Characterization of expanded intermediate cell mass in zebrafish chordin morphant embryos
    Anskar Y H Leung
    Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
    Dev Biol 277:235-54. 2005
    ..BMP4, but not BMP2b or 7, was involved in this process. The results provide ground for further research into the mechanisms of embryonic hematopoietic cell expansion...
  23. ncbi request reprint Zebrafish as a genomics research model
    Eleanor Chen
    Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, University of Minnesota, 6 160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
    Curr Pharm Biotechnol 5:409-13. 2004
    ....
  24. ncbi request reprint Functional genomics tools for the analysis of zebrafish pigment
    Michael A Pickart
    Department of Oral Sciences and Minnesota Craniofacial Research Training Program MinnCResT, University of Minnesota, Minneapolis, MN, USA
    Pigment Cell Res 17:461-70. 2004
    ....
  25. pmc Enhancer trapping in zebrafish using the Sleeping Beauty transposon
    Darius Balciunas
    Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, University of Minnesota, 6 160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
    BMC Genomics 5:62. 2004
    ..Pioneering experiments in Drosophila have demonstrated the value of enhancer "trapping" using an invertebrate to address this functional genomics problem...
  26. ncbi request reprint Expression of VE-cadherin in zebrafish embryos: a new tool to evaluate vascular development
    Jon D Larson
    Discovery Genomics, Incorporated, Minneapolis, Minnesota, USA
    Dev Dyn 231:204-13. 2004
    ..This loss can be restored in embryos supplemented with either zebrafish or human VEGF-A, the latter indicating that genes crucial to angiogenesis have highly conserved functional activities in vertebrates...
  27. pmc Identifying secretomes in people, pufferfish and pigs
    Eric W Klee
    Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
    Nucleic Acids Res 32:1414-21. 2004
    ....
  28. ncbi request reprint Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon
    Ann E Davidson
    The Arnold and Mabel Beckman Center for Transposon Research, Institute of Human Genetics, University of Minnesota, Minneapolis, MN 55455, USA
    Dev Biol 263:191-202. 2003
    ....
  29. ncbi request reprint Syndecan-2 is essential for angiogenic sprouting during zebrafish development
    Eleanor Chen
    Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
    Blood 103:1710-9. 2004
    ..Syndecan-2 as a novel angiogenic factor is a potential candidate for use in the development of angiogenesis-based therapies...
  30. ncbi request reprint Nonconventional antisense in zebrafish for functional genomics applications
    Stephen C Ekker
    University of Minnesota, Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, Minneapolis, Minnesota 55455, USA
    Methods Cell Biol 77:121-36. 2004
  31. ncbi request reprint Sleeping Beauty transposon for efficient gene delivery
    Spencer Hermanson
    The Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
    Methods Cell Biol 77:349-62. 2004
  32. pmc Harnessing a high cargo-capacity transposon for genetic applications in vertebrates
    Darius Balciunas
    The Arnold and Mabel Beckman Center for Transposon Research, Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS Genet 2:e169. 2006
    ..Together, Tol2 provides a novel nonviral vector for the delivery of large genetic payloads for gene therapy and other transgenic applications...
  33. ncbi request reprint The transcription factors Scl and Lmo2 act together during development of the hemangioblast in zebrafish
    Lucy J Patterson
    Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headington, Oxford, United Kingdom
    Blood 109:2389-98. 2007
    ..Thus, expression of these critical regulators is dependent on continued expression of upstream regulators, which may include cell-extrinsic signals...
  34. ncbi request reprint Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development
    Sridhar Sivasubbu
    University of Minnesota, Department of Genetics, Cell Biology and Development, Arnold and Mabel Beckman Center for Transposon Research, 321 Church St SE, 6 160 Jackson Hall, Minneapolis, MN 55455, USA
    Mech Dev 123:513-29. 2006
    ..In principle this gene-breaking strategy is scalable for functional genomics screens and can be used in Sleeping Beauty transposon and other gene delivery systems in the zebrafish...
  35. pmc Functional analysis of zebrafish microfibril-associated glycoprotein-1 (Magp1) in vivo reveals roles for microfibrils in vascular development and function
    Eleanor Chen
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
    Blood 107:4364-74. 2006
    ..The essential role for MAGP1 in vascular morphogenesis and function also supports a wide range of clinical applications, including therapeutic targets in vascular disease and cardiovascular tissue engineering...
  36. ncbi request reprint Regulation of primitive hematopoiesis in zebrafish embryos by the death receptor gene
    Tommy T Kwan
    Department of Medicine, University of Hong Kong, Hong Kong
    Exp Hematol 34:27-34. 2006
    ..We investigated the regulatory mechanism of primitive hematopoiesis in zebrafish (Danio rerio) embryos with particular reference to the role of a death receptor (zDR) gene, based on a morpholino (MO) knockdown approach...
  37. pmc Wnt5 signaling in vertebrate pancreas development
    Hyon J Kim
    Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Biol 3:23. 2005
    ..Signaling by the Wnt family of secreted glycoproteins through their receptors, the frizzled (Fz) family of seven-pass transmembrane proteins, is critical for numerous cell fate and tissue polarity decisions during development...
  38. pmc Functional analysis of human hematopoietic stem cell gene expression using zebrafish
    Craig E Eckfeldt
    Division of Hematology, Oncology, and Transplantation, Department of Medicine, Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA
    PLoS Biol 3:e254. 2005
    ....
  39. ncbi request reprint A unique role for 6-O sulfation modification in zebrafish vascular development
    Eleanor Chen
    Arnold and Mabel Beckman Center for Transposon Research, Department of Genetics, Cell Biology and Development, University of Minnesota, 6 160 Jackson Hall, Minneapolis, MN 55455, USA
    Dev Biol 284:364-76. 2005
    ..Our analysis of two zebrafish HS6ST genes suggests that a wide range of biological processes may be regulated by an array of sulfation-modifying enzymes in the vertebrate genome...
  40. ncbi request reprint Lateral line, nervous system, and maternal expression of Frizzled 7a during zebrafish embryogenesis
    Saulius Sumanas
    Department of Genetics, Cell and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
    Mech Dev 115:107-11. 2002
    ..00cR, LOD score 14.1). To prove that fz7 and fz7a are indeed different genes we mapped fz7 as well using the same LN54 panel. Fz7 mapped to linkage group 9 with a LOD of 12.5, 27.31 cR from wnt 10a in between markers IBD2759 and fb50e04...

Research Grants21

  1. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2006
    ..The zebrafish offers the first opportunity for a comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  2. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2003
    ..The zebrafish offers the first comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  3. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2004
    ..The zebrafish offers the first opportunity for a comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  4. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2005
    ..5) Develop lines of zebrafish that have genes containing the transposon-traps for further mapping of genetic pathways in zebrafish. ..
  5. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2005
    ..The zebrafish offers the first opportunity for a comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  6. Intron-based Mutagenic Transposons for Zebrafish
    Stephen Ekker; Fiscal Year: 2009
    ....
  7. Intron-based Mutagenic Transposons for Zebrafish
    Stephen Ekker; Fiscal Year: 2009
    ....
  8. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2004
    ..5) Develop lines of zebrafish that have genes containing the transposon-traps for further mapping of genetic pathways in zebrafish. ..
  9. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2003
    ..The zebrafish offers the first comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  10. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2003
    ..5) Develop lines of zebrafish that have genes containing the transposon-traps for further mapping of genetic pathways in zebrafish. ..
  11. ROLE OF FRIZZLED RECEPTORS AND EMBRYOGENESIS
    Stephen Ekker; Fiscal Year: 1999
    ..Using these tools, we will identify the signaling cascades mediated by this family of receptor- like molecules in an attempt to understand in a broader context the role this new gene family plays in development. ..
  12. ROLE OF FRIZZLED RECEPTORS AND EMBRYOGENESIS
    Stephen Ekker; Fiscal Year: 2000
    ..Using these tools, we will identify the signaling cascades mediated by this family of receptor- like molecules in an attempt to understand in a broader context the role this new gene family plays in development. ..
  13. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2001
    ..5) Develop lines of zebrafish that have genes containing the transposon-traps for further mapping of genetic pathways in zebrafish. ..
  14. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2001
    ..The zebrafish offers the first comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  15. ROLE OF FRIZZLED RECEPTORS AND EMBRYOGENESIS
    Stephen Ekker; Fiscal Year: 2001
    ..Using these tools, we will identify the signaling cascades mediated by this family of receptor- like molecules in an attempt to understand in a broader context the role this new gene family plays in development. ..
  16. Systematic Vertebrate Functional Genomics
    Stephen Ekker; Fiscal Year: 2002
    ..The zebrafish offers the first comprehensive analysis of these processes using as template an entire vertebrate genome. ..
  17. Insertional Mutagenesis in Zebrafish by SB Transposons
    Stephen Ekker; Fiscal Year: 2002
    ..5) Develop lines of zebrafish that have genes containing the transposon-traps for further mapping of genetic pathways in zebrafish. ..
  18. Intron-based Mutagenic Transposons for Zebrafish
    STEPHEN CARL EKKER; Fiscal Year: 2010
    ....