Garrett A . Soukup, PhD

Department

Biomedical Sciences

Position

Professor

Books

• Catalytic RNA
  Soukup Garrett A., Preface [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Chapter Five: The Structural and Functional Uniqueness of the glmS Ribozyme [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Chapter Two: Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Cata [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Chapter One: The Hammerhead Ribozyme: Structure, Catalysis, and Gene Regulation [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Chapter Six: The Role of snRNAs in Spliceosomal Catalysis [Book Chapter] 2013
• Soukup Garrett A, Catalytic RNA 2013
• Catalytic RNA
  Soukup Garrett A, Chapter Four: HDV Family of Self-Cleaving Ribozymes [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Chapter Three: A Mechanistic Comparison of the Varkud Satellite and Hairpin Ribozymes [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Contributors [Book Chapter] 2013
• Catalytic RNA
  Soukup Garrett A, Color Plate [Book Chapter] 2013
• Non-Protein Coding RNAs
  Soukup Garrett A., Structure and mechanism of the glmS ribozyme [Book Chapter] 2009
• Nucleic acid switches and sensors
  Soukup Garrett A., Allosteric ribozymes as molecular switches and sensors [Book Chapter] 2006

Articles

• McCarthy T. J., Plog M. A., Soukup Garrett A., Jansen J. A., Floy S. A., Ligand Requirements for glmS Ribozyme Self-Cleavage (Erratum) 2006
• McCarthy Tom J., Plog Melissa A., Floy Shennen A., Jansen Joshua A., Soukup Juliane K., Soukup Garrett A., Ligand Requirements for glmS Ribozyme Self-Cleavage (DOI:10.1016/j.chembiol.2005.09.006) 2006

Publications

• Molecular Neurobiology
  Banks Samantha A., Pierce Marsha L., Soukup Garrett A., Sensational MicroRNAs
  57:1, p. 358 - 371 2020
• Scientific Reports
  Weston Michael D., Pyakurel Umesh, Tarang Shikha, Pierce Marsha L., Rocha-Sanchez Sonia M., McGee Jo Ann, Walsh Edward J., Soukup Garrett A., A mouse model of MIR-96, MIR-182 and MIR-183 misexpression implicates MIRNAs in cochlear cell fate and homeostasis
  8:1 2018
• Biophysical journal
  Strauss-Soukup Juliane, Del Vecchio Katie, McDevitt Molly, Holmes Zachariah, Stoupa Samantha, Monahan Jodi, Soukup Garrett, Ornithine Decarboxylase Antizyme Pseudoknot RNA Binding to Spermine Regulates Gene Expression
  114:3, p. 438a - 438a 2018
• Plos One
  Ebeid Michael, Beisel Kirk W., Kwan Kelvin, Soukup Garrett A., Pecka Jason L., Sripal Prashanth, Transcriptome-Wide Comparison of the Impact of Atoh1 and miR-183 Family on Pluripotent Stem Cells and Multipotent Otic Progenitor Cells
  12:7, p. E0180855 - E0180855 2017
• Molecular therapy
  Kim Ju-hyun, Soukup Garrett A., Jeong Seonyeong, Kertsburg Alexis, Lee Seong-Wook, 139. Controllable Target-Specific Transgene Induction Using an Allosteric trans-Splicing Ribozyme
  23, p. S56 - S57 2015
• PLoS One
  Zhang Qian, He David Z. Z., Liu Huizhan, Soukup Garrett A., Identifying microRNAs involved in aging of the lateral wall of the cochlear duct
  9:11, p. e112857 - e112857 2014
• Journal of Neuroscience
  Liu H., Beisel K. W., Pecka J. L., Zhang Q., Soukup G. A., He D. Z. Z., Characterization of transcriptomes of cochlear inner and outer hair cells
  34:33, p. 11085 - 11095 2014
• Journal of Neuroscience
  Liu Huizhan, Soukup Garrett A., Pecka Jason L., Zhang Qian, Beise Kirk W., He David Z. Z., Characterization of Transcriptomes of Cochlear Inner and Outer Hair Cells
  34:33, p. 11085 - 11095 2014
• ACS Chemical Biology
  Kim Juhyun, Jeong Seonyeong, Kertsburg Alexis, Soukup Garrett A., Lee Seong-Wook, Conditional and target-specific transgene induction through RNA replacement using an allosteric trans-splicing ribozyme
  9:11, p. 2491 - 2495 2014
• Soukup Garrett A., Preface. Catalytic RNA. 2013
• PloS one
  Zhang Qian, Liu Huizhan, McGee Jo Ann, Walsh Edward J., Soukup Garrett A., He David Z.Z., Identifying MicroRNAs Involved in Degeneration of the Organ of Corti during Age-Related Hearing Loss
  8:4 2013
• Nebraska Academy of Sciences, PO Box 880410 Lincoln NE 68588-0410 United States. [np]. Apr 2012
  Holmes Zachariah, Soukup Juliane, Soukup Garrett, Vecchio Katie, Monaharr Jodi, Carlson Chris, EFFECT OF MICRORNA-183 FAMILY ON EXPRESSION OF GENES THAT REINFORCE NEUROSENSORY CELL FATE IN THE INNER EAR 2012
• Indian Journal of Human Genetics
  Barritt Laura C., Miller Joseph M., Scheetz Laura R., Gardner Kelsey, Pierce Marsha L., Soukup Garrett A., Rocha-Sanchez Sonia M., Conditional deletion of the human ortholog gene Dicer1 in Pax2-Cre expression domain impairs orofacial development
  18:3, p. 310 - 319 2012
• Genesis
  Kersigo Jennifer, D'Angelo Alex, Gray Brian D., Soukup Garrett A., Fritzsch Bernd, The role of sensory organs and the forebrain for the development of the craniofacial shape as revealed by Foxg1-cre-mediated microRNA loss
  49:4, p. 326 - 341 2011
• Developmental Dynamics
  Weston Michael D., Pierce Marsha L., Soukup Garrett A., Jensen-Smith H. C., Fritzsch B., Rocha-Sanchez Sonia M., Beisel Kirk W., MicroRNA-183 family expression in hair cell development and requirement of microRNAs for hair cell maintenance and survival
  240:4, p. 808 - 819 2011
• International Journal for Parasitology
  Gong Ai-Yu, Hu Guoku, Zhou Rui, Liu Jun, Feng Yaoyu, Soukup Garrett A., Chen Xian-Ming, MicroRNA-122 controls expression of intercellular adhesion molecule-1 in epithelial cells in response to Cryptosporidium parvum infection
  41:3/4, p. 397 - 403 2011
• Chembiochem
  Klawuhn K., Soukup Garrett A., Jansen J. A., Souchek J., Analysis of Metal Ion Dependence in glmS Ribozyme Self-Cleavage and Coenzyme Binding
  11:18, p. 2567 - 2571 2010
• Genome Medicine
  Weston Michael D., Soukup Garrett A., MicroRNAs sound off
  1:6, p. 59 2009
• Brain Research
  Soukup Garrett A., Little but loud: Small RNAs have a resounding affect on ear development
  1277, p. 104 - 114 2009
• Developmental Biology
  Soukup Garrett A., Weston Michael D., Fritzsch Bernd, Pierce Marsha L., Jahan Israt, McManus Michael T., Harfe Brian D., Residual microRNA expression dictates the extent of inner ear development in conditional Dicer knockout mice
  328:2, p. 328 - 341 2009
• Journal of Immunology
  Gong Ai Yu, Chen Xian Ming, Zhou Rui, Hu Guoku, Li Xiaoqing, Splinter Patrick L., Dong Haidong, O'Hara Steven P., LaRusso Nicholas F., Soukup Garrett A., MicroRNA-513 regulates B7-H1 translation and is involved in IFN-γ-induced B7-H1 expression in cholangiocytes
  182:3, p. 1325 - 1333 2009
• Methods in Molecular Biology
  Soukup Garrett A., Identification of metabolite-riboswitch interactions using nucleotide analog interference mapping and suppression
  540, p. 193 - 206 2009
• Cell and Tissue Research
  Beisel Kirk W., Hansen Laura A., Soukup Garrett A., Fritzsch Bernd, Regenerating cochlear hair cells: quo vadis stem cell
  333:3, p. 373 - 379 2008
• Panminerva Medica
  Pauley S., Kopecky B., Beisel K., Soukup G., Fritzsch B., Stem cells and molecular strategies to restore hearing
  50:1, p. 41 - 53 2008
• Evolution & Development
  Pierce Marsha L., Gabel H. W., Weston Michael D., Fritzsch Bernd, Ruvkun G., Soukup Garrett A., MicroRNA-183 family conservation and ciliated neurosensory organ expression
  10:1, p. 106 - 113 2008
• International Journal of Developmental Biology
  Fritzsch Bernd, Beisel Kirk W., Pauley S., Soukup Garrett A., Molecular evolution of the vertebrate mechanosensory cell and ear
  51:6-7, p. 663 - 678 2007
• Brain Research
  Weston Michael D., Soukup Garrett A., Beisel Kirk W., Pierce Marsha L., Rocha-Sanchez Sonia M., MicroRNA gene expression in the mouse inner ear
  1111:1, p. 95 - 104 2006
• Nature Structural and Molecular Biology
  Jansen Joshua A., McCarthy Tom J., Soukup Garrett A., Soukup Juliane K., Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme
  13:6, p. 517 - 523 2006
• Nucleic Acids Research
  Soukup Garrett A., Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure
  34:3, p. 968 - 975 2006
• Chemistry and Biology
  McCarthy Tom J., Plog Melissa A., Floy Shennen A., Jansen Joshua A., Soukup Garrett A., Soukup Juliane K., Ligand requirements for glmS ribozyme self-cleavage
  12:11, p. 1221 - 1226 2005
• Chemistry and Biology
  Soukup Garrett A., Aptamers meet allostery
  11:8, p. 1031 - 1032 2004
• Current Opinion in Structural Biology
  Soukup Juliane K., Soukup Garrett A., Riboswitches exert genetic control through metabolite-induced conformational change
  14:3, p. 344 - 349 2004
• American Journal of PharmacoGenomics
  Steele David, Soukup Garrett A., Kertsburg Alexis, Engineered catalytic RNA and DNA
  3:2, p. 131 - 144 2003
• American Journal of PharmacoGenomics
  Steele David, Kertsburg Alexis, Soukup Garrett A., Engineered catalytic RNA and DNA : new biochemical tools for drug discovery and design
  3:2, p. 131 - 144 2003
• Nucleic Acids Research
  Kertsburg Alexis, Soukup Garrett A., A versatile communication module for controlling RNA folding and catalysis
  30:21, p. 4599 - 4606 2002
• Nucleic Acids Research
  Kertsburg Alexis, Soukup Garrett A., A versatile communication module for controlling RNA folding and catalysis
  30:21, p. 4599 - 4606 2002
• Nucleic Acids Research
  Jose Antony M., Soukup Garrett A., Breaker Ronald R., Cooperative binding of effectors by an allosteric ribozyme
  29:7, p. 1631 - 1637 2001
• RNA
  Soukup Garrett A., Breaker Ronald R., Derose Elizabeth C., Koizumi Makoto, Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes
  7:4, p. 524 - 536 2001
• Current Opinion in Structural Biology
  Soukup Garrett A., Breaker Ronald R., Allosteric nucleic acid catalysts
  10:3, p. 318 - 325 2000
• Journal of Molecular Biology
  Soukup Garrett A., Emilsson Gail A.M., Breaker Ronald R., Altering molecular recognition of RNA aptamers by allosteric selection
  298:4, p. 623 - 632 2000
• Trends in Biotechnology
  Soukup Garrett A., Breaker Ronald R., Nucleic acid molecular switches
  17:12, p. 469 - 476 1999
• RNA
  Soukup Garrett A., Breaker Ronald R., Relationship between internucleotide linkage geometry and the stability of RNA
  5:10, p. 1308 - 1325 1999
• Structure
  Soukup Garrett A., Breaker Ronald R., Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization
  7:7, p. 783 - 791 1999
• Proceedings of the National Academy of Sciences of the United States of America
  Soukup Garrett A., Breaker Ronald R., Engineering precision RNA molecular switches
  96:7, p. 3584 - 3589 1999
• Nucleic acids symposium series
  Koizumi M., Breaker R. R., Soukup G. A., Kerr J. N., Allosteric ribozymes sensitive to the second messengers cAMP and cGMP., p. 275 - 276 1999
• Nature Structural Biology
  Koizumi Makoto, Breaker Ronald R., Soukup Garrett A., Kerr Jo Nita Q., Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP
  6:11, p. 1062 - 1071 1999
• Nucleic Acids Research
  Soukup Garrett A., Maher L. James, Selection and characterization of RNAs that relieve transcriptional interference in Escherichia coli
  26:11, p. 2715 - 2722 1998
• Journal of Molecular Biology
  Soukup Garrett A., Maher L. James, Ellington Andrew D., Selection of RNAs that bind to duplex DNA at neutral pH
  259:2, p. 216 - 228 1996
• Bioconjugate Chemistry
  Soukup Garrett A., Maher L. James, Cerny Ronald L., Preparation of Oligonucleotide-Biotin Conjugates with Cleavable Linkers
  6:1, p. 135 - 138 1995

Presentations

• "Neurosensory microRNA-183 family function in mouse", Department of Biomedical Sciences, Creighton University, Omaha, NE. 2019
• "Significance of the Neurosensory MicroRNA-183 Family", Neurosensory CoBRE, External Advisory Committee Retrospective, University of Nebraska Medical Center, Omaha, NE. 2019
• "Requirement of microRNA-183 family for hair cell development and maintenance." Joint Meeting of the Midwest Auditory Research Conference and the Midwest Auditory Neuroscience Symposium, Omaha, NE. 2015
• "Requirement of microRNAs for Hair Cell Development and Maintenance in the Mouse Inner Ear.", Department of Biomedical Sciences, Creighton University, Omaha, NE. 2015
• "MicroRNAs in Hair Cell Development and Maintenance." Association for Research in Otolaryngology Midwinter Meeting, Baltimore, MD. 2015
• "Role of microRNAs in development and maintenance of hair cells in the mouse inner ear." Institute of Molecular Genetics, Prague, Czech Republic. 2015
• "Small RNAs in development and maintenance of sensory hair cells in the inner ear.", Department of Biology, University of Iowa, Iowa City, IA. 2014
• "Exploring the ups (overexpression) and downs (knockout) of microRNA-183 family in neurosensory cell development." Neurosensory CoBRE Seminar, University of Nebraska Medical Center, Omaha, NE. 2013
• "Temporal-Spatial Expression of microRNAs in Mouse Inner Ear Sensory Epithelium." Association for Research in Otolaryngology Midwinter Meeting, Baltimore, MD. 2013
• "Effects of small RNA depletion on development of mammalian inner ear and sensory hair cell differentiation and maintenance." Zing Conference on Nucleic Acids, Xcaret, Mexico. 2012
• "Hair cell microRNAs effect downregulation of factors that promote supporting cell differentiation." Association for Research in Otolaryngology Midwinter Meeting, San Diego, CA. 2012
• "MicroRNAs as effectors of sensory cell development and function.", Department of Chemistry, Creighton University, Omaha, NE. 2012
• "Effects of microRNA depletion on hair cell development and maintenance and the mechanisms of hair cell miR-183 family members." 8th Molecular Biology of Hearing and Deafness Conference, Hinxton, United Kingdom. 2011
• "Effects of microRNA depletion on development and maintenance of hair cells in mouse inner ear." Central Region IDeA Conference, Omaha, NE. 2011
• "Hair cell microRNA depletion affects hair cell maintenance and causes progressive hearing loss." Association for Research in Otolaryngology Midwinter Meeting, Baltimore, MD. 2011
• "A putative mammalian riboswitch in the spermine biosynthetic pathway." Zing Conference on Nucleic Acids, Puerto Morelos, Mexico. 2010
• "MicroRNA-associated Argonaute protein expression in the mouse inner ear." Association for Research in Otolaryngology Midwinter Meeting, Los Angeles, CA. 2010
• "MicroRNAs in the development and maintenance of inner ear sensory epithelia.", Biology of the Inner Ear: Experimental and Analytical Approaches, Marine Biological Laboratories, Woods Hole, Massachusetts, 2009 2009
• "MicroRNA expression and function in the developing mouse inner ear and maturing hair cells." 7th Molecular Biology of Hearing and Deafness Conference. Boston, MA. 2009
• "MicroRNA expression and function in development of neurosensory cells in mouse inner ear." Department of Biology, University of Nebraska at Omaha, Omaha, NE. 2008
• "Characterization of microRNA expression in Snell Dwarf mouse fibroblasts as a model of cellular longevity and stress resistance." Nebraska Research and Innovation Conference, Lincoln, NE. 2008
• "Regulation of gene expression by small RNAs.", Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE. 2008
• "Significance of microRNAs in development and maintenance of the mouse inner ear." The Mouse as an Instrument for Ear Research III, The Jackson Laboratory, Bar Harbor, ME. 2008
• "Expression and function of microRNAs in the developing mouse inner ear." Association for Research in Otolaryngology Midwinter Meeting, Phoenix, AZ. 2008
• "Expression and function of microRNAs in the developing mouse inner ear.", Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE. 2007
• "Expression and function of microRNAs in the developing mouse inner ear.", Department of Biomedical Sciences, Creighton University, Omaha, NE 2007
• Expression and function of microRNAs in the developing mouse inner ear. 6th Molecular Biology of Hearing and Deafness Conference, Hinxton, United Kingdom. 2007
• "Phylogenetic Conservation and Expression of Neurosensory MicroRNAs in Mechanosensory Organs." Association for Research in Otolaryngology (ARO) Mid-Winter Meeting, Denver, CO 2007
• "Riboswitch Regulation of Gene Expression." Nebraska INBRE Program, Omaha, NE 2006
• "Structure and Mechanism of a Metabolic Ribozyme." Federation of American Societies for Experimental Biology (FASEB) Summer Research Conference on Nucleic Acid Enzymes, Saxtons River, VT 2006
• "MicroRNA Expression in the Mouse Inner Ear." Association for Research in Otolaryngology (ARO) Mid-Winter Meeting, Baltimore, MD 2006
• "Coenzyme function of glucosamine-6-phosphate in the glmS ribozyme." Nebraska INBRE Annual Meeting, Grand Island, NE. 2005
• "MicroRNA Regulation of Gene Expression." Nebraska INBRE Program, Omaha, NE 2005
• "Coenzyme function of glucosamine-6-phosphate in the glmS ribozyme." Gordon Research Conference on Nucleic Acids, Newport, RI. 2005
• "MicroRNA expression in a developing mammalian neurosensory organ." Promoted Talk at Gordon Research Conference on Nucleic Acids, Newport, RI. 2005
• "Investigation of microRNA expression in mouse ear development." Association for Research in Otolaryngology Mid-Winter Meeting, New Orleans, LA. 2005
• "Core requirements of a natural metabolite-responsive ribozyme reveal a putative pseudoknot structure." Nebraska INBRE Annual Meeting, Grand Island, NE 2004
• "RNA catalysts in biology." Nebraska BRIN/INBRE program, Omaha, NE. 2004
• "Core requirements of a natural metabolite-reponsive ribozyme reveal a putative pseudoknot structure." RNA Conference, Madison, WI 2004
• "Development of self-cleaving and self-splicing allosteric ribozymes for regulating RNA function and gene expression." Gordon Research Conference: Nucleic Acids, Newport, RI. 2003
• "RNA interference: The sound of silence." Department of Biomedical Sciences, Creighton University, Omaha, NE. 2003
• "A versatile communication module for controlling RNA folding and catalysis", RNA Conference, Madison, WI 2002
• "RNA as target and tool for genetic regulation and biosensor development", AAAS Southwest and Rocky Mountain Regional Meeting, Omaha, NE 2001
• "Allosteric Ribozymes: Structural Dynamics and the Challenge of Selection", Archemix Corporation, Boston, Massachusetts. 2001
• "Allosteric Ribozymes: Biotechnology and Biomedicine", Veterans Affairs Medical Center, Omaha, Nebraska. 2001