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Tom Cooper Lab

Previous Lab Members

Master
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Postdoctoral Fellows / Junior Faculty

Content

Ginny Morriss, Ph.D.

Postdoctoral Fellow
In the lab: September 2012-May 2019
Funding: IRACDA Postdoctoral Fellow, NIH and Postdoctoral Fellowship, Myotonic Dystrophy Foundation.
After leaving the Cooper lab: Assistant Professor, Department of Biological Sciences, University of Mary Washington
Publications:

  • Morriss, G.R., Rajapakshe, K., Huang, S., Coarfa, C. and Cooper, T.A. (2018) Mechanisms of skeletal muscle wasting in a mouse model for myotonic dystrophy type 1. Hum. Mol. Genet. 27, 2789-2804.
  • Morriss, G.R. and Cooper, T.A. (2017) Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Human Genetics 136, 1247­1263.

Ravi Singh, Ph.D.

Postdoctoral Fellow / Instructor
In the lab: December 2009 – September 2018
Funding: Postdoctoral Fellowship, American Heart Association, Southwest Affiliate. Development Award, American Heart Association (National)
After leaving the Cooper lab: Assistant Professor, Medical College of Wisconsin, Milwaukee
Publications:

  • Singh, R. and Cooper, T.A. (2012) Pre-mRNA splicing in disease and therapeutics. Trends in Molecular Medicine 18, 472-482.
  • -Kalsotra, A., Singh, R.K., Gurha, P., Ward, A.J., Creighton, C. and Cooper, T.A. (2014) The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue dramatically altering miRNA and mRNA expression. Cell Reports 6, 336-345.
  • Singh, R.K., Zheng, X., Bland, C.S., Kalsotra, A., Scavuzzo, M.A., Curk, T., Ule, J., Li, W. and Cooper, T.A. (2014) Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol. Cell 55, 592-603.
  • Gennarino, V.A., Singh, R, White, J.J., De Maio, A., Han, K., Kim, J-Y., Jafar-Nejad, P., di Ronza, A., Kang, H., Sayegh, L.S., Cooper, T.A., Orr, H.T., Sillitoe, R.V., and Zoghbi, H.Y. (2015) Pumilio1 haploinsufficiency leads to SCA1-like neurodegeneration by increasing wild-type ataxin1 levels. Cell 160, 1087-1098. PMC4383046
  • Pedrotti, S., Giudice, J., Dagnino-Acosta, A., Knoblauch, M., Singh, R.K., Hanna, A., Mo, Q., Hicks, J., Hamilton, S.L., Cooper, T.A. (2015) The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function. Human Molecular Genetics 24, 2360-2374.
  • -Singh, R.K., Kolonin, A.M., Fiorotto, M.L. and Cooper, T.A. (2018) Rbfox splicing factors maintain skeletal muscle mass by regulating calpain3 and proteostasis. Cell Reports 24, 197-208.

Lydia Sharp, M.D.

Instructor
In the lab: July 2014 – July 2016
After leaving the Cooper lab: Assistant Professor, Department of Neurology, Baylor College of Medicine,
Publications:

  • Sharp, L., Cox, D.C. and Cooper, T.A. (2019) Endurance exercise leads to beneficial effects in a mouse model of myotonic dystrophy type 1. Muscle and Nerve 60, 779–789

Jimena Giudice, Ph.D.

Postdoctoral Fellow
In the lab: August 2011 - February 2016
Funding: Postdoctoral Fellowship, Pew Latin American Fellows Program; Postdoctoral Fellowship, American Heart Association, Southwest Affiliate
After leaving the Cooper lab: Assistant Professor Cell Biology and Physiology, University of North Carolina at Chapel Hill
Publications:

  • Giudice, J, Zheng, X., Wang, E.T., Scavuzzo, M.A., Ward, A.J., Kalsotra, A., Wei, W, Wehrens, X.H.T., Burge, C.B., Li, W. and Cooper, T.A. (2014) Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Communications 5, 3603. PMC4018662
  • Giudice, J. and Cooper, T. A. (2014) RNA binding proteins in heart development. Adv Exp Med. Biol. 825, 389-429.
  • Pedrotti, S., Giudice, J., Dagnino-Acosta, A., Knoblauch, M., Singh, R.K., Hanna, A., Mo, Q., Hicks, J., Hamilton, S.L., Cooper, T.A. (2015) The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function. Human Molecular Genetics 24, 2360-2374. PMC4380076.
  • Wang, E.T., Ward, A.J., Giudice, J., Treacy, D., Wang, T.T., Housman, D.E., Cooper, T.A., Burge, C.B. (2015) Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Research 25, 858-871. PMC4448682
  • Giudice, J., Xia, Z., Li, W. & Cooper, T.A. Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1. Sci. Rep. 6, 35550 (2016).
  • Giudice J., Loehr J.A., Rodney G.G., and Cooper T.A. (2016) Alternative splicing of four trafficking genes regulates myofiber structure and skeletal muscle physiology. Cell Reports (In press).

Simona Pedrotti, Ph.D.

Postdoctoral Fellow
In the lab: March 2011 - August 2014
After leaving the Cooper lab: Postdoctoral fellow, San Raffaele Scientific Institute, Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, Milan Italy
Publications:

  • Pedrotti, S. and Cooper, T.A. (2014) (Mis)-splicing in disease. Journal of Pathology 233, 1-3.
  • Pedrotti, S., Giudice, J., Dagnino-Acosta, A., Knoblauch, M., Singh, R.K., Hanna, A., Mo, Q., Hicks, J., Hamilton, S.L., Cooper, T.A. (2015) The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function. Human Molecular Genetics 24, 2360-2374.”

Tina Gao, Ph.D.

Postdoctoral Fellow
In the lab: September 2011 - December 2012
Funding: Postdoctoral Fellowship, Myotonic Dystrophy Foundation
After leaving the Cooper lab: Associate Professor, Neuroscience Institute, Zhejiang University School of Medicine, Hangzhou, China.
Publications:

  • Gao, Z. and Cooper, T.A. (2013) Re-expression of PKM2 in type 1 myofibers correlates with altered glucose metabolism in myotonic dystrophy. Proc Natl Acad Sci U.S.A. 110, 13570-13575.
  • Gao, Z. and Cooper, T.A. (2012) Antisense oligonucleotides: rising stars in eliminating RNA toxicity in myotonic dystrophy. Human Gene Therapy 24, 499-507.

Auinash Kalsotra, Ph.D.

Postdoctoral Fellow/Instructor
In the lab: July 2006 - November 2012
Funding: Postdoctoral Fellowship, Myotonic Dystrophy Foundation; American Heart Association Development Award
After leaving the Cooper lab: Assistant Professor, University of Illinois, Urbana-Champaign
Publications:

  • Kalsotra, A., Singh, R.K., Gurha, P., Ward, A.J., Creighton, C. and Cooper, T. A. (2014) The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue dramatically altering miRNA and mRNA expression. Cell Reports 6, 336-345.
  • Giudice, J, Zheng, X., Wang, E.T., Scavuzzo, M.A., Ward, A.J., Kalsotra, A., Wei, W, Wehrens, X.H.T., Burge, C.B., Li, W. and Cooper, T.A. (2014) Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Communications 5, 3603.
  • Singh, R.K., Zheng, X., Bland, C.S., Kalsotra, A., Scavuzzo, M.A., Curk, T., Ule, J., Li, W. and Cooper, T. A. (2014) Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol. Cell 55, 592-603.
  • Kalsotra, A. and Cooper, T. A. (2011) Functional consequences of developmentally regulated alternative splicing Nature Rev. Genet. 12, 715-729.
  • Kalsotra, A., Wang, K, Li, P.-F., and Cooper, T. A. (2010) MicroRNAs coordinate an alternative splicing network during mouse postnatal heart development. Genes Dev. 24, 653-658.
  • Kalsotra, A., Xiao, X., Ward, A.J., Castle, J.C., Johnson, J.M., Burge, C.B., and Cooper, T.A. (2008) A conserved program of regulated alternative splicing during vertebrate heart development. Proc. Nat’l Acad. Sci. 105, 20333-20338.
  • Castle, J.C., Zhang, C., Shah, J.K, Kulkarni, A.V., Kalsotra, A., Cooper, T.A ., and Johnson, J.M. (2008) Differential expression of 24,426 human alternative splicing events and predicted cis-regulation in 48 tissues and cell lines. Nat. Genet. 40, 1416-1425.

Muge Kuyumcu-Martinez, Ph.D.

Postdoctoral Fellow/Instructor
In the lab: January 2004 - October 2010
Funding: NRSA postdoctoral fellowship, NIH (NIAMS); American Heart Association Development Award
After leaving the Cooper lab: Assistant Professor, University of Texas Medical Branch, Galveston
Publications:

  • Wang, G.S., Kuyumcu-Martinez, N.M., Mathur, N., Wehrens, X.H., and Cooper, T.A. (2009) Protein kinase C inhibition ameliorates the cardiac phenotype of a mouse model for myotonic dystrophy, type 1. J. Clin. Invest. 119,3797-3806.
  • Kuyumcu-Martinez , N.M. , Wang, G.S., and Cooper, T.A. (2007) Increased steady state levels of CUG-BP1 in Myotonic Dystrophy 1 are due to PKC-mediated hyper-phosphorylation. Mol. Cell 28, 68-78.
  • Kuyumcu-Martinez NM, Cooper TA. (2006) Misregulation of alternative splicing causes pathogenesis in myotonic dystrophy. Prog Mol Subcell Biol. 44, 133-159.

Young-Hwa Goo, Ph.D.

Postdoctoral Fellow
In the lab: July 2004 - January 2009
Funding: American Heart Association, Texas Affiliate
After leaving the Cooper lab: Assistant Professor, Center for Cardiovascular Sciences, Albany Medical College, Albany, NY
Publications:

  • Grammatikakis, I. Goo, Y.H., Echeverria, G.V., and Cooper, T.A. (2011) Identification of MBNL1 and MBNL3 domains required for alternative splicing activation and repression. Nucl. Acids Res. 39, 2769-2780.
  • Goo, Y.H. and Cooper, T.A. (2009) CUGBP2 directly interacts with U2 17S snRNP components and promotes U2 snRNA binding to cardiac troponin T pre-mRNA. Nucl. Acids Res. 37, 4275-4286.

Guey-Shin Wang, Ph.D.

Postdoctoral fellow
In the lab: April 2005 - July 2009
Funding: American Heart Association, Texas Affiliate
After leaving the Cooper lab: Faculty, Cardiovascular Research Division of the Institute of Biomedical Sciences at Academia Sinica in Taipei, Taiwan
Publications:

  • Wang, G.S., Kuyumcu-Martinez, N.M., Mathur, N., Wehrens, X.H., and Cooper, T.A. (2009) Protein kinase C inhibition ameliorates the cardiac phenotype of a mouse model for myotonic dystrophy, type 1. J. Clin. Invest. 119,3797-3806.
  • Wang, G.S. and Cooper T.A. (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nature Rev. Genet. 8, 749-761.
  • Wang, G.S., Kearney, D.L., De Biasi, M., Taffet, G.E., and Cooper, T.A. (2007) Elevated CUGBP1 is an early event in an inducible heart-specific mouse model of myotonic dystrophy. J. Clin. Invest. 117, 2802-2811.

Andrea N. Ladd, Ph.D.

Postdoctoral Fellow
In the lab: June 1999 - May 2005
Funding: Postdoctoral NRSA from NIH/NIAMS; Muscular Dystrophy Association Development Grant
After leaving the Cooper lab: Associate Staff, Department of Cell Biology, Cleveland Clinic Foundation, Lerner Research Institute
Publications:

  • Ladd, A.L. Stenberg, M.G., Swanson, M.S., and Cooper, T.A. (2005) A dynamic balance between activation and repression regulates pre-mRNA alternative splicing during heart development. Dev. Dyn. 233, 783-793.
  • Ladd, A.N., Taffet, G.E., Hartley, C., Kearney, D.L. and Cooper, T.A. (2005) Cardiac-specific repression of CELF activity disrupts alternative splicing and causes cardiomyopathy. Mol. Cell. Biol. 25, 6267-6278.
  • Ladd, A.N. and Cooper, T.A. (2004) Nuclear-cytoplasmic localization of the RNA binding protein ETR-3 is controlled by multiple localization elements. J. Cell Science 117, 3519-3529.
  • Ladd, A.N., Nguyen, N.H. Malhotra, K and Cooper, T.A. (2004) CELF6, a member of the CELF family of RNA binding proteins, regulates MSE-dependent alternative splicing. J. Biol. Chem. 279,17756-17764.
  • Ladd, A.N., Cooper, T.A. (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biology 3, 8.1-8.16.
  • Ladd, A.N., Charlet-B., N., and Cooper, T.A. (2001) The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing Mol. Cell. Biol. 21,1285-1296

Jin Han, Ph.D.

Postdoctoral Fellow
In the lab: January 2002 - March 2005
Funding: American Heart Association, Western Division
After leaving the Cooper lab: Health Science Associate, MSD Korea, Subsidiary of Merck & Co., Inc., Seoul , Korea
Publications:

  • Singh, G., Charlet-B. N., Han, J., Cooper, T.A. (2004) ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo. Nucleic Acids Res. 32(3):1232-1241.
  • Han, J. and Cooper, T.A. (2005) Characterization of CELF splicing activation and repression domains in vivo. Nucl. Acids Res. 33, 2769-2780.

Sherri D. Fraser, Ph.D.

Postdoctoral Fellow
In the lab: February 1997 - January 1999
Funding: Postdoctoral Fellowship, Muscular Dystrophy Association (Canada)
After leaving the Cooper lab: Model Organism Research for Paediatric Health (MORPH) Coordinator
Publications:

  • Stickeler, E., Fraser, S.D., Honig, A., Chen, A.L., Berget, S.M. and Cooper, T.A. (2001) The RNA binding protein YB-1 recognizes A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4. EMBO J. 20, 3821-3830

Anne Philips, Ph.D.

Postdoctoral Fellow
In the lab: March 1996 - December 2000
After leaving the Cooper lab: Lexicon Genetics Inc., The Woodlands, TX
Publications:

  • Philips, A.V., Timchenko, L.T., and Cooper, T.A. (1998) Disruption of splicing regulated by a CUG-binding protein in myotonic dystrophy. Science 280, 737-741.
  • Philips, A.V. and Cooper, T.A. (2000) RNA and human disease. Cell. Mol. Life Sci. 57, 235-249.
  • Savkur, R., Philips, A.V., and Cooper, T.A. (2001) Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy. Nature Genetics 29, 40-47.
  • Charlet-B., Singh, G, N., Philips, A.V., Grice, E.A., and Cooper, T.A (2002). Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell 10, 45-53.
  • Savkur, R.S., Philips, A.V., Cooper, T.A., Dalton, J.C., Moseley, M.L., Ranum, L.P.W., Day, J.W. (2004) Insulin receptor splicing alteration in myotonic dystrophy type 2. Am. J. Hum. Genet. 74:1309-1313.

Rajesh S. Savkur, Ph.D.

Postdoctoral Fellow
In the lab: March 1999 - March 2003
After leaving the Cooper lab: Chief Scientist, Jehangir Clinical Development Center, India.”
Publications:

  • Ho, T., Savkur, R.S., Poulos, M., Mancini., M.M., Swanson, M.S., and Cooper, T.A. (2005) Co-localization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy J. Cell Science 118, 2923-2933.
  • Savkur, R.S., Philips, A.V., Cooper, T.A., Dalton, J.C., Moseley, M.L., Ranum, L.P.W., Day, J.W. (2004) Insulin receptor splicing alteration in myotonic dystrophy type 2. Am. J. Hum. Genet. 74:1309-1313.
  • Savkur, R., Philips, A.V., and Cooper, T.A. (2001) Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy. Nature Genetics 29, 40-47.
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Graduate Students

Content

Diana Cox

Ph.D. Student, Department of Biochemistry and Molecular Biology
In the lab: July 2017 August 2020
Funding: NIH NRSA F31 AR073088
After leaving the Cooper lab: Research Scientist, Eclipse Bioinnovations
Publications:

  • Sharp, L., Cox, D.C. and Cooper, T.A. (2019) Endurance exercise leads to beneficial effects in a mouse model of myotonic dystrophy type 1. Muscle and Nerve 60, 779–789.
  • Cox, D.C., Xiangnan, G., Xia, Z., and Cooper, T.A. (2020) Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting. Hum. Mol. Genet. 29, 1729-1744.
  • Cox, D.C. and Cooper, T.A. (2016) Non-canonical RAN translation of CGG repeats has canonical requirements. Mol. Cell 62, 155-156

Paul Pang

Ph.D. Student, Integrative Molecular and Biomedical Sciences
In the lab: July 2016 ­ July 2019
Funding: NIH T32 HL07676 ³Molecular Physiology of the Cardiovascular System², Department of Molecular Physiology and Biophysics. NIH NRSA F31 HL140879
After leaving the Cooper lab: Postdoctoral fellow, Stanford University, lab of Dr. Joseph Wu.
Publications:

  • Pang, P.D., Alsina, K.M., Cao, S., Koushik, A.B., Wehrens, X.H.T., Cooper, T.A. (2018) CRISPR-mediated expression of the fetal Scn5a isoform in adult mice causes conduction defects and arrhythmias. J. Amer. Heart Assoc. 19, e010393.

Kassie Manning

Ph.D. Student, Integrative Molecular and Biomedical Sciences
In the lab: July 2013 – July 2017
Funding: NSF Predoctoral Fellowship; selected for stipend support from the IMBS graduate program training grant, National Institutes of Health 5 T32 GM008231
After leaving the Cooper lab: Associate Consultant; McKinsey and Company
Publications:

  • Manning, K.S. and Cooper, T.A. (2017) The roles of RNA processing in translating genotype to phenotype. Nature Reviews Mol. Cell. Biology 18, 102–114.
  • Manning, K.S., Rao, A.N., Castro, M. and Cooper, T.A. (2017) BNANC gapmers revert splicing defects and reduce RNA foci with low toxicity in myotonic dystrophy cell models. ACS Chem Biol. 12, 2503-2509.

Amy Brinegar

Ph.D. Student, Department of Molecular and Cellular Biology
In the lab: May 2012 – July 2017
After leaving the Cooper lab: Staff Scientist, Expansion Therapeutics
Publications:

  • Brinegar, A.E. and Cooper, T.A. (2016) Roles for RNA-binding proteins in development and disease. Brain Research 1647, 1-8.
  • Brinegar, A.E., Zheng, X., Loehr J.A., Li, W., Rodney G.G., and Cooper T.A. Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. eLife 6:e27192.

Gloria Vittone Echeverria

Ph.D. Student, Interdepartmental Program in Cell and Molecular Biology
In the lab: July 2009 - October 2013
Funding: NSF Graduate Research Fellowship Award
After leaving the Cooper lab: Postdoctoral Fellow, MD Anderson Cancer Center
Publications:

  • Echeverria, G.V., and Cooper, T.A. (2014) Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron. Nucleic Acids Res. 42, 1893-1903.
  • Echeverria, G. V. and Cooper, T. A. (2012) RNA-binding proteins in microsatellite expansion disorders: mediators of RNA toxicity. Brain Research 1462, 100-111.
  • Grammatikakis I., Goo Y., Echeverria G.V., and Cooper T.A. (2011). Identification of MBNL1 and MBNL3 domains required for alternative splicing activation and repression. Nucleic Acids Research. 39(7):2769-80.

Chris Bland

Ph.D. Student, Interdepartmental Program in Cell and Molecular Biology
In the lab: July 2006 - December 2010
Funding: The Ford Foundation
After leaving the Cooper lab: Senior Medical Science Liaison, Solid Tumor Oncology at The Janssen Pharmaceutical Companies of Johnson & Johnson
Publications:

  • Meerbrey, K.L., Hu, G., Kessler, J.D., Roarty, K., Li, M.Z., Fang, J.E., Herschkowitz, J.I., Burrows, A.E., Ciccia, A., Sun, T., Schmitt, E.M., Bernardi, R.J., Fu, X., Bland, C.S., Cooper, T.A., Schiff, R., Rosen, J.M., Westbrook, T.F., Elledge, S.J. (2011) The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo. Proc Natl Acad Sci U S A. 108, 3665-3670.
  • Bland, C.S., Wang, E.T., Vu, A., David, M.P., Castle, J.C., Johnson, J.M., Burge, C.B., and Cooper, T.A. (2010) Global regulation of alternative splicing during myogenic differentiation. Nucl. Acids Res. 38, 7651-7654.
  • Bland C.S., Cooper T.A. Micromanaging alternative splicing during muscle differentiation. Dev Cell. 2007 Feb;12(2):171-172.

Yannis Grammatikakis

Ph.D. Student, Department of Molecular and Cellular Biology
In the lab: July 2007 - December 2011
After leaving the Cooper lab: Research Scientist I, Molecular Oncology Department, Moffitt Cancer Center, Tampa FL
Publications:

  • Grammatikakis, I., Goo, Y.H., Echeverria, G.V., and Cooper, T.A. (2011) Identification of MBNL1 and MBNL3 domains required for alternative splicing activation and repression. Nucl. Acids Res. 39, 2769-2780.

Amanda Ward

Ph.D. Student, Department of Molecular and Cellular Biology
In the lab: July 2008 - July 2011
Funding: NRSA postdoctoral fellowship, NIH (NIAMS)
After leaving the Cooper lab: MIT (Phil Sharp, mentor)
Publications:

  • Giudice, J, Zheng, X., Wang, E.T., Scavuzzo, M.A., Ward, A.J., Kalsotra, A., Wei, W, Wehrens, X.H.T., Burge, C.B., Li, W. and Cooper, T.A. (2014) Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Communications 5, 3603.
  • Kalsotra, A., Singh, R.K., Gurha, P., Ward, A.J., Creighton, C. and Cooper, T. A. (2014) The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue dramatically altering miRNA and mRNA expression Cell Reports 6, 336-345.
  • Orengo, J.P., Ward, A.J., and Cooper T.A. (2011) Alternative splicing misregulation secondary to skeletal muscle regeneration. Annals Neurology 69, 681-690.
  • Ward, A.J., Rimer, M., Killian, J.M., Dowling, J.J., Cooper, T.A. (2010) CUGBP1 overexpression in mouse skeletal muscle reproduces features of myotonic dystrophy type 1. Hum Mol Genet. 19, 3614-3622.
  • Ward, A.J. and Cooper, T.A. (2010) The pathobiology of alternative splicing. J. Path. 220, 152-163.
  • Kalsotra, A., Xiao, X., Ward, A.J., Castle, J.C., Johnson, J.M., Burge, C.B., and Cooper, T.A. (2008) A conserved program of regulated alternative splicing during vertebrate heart development. Proc. Nat'l Acad. Sci. 105, 20333-20338.

Johanna Lee

Ph.D. Student, Interdepartmental Program in Cell and Molecular Biology
In the lab: July 2007 - January 2012
Funding: Shanna and Andrew Linbeck Family Charitable Fund
After leaving the Cooper lab: Science Writer, Promega Corporation
Publications:

  • Lee, J.E., Bennett, C.F. and Cooper, T.A. (2012) RNase H-mediated degradation of toxic RNA in myotonic dystrophy type 1. Proc. Nat'l Acad. Sci. 109, 4221-4226.
  • Lee, J.E. and Cooper, T.A. (2009) Pathogenic Mechanisms of Myotonic Dystrophy. Biochem Soc Trans. 37, 1281-1286.

James Orengo

M.D./Ph.D. Student, Molecular and Cellular Biology
In the lab: June 2005 - December 2008
Funding: Predoctoral NRSA from NIH/NINDS
After leaving the Cooper lab: Neurology Fellow, Stanford University
Publications:

  • Orengo, J.P., Ward, A.J., and Cooper T.A. (2011)Alternative splicing misregulation secondary to skeletal muscle regeneration. Annals Neurology69, 681-690.
  • Orengo, J.P., Chambon, P., Metzger, D., Mosier, D.R., Snipes, G.J. and Cooper, T.A. (2008) Expanded CTG repeats within the DMPK 3’ UTR causes severe skeletal muscle wasting in an inducible mouse model for myotonic dystrophy. Proc. Nat’l Acad. Sci. 105, 2646-2651.
  • Orengo, J.P. and Cooper, T.A. (2007) Alternative splicing in disease, In Alternative Splicing In The Post-Genomic Era, B.R. Graveley and B. Blencowe, eds. Landes Publishing; pp. 212-223.
  • Orengo, J., Bundman, D., and Cooper, T.A. (2006) A bichromatic fluorescent reporter for cell-based screens of alternative splicing. Nucl. Acids Res. 34, e148.

Misha Koshelev

M.D./Ph.D. Student, Interdepartmental Program in Cell and Molecular Biology
In the lab: June 2006 - March 2009
Funding: Predoctoral NRSA from NIH/NINDS
After leaving the Cooper lab: Dermatology resident, Baylor College of Medicine
Publications:

  • Koshelev, M.V., Sarma, S., Wehrens, X.H.T., and Cooper, T.A. (2010) Heart-specific expression of CUGBP1 in transgenic mice reproduces electrocardiographic and functional abnormalities of DM1. Hum. Mol. Genet. 19, 1066-1075.

Margie (Parker) David

Ph.D. Student, Department of Biochemistry and Molecular Biology
In the lab: August 2004 - January 2006
After leaving the Cooper lab: medical student
Publications:

  • Bland, C.S., Wang, E.T., Vu, A., David, M.P., Castle, J.C., Johnson, J.M., Burge, C.B., and Cooper, T.A. (2010)Global regulation of alternative splicing during myogenic differentiation. Nucl. Acids Res.38, 7651-7654.

Thai Ho

M.D./Ph.D. Student, Department of Molecular and Cellular Biology
In the lab: May 2002 - April 2005
Funding: The Robert and Janice McNair Foundation
After leaving the Cooper lab: Faculty, Mayo Clinic Arizona
Publications:

  • Ho, T., Savkur, R.S., Poulos, M., Mancini., M.M., Swanson, M.S., and Cooper, T.A. (2005) Co-localization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy J. Cell Science 118, 2923-2933.
  • Ho, T., Bundman, D., Armstrong, D.L., and Cooper, T.A. (2005) Transgenic mice expressing CUG-BP1 reproduce the myotonic dystrophy pattern of splicing. Hum. Mol. Genet. 14, 1539-1547.
  • Ho T., Charlet N-B, Poulos MG, Singh GS, Swanson MS, Cooper TA. (2004) Muscleblind proteins regulate alternative splicing. EMBO J. 23, 3103-3112

Nicolas Charlet Berguerand

International Graduate Student
In the lab: November 1999 - July 2002
After leaving the Cooper lab: Team Leader, IGBMC, Strasbourg, France
Publications:

  • Ladd, A.N., Charlet-B., N., and Cooper, T.A. (2001) The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing Mol. Cell. Biol. 21,1285-1296.
  • Ryan, K.J., Charlet-B., N., and Cooper, T.A. (2000) Binding of PurH to a muscle-specific splicing enhancer correlates with exon inclusion in vivo. J. Biol. Chem. 275, 20618-20626.
  • Charlet-B., N., Singh, G, N., Logan, P.E., and Cooper, T.A. (2002) Dynamic antagonism between CELF proteins and PTB regulate splicing of a muscle-specific exon in both muscle and nonmuscle cells. Mol. Cell 9, 649-658.
  • Charlet-B., N., Singh, G, N., Philips, A.V., Grice, E.A., and Cooper, T.A (2002). Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell 10, 45-53.
  • Singh, G., Charlet-B., N., N., Han, J., and Cooper, T.A. (2004) ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo. Nucl. Acids Res. 32, 1232-1241.
  • Ho, T.,Charlet-B., N., Poulos, M., Singh, G., Swanson, M.S., and Cooper, T.A. (2004) Muscleblind proteins regulate alternative splicing. EMBO J. 23, 3103-3112.

Kathy Ryan

Graduate Student
In the lab: July 1993 - December 1998
After leaving the Cooper lab: Assistant Professor, Department of Biology, Texas A&M University.
Publications:

  • Ryan, K.J., Charlet-B., N., and Cooper, T.A. (2000) Binding of PurH to a muscle-specific splicing enhancer correlates with exon inclusion in vivo. J. Biol. Chem. 275, 20618-20626.
  • Ryan, K.J. and Cooper, T.A. (1996) Muscle-specific splicing enhancers regulate inclusion of the cardiac troponin T alternative exon in embryonic skeletal muscle. Mol. Cell. Biol. 16, 4014-4023

Lydia Coulter

Graduate Student
In the lab: May 1995 - December 1996
After leaving the Cooper lab: Department of Biostatistics, Emory University
Publications:

  • Coulter, L., Landree, M., and Cooper, T.A. (1997) Identification of a new class of exonic splicing enhancers by in vivo selection. Mol. Cell. Biol. 17, 2143-2150.

Penny Logan

Graduate Student
In the lab: July 1997 - December 1999
After leaving the Cooper lab: Lexicon Genetics Inc., The Woodlands, Texas
Publications:

  • Charlet-B., Singh, G, N., Logan, P.E., and Cooper, T.A. (2002) Dynamic antagonism between CELF proteins and PTB regulate splicing of a muscle-specific exon in both muscle and nonmuscle cells. Mol. Cell 9, 649-658
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Research Staff

Content

Jennifer Graham
Research Assistant I
In the lab: June 2017 - May 2019
After leaving the Cooper lab: Pathologists¹ Assistant Masters program, Quinnipiac University

Amrita Koushik, Ph.D.
Staff Scientist
In the lab: January 2015 – July 2017
After leaving the Cooper lab: MBA program at Jones Graduate School of Business, Rice University

Roberta Palau
Research Technician III
In the lab: March 2016 – June 2017
After leaving the Cooper lab: Medical Student, David Geffen School of Medicine at UCLA

Adrienne Joseph
Research Technician III
In the lab: August 2016 – June 2017
After leaving the Cooper lab: Medical Student, UT Southwestern Medical School

Arseniy Kolonin
Research Assistant I
In the lab: May 2014 – December 2016, March-June 2017
After leaving the Cooper lab: Masters program, Texas State University

Anha Pham
Research Technician II,
In the lab: August 2015-May 2016.
After leaving the Cooper lab: Forensics Analyst, Houston Police Department

Chaitali Chakraborty
Research Assistant II
In the lab: July 2009 - August 2014

Marissa (Ruddy) Scavuzzo
Research Technician II
In the lab: January 2012-June 2013
After leaving the Cooper lab: Graduate student, Baylor College of Medicine

Donnie Bundman
Research Associate
In the lab: March 2002-September 2013

Joey Cienfuegos
Research Technician II
713-798-5021
In the lab: March 2009-August 2010

Anthony Vu
Research Assistant
In the lab: August 2007 - May 2009
After leaving the Cooper lab: Dental student, NYU

Duyen Tran
Research Assistant
In the lab: August 2004- February 2007

Gopal Singh, Ph.D.
Research Associate
In the lab: July 1999 - May 2006

Kusal Mihindukulasuriya
Nicole Nguyen
Margo Thomas
Keynae Agnew
Claire Lo
Linda Li
Jackie Ramchatesingh
Angie Lee
Ruishu Xu