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Molecular Cell Biology Alumni |
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Molecular Cell Biology Alumni |
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Molecular Cell Biology |
Roman Alpatov, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Biological Sciences, University of Michigan, Dearborn | |
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Enrolled |
August 2000 - December 2005 |
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Dissertation Title |
Pinin at the Interface of Gene Regulatory Machines | |
| Professional Positions | ||
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Publications |
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| Joo JH, Alpatov R, Munguba GC, Jackson MR, Hunt ME, Sugrue SP. Reduction of Pnn by RNAi induces loss of cell-cell adhesion between human corneal epithelial cells. Mol Vis. 2005 Feb 18;11:133-42. abstract | ||
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Alpatov R, Munguba GC, Caton P, Joo JH, Shi Y, Shi Y, Hunt ME, Sugrue SP. Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene. Mol Cell Biol. 2004 Dec;24(23):10223-35. abstract |
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Zimowska G, Shi J, Munguba G, Jackson MR, Alpatov R, Simmons MN, Shi Y, Sugrue SP. Pinin/DRS/memA interacts with SRp75, SRm300 and SRrp130 in corneal epithelial cells. Invest Ophthalmol Vis Sci. 2003 Nov;44(11):4715-23. abstract |
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Darwin N. Ang, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Florida State University | |
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Enrolled |
August 1996 - August 1999 |
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Dissertation Title |
An alternative to the origins of life theories: Functionally endowed DNA molecules capable of improved catalysis |
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| Professional Positions | ||
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Publications |
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Battersby TR, Ang DN, Burgstaller P, Jurczyk SC, Bowser MT, Buchanan DD, Kennedy RT, Benner SA. Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog. J Am Chem Soc. 1999;121(42):9781-9. abstract |
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Abstracts Presented at Meetings Through Graduate Studies |
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Ang, D. N., Suh, B., Westermann-Clark, E., Battersby, T., Benner, S. A. An alternative to the origins of life theories: Amino acid-like DNA molecules with catalytic activity. FASEB J. 13:, A1415 Suppl. S (1999). |
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Jason Butler, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Zoology, University of Florida | |
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Enrolled |
August 2002 |
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Dissertation Title |
The Role of Stromal Cell-Derived Factor 1 in Diabetic Retinopathy | |
| Professional Positions | Postdoctoral Fellow, Weill Medical College at Cornell University, Dept of Genetic Medicine, August 2006 | |
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Publications |
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Butler JM, Guthrie SM, Koc M, Afzal A, Caballero S, Brooks HL, Mames RN, Segal MS, Grant MB, Scott EW. SDF-1 is both necessary and sufficient to promote proliferative retinopathy. J Clin Invest. 2005 Jan;115(1):86-93. abstract |
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Sengupta N, Caballero S, Mames RN, Butler JM, Scott EW, Grant MB. The role of adult bone marrow-derived stem cells in choroidal neovascularization. Invest Ophthalmol Vis Sci. 2003 Nov;44(11):4908-13. abstract |
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Abstracts Presented at Meetings Through Graduate Studies |
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| Keystone Symposia (From Stem Cells to Therapy) Keystone, CO, March 2003 | ||
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Honors & Awards |
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Ruth L. Kirschstein National Research Service Award Fellowship for Minority Students (F31) 2004-2007 |
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Jie Deng, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | ||
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Enrolled |
August 1999 - April 2005 |
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| Dissertation Title | Neurogenesis of Adult Stem Cells from the Liver and Bone Marrow | |
| Professional Positions | Postdoctoral Fellow, UF, Department of Anatomy and Cell Biology | |
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Publications |
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Laywell ED, Kearns SM, Zheng T, Chen KA, Deng J, Chen HX, Roper SN, Steindler DA. Neuron-to-astrocyte transition: Phenotypic fluidity and the formation of hybrid asterons in differentiating neurospheres. J Comp Neurol. 2005 Dec 19;493(3):321-33. abstract |
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Deng J, Steindler DA, Laywell ED, Petersen BE. Neural trans-differentiation potential of hepatic oval cells in the neonatal mouse brain. Exp Neurol. 2003 Aug;182(2):373-82. abstract |
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Petersen BE, Grossbard B, Hatch H, Pi L, Deng J, Scott EW. Mouse A6-positive hepatic oval cells also express several hematopoietic stem cell markers. Hepatology. 2003 Mar;37(3):632-40. abstract |
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Alaric Falcon, Ph.D. |
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Advanced Concentration |
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Mentor |
John P. Aris, Ph.D. | |
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Department |
Anatomy & Cell Biology | |
| Previous Education | B.S., Biochemistry, University of Florida | |
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Enrolled |
August 1999 - May 2004 | |
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Dissertation Title |
Building
an episomal model of aging in Saccharomyces cerevisiae |
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| Professional Positions | ||
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Publications |
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| Falcon AA, Aris JP. Plasmid accumulation reduces life span in Saccharomyces cerevisiae. J Biol Chem. 2003 Oct 24;278(43):41607-17. Epub 2003 Aug 06. abstract | ||
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Abstracts Presented at Meetings |
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Cold Springs Harbor Laboratory, Molecular Biology of Aging, "Plasmids reduce yeast life spans", 2002 |
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Honors & Awards |
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Ellison Medical Foundation, Sponsorship to Molecular Biology of Aging Course, Marine Biological Laboratory, Woods Hole, MA, 2001 |
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Eillison Medical Foundation, New Opportunities Award, 2002 |
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Eric A. Gaucher, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., University of Missouri, Columbia, MO | |
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Enrolled |
August 1997 - May 2002 |
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Dissertation Title |
Higher order models and comparative evolutionary analyses for detecting functional divergence among genomic sequences |
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| Professional Positions | Postdoctoral Associate, Universityof Florida | |
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Publications |
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Gaucher EA, Thomson JM, Burgan MF, Benner SA. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature. 2003 Sep 18;425(6955):285-8. abstract |
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Gaucher EA, Miyamoto MM, Benner SA. Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics. 2003 Apr;163(4):1549-53. abstract |
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Gaucher EA, Gu X, Miyamoto MM, Benner SA. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci. 2002 Jun;27(6):315-21. abstract |
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Benner SA, Caraco MD, Thomson JM, Gaucher EA. Planetary biology--paleontological, geological, and molecular histories of life. Science. 2002 May 3;296(5569):864-8. abstract |
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Gaucher EA, Das UK, Miyamoto MM, Benner SA. The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Mol Biol Evol. 2002 Apr;19(4):569-73. abstract |
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Benner SA, Gaucher EA. Evolution, language and analogy in functional genomics. Trends Genet. 2001 Jul;17(7):414-8. abstract |
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Gaucher EA, Miyamoto MM, Benner SA. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):548-52. abstract |
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Steven Guthrie, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Biology/Philosophy, Albright College | |
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Enrolled |
August 2001 - April 2005 |
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| Dissertation Title | Hemangioblasts: From Hematopoietic Stem Cells to Endothelial Progenitor Cells and their Effector Molecules | |
| Professional Positions | ||
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Publications |
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Butler JM, Guthrie SM, Koc M, Afzal A, Caballero S, Brooks HL, Mames RN, Segal MS, Grant MB, Scott EW. SDF-1 is both necessary and sufficient to promote proliferative retinopathy. J Clin Invest. 2005 Jan;115(1):86-93. abstract |
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Guthrie SM, Curtis LM, Mames RN, Simon GG, Grant MB, Scott EW. The nitric oxide pathway modulates hemangioblast activity of adult hematopoietic stem cells. Blood. 2005 Mar 1;105(5):1916-22. abstract |
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Guthrie SM, Caballero S, Mames RN, Grant MB, Scott EW. Analysis of the vascular potential of hematopoietic stem cells. Methods Mol Med. 2005;105:369-80. abstract |
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Fisher RC, Slayton WB, Chien C, Guthrie SM, Bray C, Scott EW. PU.1 supports proliferation of immature erythroid progenitors. Leuk Res. 2004 Jan;28(1):83-9. abstract |
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Cogle CR, Wainman DA, Jorgensen ML, Guthrie SM, Mames RN, Scott EW. Adult human hematopoietic cells provide functional hemangioblast activity. Blood. 2004 Jan 1;103(1):133-5. abstract |
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Cogle CR, Guthrie SM, Sanders RC, Allen WL, Scott EW, Petersen BE. An overview of stem cell research and regulatory issues. Mayo Clin Proc. 2003 Aug;78(8):993-1003. abstract |
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Grant MB, Caballero S, Brown GA, Guthrie SM, Mames RN, Vaught T, Scott EW. The contribution of adult hematopoietic stem cells to retinal neovascularization. Adv Exp Med Biol. 2003;522:37-45. abstract |
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Grant MB, May WS, Caballero S, Brown GA, Guthrie SM, Mames RN, Byrne BJ, Vaught T, Spoerri PE, Peck AB, Scott EW. Adult hematopoietic stem cells provide functional hemangioblast activity during retinal neovascularization. Nat Med. 2002 Jun;8(6):607-12. abstract |
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Cynthia L. Hendrickson, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | ||
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Enrolled |
August 1998 - December 2003 |
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Dissertation Title |
DNA polymerase incorporation of an expanded genetic alphabet : an analysis of substrate recognition with evolutionary implication |
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| Professional Positions | Postdoctoral Associate, National Institutes of Health | |
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Publications |
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Hendrickson CL, Devine KG, Benner SA. Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine. Nucleic Acids Res. 2004 Apr 23;32(7):2241-50. abstract |
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Roychowdhury A, Illangkoon H, Hendrickson CL, Benner SA. 2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase. Org Lett. 2004 Feb 19;6(4):489-92. abstract |
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Irene Hurst, D.D.S., Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | D.D.S., Science Education/Biology, University of South Florida | |
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Enrolled |
August 2001 - August 2006 |
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Dissertation Title |
The Actin-Related Protein 2/3 Complex and Osteoclast Bone Resorption | |
| Professional Positions | ||
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Publications |
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Holliday LS, Bubb MR, Jiang J, Hurst IR, Zuo J. Interactions between vacuolar H+-ATPases and microfilaments in osteoclasts. J Bioenerg Biomembr. 2005 Dec;37(6):419-23. abstract |
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Hurst IR, Zuo J, Jiang J, Holliday LS. Actin-related protein 2/3 complex is required for actin ring formation. J Bone Miner Res. 2004 Mar;19(3):499-506. Epub 2003 Dec 22. abstract |
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Jiang J, Zuo J, Hurst IR, Holliday LS. The synergistic effect of peptidoglycan and lipopolysaccaride on osteoclast formation. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2003 Dec;96(6):738-43. abstract |
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Chen SH, Bubb MR, Yarmola EG, Zuo J, Jiang J, Lee BS, Lu M, Gluck SL, Hurst IR, Holliday LS. Vacuolar H(super)+-ATPase binding to microfilaments: regulation in response to phosphatidylinositol 3-kinase activity and detailed characterization of the Aactin binding site in subunit B. J Biol Chem. 2003 Dec 8 [Epub ahead of print] abstract |
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Abstracts Presented at Meetings Through Graduate Studies |
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Honors & Awards |
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JeongHoon Joo, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Biology, Dongguk University (S. Korea) | |
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Enrolled |
August 2001 - August 2006 |
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Dissertation Title |
Functional analysis of pinin by targeted disruption in cultured cells and mice | |
| Professional Positions | ||
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Publications |
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Joo JH, Alpatov R, Munguba GC, Jackson MR, Hunt ME, Sugrue SP. Reduction of Pnn by RNAi induces loss of cell-cell adhesion between human corneal epithelial cells. Mol Vis. 2005 Feb 18;11:133-42. abstract |
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Alpatov R, Munguba GC, Caton P, Joo JH, Shi Y, Shi Y, Hunt ME, Sugrue SP. Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene. Mol Cell Biol. 2004 Dec;24(23):10223-35. abstract |
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Abstracts Presented at Meetings Through Graduate Studies |
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Honors & Awards |
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Youngmi Jung, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | ||
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Enrolled |
August 2002 - August 2006 |
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Dissertation Title |
Role of somatostatin in the migration of hepatic oval cells in the injured liver model of rats |
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| Professional Positions | ||
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Publications |
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Jung Y, Oh SH, Zheng D, Shupe TD, Witek RP, Petersen BE. A potential role of somatostatin and its receptor SSTR4 in the migration of hepatic oval cells. Lab Invest. 2006 Mar 13; [Epub ahead of print] abstract |
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Sean Kearns, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Interdisciplinary Studies, University of Florida | |
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Enrolled |
August 2001 - August 2006 |
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Dissertation Title |
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| Professional Positions | ||
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Publications |
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Laywell ED, Kearns SM, Zheng T, Chen KA, Deng J, Chen HX, Roper SN, Steindler DA. Neuron-to-astrocyte transition: Phenotypic fluidity and the formation of hybrid asterons in differentiating neurospheres. J Comp Neurol. 2005 Dec 19;493(3):321-33. abstract |
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Kearns SM, Laywell ED, Kukekov VK, Steindler DA. Extracellular matrix effects on neurosphere cell motility. Exp Neurol. 2003 Jul;182(1):240-4. abstract |
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Honors & Awards |
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First Place, Molecular Cell Biology Advanced Concentration, Medical Guild Graduate Student Research Concentration, 2005 |
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Bronze Medal Finalist, Medical Guild Graduate Student Research Competition, 2005 |
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Liya Pi, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | M.S., Genetics, Lanzhou University (P.R. China) | |
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Enrolled |
August 2000 - April 2005 |
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| Dissertation Title | The Role of Connective Tissue Growth Factor (CTGF) in Oval Cell Aided Liver Regeneration in the 2-AAF/PHX Model | |
| Professional Positions | ||
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Publications |
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Pi LY, Oh SH, Shupe T, Petersen BE Connective tissue growth factor is expressed in Thy1+ oval cells and is required for liver regeneration following 2-acetylaminofluorene / partial hepatectomy in Rats. In preparation. |
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Petersen BE, Grossbard B, Hatch H, Pi L, Deng J, Scott EW. Mouse A6-positive hepatic oval cells also express several hematopoietic stem cell markers. Hepatology. 2003 Mar;37(3):632-40. abstract |
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| Honors & Awards | ||
| Excellent International Student Award 2004 | ||
Nemanja Rodic, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Molecular Biology, University of Central Florida | |
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Enrolled |
August 2001 - August 2005 |
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Dissertation Title |
Identification and Initial Characterization of DNA Methylation Controlled Genes in Embryonic Stem Cells (PDF) |
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| Professional Positions | Medical Student, College of Medicine, UF | |
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Publications |
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Rodic N, Oka M, Hamazaki T, Murawski MR, Jorgensen M, Maatouk DM, Resnick JL, Li E, Terada DNA methylation is required for silencing of Ant4, an adenine nucleotide translocase selectively expressed in mouse embryonic stem cells and germ cells. Stem Cells. 2005 Jul 28; [Epub ahead of print] abstract |
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Oka M, Meacham AM, Hamazaki T, Rodic N, Chang LJ, Terada N. De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2'-deoxycytidine. Oncogene. 2005 Apr 28;24(19):3091-9. abstract |
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Rodic N, Rutenberg MS, Terada N. Cell fusion and reprogramming: resolving our transdifferences. Trends Mol Med. 2004 Mar;10(3):93-6. Review. abstract |
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Yu-Jiang Shi, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | ||
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Enrolled |
August 1996 - May 2000 |
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Dissertation Title |
The biological function of Pinin/DRS/memA and its involvement in tumorigenesis |
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| Professional Positions | Postdoctoral Associate, Department of Pathology, Harvard Medical School, Boston, MA | |
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Publications |
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Zimowska G, Shi J, Munguba G, Jackson MR, Alpatov R, Simmons MN, Shi Y, Sugrue SP. Pinin/DRS/memA interacts with SRp75, SRm300 and SRrp130 in corneal epithelial cells. Invest Ophthalmol Vis Sci. 2003 Nov;44(11):4715-23. abstract |
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Shi Y, Simmons MN, Seki T, Oh SP, Sugrue SP. Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1). Oncogene. 2001 Jul 5;20(30):4007-18. abstract |
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Shi Y, Tabesh M, Sugrue SP. Role of cell adhesion-associated protein, pinin (DRS/memA), in corneal epithelial migration. Invest Ophthalmol Vis Sci. 2000 May;41(6):1337-45. abstract |
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Shi Y, Ouyang P, Sugrue SP. Characterization of the gene encoding pinin/DRS/memA and evidence for its potential tumor suppressor function. Oncogene. 2000 Jan 13;19(2):289-97. abstract |
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Matthew N. Simmons, Ph.D., M.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Stanford University | |
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Enrolled |
August 1997 - May 2001 (Ph.D.) |
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Dissertation Title |
Pnn nuclear and centrosomal localization and implications in the regulation of epitheliogenesis |
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| Professional Positions | Medical Student, Stanford University School of Medicine | |
| Resident, Dept. Urology, Cleveland Clinic Foundation, Cleveland, OH | ||
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Publications |
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Zimowska G, Shi J, Munguba G, Jackson MR, Alpatov R, Simmons MN, Shi Y, Sugrue SP. Pinin/DRS/memA interacts with SRp75, SRm300 and SRrp130 in corneal epithelial cells. Invest Ophthalmol Vis Sci. 2003 Nov;44(11):4715-23. abstract |
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Shi Y, Simmons MN, Seki T, Oh SP, Sugrue SP. Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1). Oncogene. 2001 Jul 5;20(30):4007-18. abstract |
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John M. Thomson, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., University of Georgia | |
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Enrolled |
August 1997 - December 2002 |
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Dissertation Title |
Interpretive proteomics: experimental paleogenetics as a tool to analyze function and discover pathways in yeast |
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| Professional Positions | Postdoctoral Associate, University of North Carolina (Chapel Hill) | |
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Publications |
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Gaucher EA, Thomson JM, Burgan MF, Benner SA. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature. 2003 Sep 18;425(6955):285-8. abstract |
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Benner SA, Caraco MD, Thomson JM, Gaucher EA. Planetary biology--paleontological, geological, and molecular histories of life. Science. 2002 May 3;296(5569):864-8. abstract |
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Honors & Awards |
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Medical Guild Award for Research Excellence, UF College of Medicine, 2002 |
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Rafel Witek, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | B.S., Microbiology, University of Georgia | |
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Enrolled |
August 2001 - April 2005 |
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| Dissertation Title | Novel application of gene therapy and somatic stem cells in the treatment of metabolic liver disorders | |
| Professional Positions | Postdoctoral Fellow, Department of Pathology, Immunology & Laboratory Medicine, UF | |
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Publications |
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Jung Y, Oh SH, Zheng D, Shupe TD, Witek RP, Petersen BE. A potential role of somatostatin and its receptor SSTR4 in the migration of hepatic oval cells. Lab Invest. 2006 May;86(5):477-89. abstract |
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Witek RP, Fisher SH, Petersen BE. Monocrotaline, an alternative to retrorsine-based hepatocyte transplantation in rodents. Cell Transplant. 2005;14(1):41-7. abstract |
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Song S, Witek RP, Lu Y, Choi YK, Zheng D, Jorgensen M, Li C, Flotte TR, Petersen BE. Ex vivo transduced liver progenitor cells as a platform for gene therapy in mice. Hepatology. 2004 Oct;40(4):918-24. abstract |
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Donghang Zheng, Ph.D. |
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Advanced Concentration |
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Mentor |
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Department |
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| Previous Education | M.S., Genetics, Shanghai Medical University (P.R. China) | |
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Enrolled |
August 2001 - April 2005 |
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| Dissertation Title | The involvement of SDF-1 in stem cell-aided liver regeneration | |
| Professional Positions | Postdoctoral Fellow, UF Dept of Pharmacology & Therapeutics, May 2006 | |
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Publications |
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Jung Y, Oh SH, Zheng D, Shupe TD, Witek RP, Petersen BE. A potential role of somatostatin and its receptor SSTR4 in the migration of hepatic oval cells. Lab Invest. 2006 Mar 13; [Epub ahead of print] abstract |
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Song S, Witek RP, Lu Y, Choi YK, Zheng D, Jorgensen M, Li C, Flotte TR, Petersen BE. Ex vivo transduced liver progenitor cells as a platform for gene therapy in mice. Hepatology. 2004 Oct;40(4):918-24. abstract |
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Hatch HM, Zheng D, Jorgensen ML, Petersen BE. SDF-1alpha/CXCR4: a mechanism for hepatic oval cell activation and bone marrow stem cell recruitment to the injured liver of rats. Cloning Stem Cells. 2002;4(4):339-51. abstract |
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last revised 9/14/06 wtm
