Scott Kennedy
| Title | Research Assistant Professor |
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| Institution | School of Medicine and Dentistry |
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| Department | Biochemistry and Biophysics |
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| Address | University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester NY 14642
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Kennedy SD, Kierzek R, Turner DH. Novel conformation of an RNA structural switch. Biochemistry. 2012 Nov 20; 51(46):9257-9.
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Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. RNA. 2011 Sep; 17(9):1664-77.
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Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised ? torsions. J Phys Chem B. 2011 Jul 28; 115(29):9261-70.
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Mutisya D, Selvam C, Kennedy SD, Rozners E. Synthesis and properties of triazole-linked RNA. Bioorg Med Chem Lett. 2011 Jun 1; 21(11):3420-2.
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Selvam C, Thomas S, Abbott J, Kennedy SD, Rozners E. Amides as excellent mimics of phosphate linkages in RNA. Angew Chem Int Ed Engl. 2011 Feb 25; 50(9):2068-70.
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Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD. RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA. Biochemistry. 2010 Jul 13; 49(27):5817-27.
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Petri ET, Celic A, Kennedy SD, Ehrlich BE, Boggon TJ, Hodsdon ME. Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity. Proc Natl Acad Sci U S A. 2010 May 18; 107(20):9176-81.
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Chen G, Kennedy SD, Turner DH. A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops. Biochemistry. 2009 Jun 23; 48(24):5738-52.
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McNanley AR, Johnson AM, Flynn MK, Wood RW, Kennedy SD, Reeder JE. Inherited pelvic organ prolapse in the mouse: preliminary evaluation of a new murine model. Int Urogynecol J Pelvic Floor Dysfunct. 2009 Jan; 20(1):19-25.
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Hart JM, Kennedy SD, Mathews DH, Turner DH. NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc. 2008 Aug 6; 130(31):10233-9.
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Gu T, Kennedy SD, Chen Z, Schneider KA, Zhong J. Functional MRI at 3T using intermolecular double-quantum coherence (iDQC) with spin-echo (SE) acquisitions. MAGMA. 2007 Dec; 20(5-6):255-64.
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Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH. NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA. Biochemistry. 2007 Nov 6; 46(44):12665-78.
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Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD. Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs. J Phys Chem B. 2007 Jun 21; 111(24):6718-27.
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Tolbert BS, Kennedy SD, Schroeder SJ, Krugh TR, Turner DH. NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs. Biochemistry. 2007 Feb 13; 46(6):1511-22.
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Wong CK, Kennedy SD, Kwok E, Zhong J. Theoretical studies of the effect of the dipolar field in multiple spin-echo sequences with refocusing pulses of finite duration. J Magn Reson. 2007 Apr; 185(2):247-58.
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Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry. 2006 Oct 3; 45(39):11776-89.
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Zheng B, Chen Z, Kennedy SD, Zhong J. iDQC MRI weighted by longitudinal relaxation in the rotating frame. Magn Reson Med. 2006 Aug; 56(2):327-33.
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Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH. An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA. Biochemistry. 2006 Jun 6; 45(22):6889-903.
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Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH. Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry. 2005 Mar 1; 44(8):2845-56.
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Znosko BM, Kennedy SD, Wille PC, Krugh TR, Turner DH. Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns. Biochemistry. 2004 Dec 21; 43(50):15822-37.
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Xu L, Appell M, Kennedy S, Momany FA, Price NP. Conformational analysis of chirally deuterated tunicamycin as an active site probe of UDP-N-acetylhexosamine:polyprenol-P N-acetylhexosamine-1-P translocases. Biochemistry. 2004 Oct 26; 43(42):13248-55.
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Kennedy SD, Zhong J. Diffusion measurements free of motion artifacts using intermolecular dipole-dipole interactions. Magn Reson Med. 2004 Jul; 52(1):1-6.
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Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH. Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Biochemistry. 2003 Dec 9; 42(48):14184-96.
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Zhong J, Chen Z, Kwok WE, Kennedy S, You Z. Optimization of blood oxygenation level-dependent sensitivity in magnetic resonance imaging using intermolecular double-quantum coherence. J Magn Reson Imaging. 2002 Dec; 16(6):733-40.
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Yan S, Kennedy SD, Koide S. Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. J Mol Biol. 2002 Oct 18; 323(2):363-75.
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Chen Z, Kennedy SD, Zhong J. Quantitation of intermolecular dipolar effects in NMR spectroscopy and high order MSE MR imaging. MAGMA. 2000 Dec; 11(3):122-8.
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Bahar S, Gunter CT, Wu C, Kennedy SD, Knauf PA. Persistence of external chloride and DIDS binding after chemical modification of Glu-681 in human band 3. Am J Physiol. 1999 Oct; 277(4 Pt 1):C791-9.
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Okamoto N, Kennedy SD, Barron-Casella EA, Casella JF, Inoko H, Kickler TS. Identification of a human heavy chain antibody fragment directed against human platelet alloantigen 1a by phage display library. Tissue Antigens. 1998 Feb; 51(2):156-63.
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Jackson JB, Piwowar EM, Parsons J, Kataaha P, Bihibwa G, Onecan J, Kabengera S, Kennedy SD, Butcher A. Detection of human immunodeficiency virus type 1 (HIV-1) DNA and RNA sequences in HIV-1 antibody-positive blood donors in Uganda by the Roche AMPLICOR assay. J Clin Microbiol. 1997 Apr; 35(4):873-6.
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Kennedy SD, Igarashi Y, Kickler TS. Measurement of in vitro P-selectin expression by flow cytometry. Am J Clin Pathol. 1997 Jan; 107(1):99-104.
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Liu D, Kennedy SD, Knauf PA. Source of transport site asymmetry in the band 3 anion exchange protein determined by NMR measurements of external Cl- affinity. Biochemistry. 1996 Dec 3; 35(48):15228-35.
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Lumadue JA, Lanzkron SM, Kennedy SD, Kuhl DT, Kickler TS. Cytokine induction of platelet activation. Am J Clin Pathol. 1996 Dec; 106(6):795-8.
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Malek A, Miller RK, Mattison DR, Kennedy S, Panigel M, di Sant'Agnese PA, Jessee L. Energy charge monitoring via magnetic resonance spectroscopy 31P in the perfused human placenta: effects of cadmium, dinitrophenol and iodoacetate. Placenta. 1996 Sep; 17(7):495-506.
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King KE, Kao KJ, Bray PF, Casella JF, Blakemore K, Callan NA, Kennedy SD, Kickler TS. The role of HLA antibodies in neonatal thrombocytopenia: a prospective study. Tissue Antigens. 1996 Mar; 47(3):206-11.
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Liu D, Knauf PA, Kennedy SD. Detection of Cl- binding to band 3 by double-quantum-filtered 35Cl nuclear magnetic resonance. Biophys J. 1996 Feb; 70(2):715-22.
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Kim HO, Kennedy SD, Kickler TS. Studies using immobilized platelet glycoproteins for detection of platelet alloantibodies. Am J Clin Pathol. 1995 Sep; 104(3):258-63.
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Liu D, Kennedy SD, Knauf PA. 35Cl nuclear magnetic resonance line broadening shows that eosin-5-maleimide does not block the external anion access channel of band 3. Biophys J. 1995 Aug; 69(2):399-408.
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Kennedy SD, Szczepaniak LS, Gibson SL, Hilf R, Foster TH, Bryant RG. Quantitative MRI of Gd-DTPA uptake in tumors: response to photodynamic therapy. Magn Reson Med. 1994 Mar; 31(3):292-301.
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Blinc A, Kennedy SD, Bryant RG, Marder VJ, Francis CW. Flow through clots determines the rate and pattern of fibrinolysis. Thromb Haemost. 1994 Feb; 71(2):230-5.
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Li H, Kennedy SD, Goldstein BM. Solid-state and solution conformations of isotiazofurin: crystallographic, computational and 1H NMR studies. Acta Crystallogr B. 1993 Aug 1; 49 ( Pt 4):729-38.
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Hillman BJ, Olson GT, Griffith PE, Sunshine JH, Joseph CA, Kennedy SD, Nelson WR, Bernhardt LB. Physicians' utilization and charges for outpatient diagnostic imaging in a Medicare population. JAMA. 1992 Oct 21; 268(15):2050-4.
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Ceckler TL, Gibson SL, Kennedy SD, Hill R, Bryant RG. Hetergeneous tumour response to photodynamic therapy assessed by in vivo localised 31P NMR spectroscopy. Br J Cancer. 1991 Jun; 63(6):916-22.
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Mendelson DA, Heinsbergen JF, Kennedy SD, Szczepaniak LS, Lester CC, Bryant RG. Comparison of agarose and cross-linked protein gels as magnetic resonance imaging phantoms. Magn Reson Imaging. 1991; 9(6):975-8.
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Hillman BJ, Joseph CA, Mabry MR, Sunshine JH, Kennedy SD, Noether M. Frequency and costs of diagnostic imaging in office practice--a comparison of self-referring and radiologist-referring physicians. N Engl J Med. 1990 Dec 6; 323(23):1604-8.
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Kennedy SD, Bryant RG. Structural effects of hydration: studies of lysozyme by 13C solids NMR. Biopolymers. 1990 Dec; 29(14):1801-6.
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Kickler T, Kennedy SD, Braine HG. Alloimmunization to platelet-specific antigens on glycoproteins IIb-IIIa and Ib/IX in multiply transfused thrombocytopenic patients. Transfusion. 1990 Sep; 30(7):622-5.
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Bryant RG, Kennedy SD, Jackson CL, Eads TM, Croasmun WR, Blaurock AE. Applications of multinuclear NMR in the solid state to structural and dynamical problems in macromolecular chemistry. Basic Life Sci. 1990; 56:255-71.
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Kennedy SD, Bryant RG. Hydration effects on dynamics of polyglycine and sodium poly(L-glutamate). Biopolymers. 1990; 30(7-8):691-701.
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Kennedy SD, Bryant RG. Manganese-deoxyribonucleic acid binding modes. Nuclear magnetic relaxation dispersion results. Biophys J. 1986 Oct; 50(4):669-76.
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Eads TM, Kennedy SD, Bryant RG. Solvent suppression in high-resolution proton nuclear magnetic resonance based on control of transverse relaxation rate. Anal Chem. 1986 Jul; 58(8):1752-6.
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Kennedy SD, Bryant RG. Proton magnetic relaxation in aqueous glycerol solutions containing manganese(II) ion. Magn Reson Med. 1985 Feb; 2(1):14-9.
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Ehman RL, Gray JE, Bryant RG, Kennedy SD, Earnest F. Spin-spin relaxation time (T2) dependence in MR saturation- and inversion- recovery images. AJR Am J Roentgenol. 1984 Oct; 143(4):903-6.
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Bryant RG, Polnaszek C, Kennedy S, Hetzler J, Hickerson D. The magnetic field dependence of water proton T1 in aqueous solutions: implications for magnetic imaging contrast media. Med Phys. 1984 Sep-Oct; 11(5):712-3.
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