• Patients & Families
• Education
• Research
• Community

• Referring Physicians
• Find a Physician
• Departments & Centers
• About URMC

• Libraries
• Alumni
• Giving

• Home
• Research
  • Research Images
  • Recent Publications
  • Laboratories
  • Facilities
• Education
• People
• Featured Alumni
• News & Events
• Available Positions
• Department intranet

Recent Publications

The following list was auto-generated 6 days ago.

• 1. Pal S
  2. Yadav AR
  3. Lifson MA
  4. Baker JE
  5. Fauchet PM
  6. Miller BL
  (2013 Jun 15). Selective virus detection in complex sample matrices with photonic crystal optical cavities. Biosens Bioelectron. 44, 229-34.
• 1. Wakabayashi H
  2. Fay PJ
  (2013 Jun 01). Molecular orientation of Factor VIIIa on the phospholipid membrane surface determined by fluorescence resonance energy transfer. Biochem J. 452, 293-301.
• 1. Simon W
  (2013 Jun 01). Letter to the Editor: The RO1 grant bottleneck. Blood Cells Mol Dis. 51, 1-2.
• 1. Wakabayashi H
  2. Fay PJ
  (2013 May 09). Modification of inter-domain interfaces within the A3C1C2 subunit of factor VIII affects its stability and activity. Biochemistry. In press.
• 1. Possin KL
  2. Feigenbaum D
  3. Rankin KP
  4. Smith GE
  5. Boxer AL
  6. Wood K
  7. Hanna SM
  8. Miller BL
  9. Kramer JH
  (2013 May 08). Dissociable executive functions in behavioral variant frontotemporal and Alzheimer dementias. Neurology. In press.
• 1. Bellaousov S
  2. Reuter JS
  3. Seetin MG
  4. Mathews DH
  (2013 Apr 24). RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. In press.
• 1. Liberman JA
  2. Salim M
  3. Krucinska J
  4. Wedekind JE
  (2013 Apr 14). Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat Chem Biol. In press.
• 1. Griffiths AE
  2. Rydkin I
  3. Fay PJ
  (2013 Apr 11). Factor VIIIa A2 Subunit Shows a High Affinity Interaction with Factor IXa: Contribution of A2 Subunit Residues 707-714 to the Interaction with Factor IXa. J Biol Chem. In press.
• 1. Grant TD
  2. Luft JR
  3. Wolfley JR
  4. Snell ME
  5. Tsuruta H
  6. Corretore S
  7. Quartley E
  8. Phizicky EM
  9. Grayhack EJ
  10. Snell EH
  (2013 Apr 10). The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA. J Mol Biol. In press.
• 1. Takeyama M
  2. Wintermute JM
  3. Manithody C
  4. Rezaie AR
  5. Fay PJ
  (2013 Apr 02). Variable contributions of basic residues forming an APC exosite in the binding and inactivation of factor VIIIa. Biochemistry. 52, 2228-35.
• 1. Grossfield A
  (2013 Apr 01). Special issue on lipid-protein interactions. Chem Phys Lipids. 169, 1.
• 1. Gleghorn ML
  2. Gong C
  3. Kielkopf CL
  4. Maquat LE
  (2013 Apr 01). Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat Struct Mol Biol. 20, 515-24.
• 1. Jenkins JL
  2. Agrawal AA
  3. Gupta A
  4. Green MR
  5. Kielkopf CL
  (2013 Apr 01). U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res. 41, 3859-73.
• 1. Wang J
  2. Gong C
  3. Maquat LE
  (2013 Apr 01). Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev. 27, 793-804.
• 1. Waugh RE
  2. Huang YS
  3. Arif BJ
  4. Bauserman R
  5. Palis J
  (2013 Apr 01). Development of membrane mechanical function during terminal stages of primitive erythropoiesis in mice. Exp Hematol. 41, 398-408.e2.
• 1. Huang C
  2. Yu YT
  (2013 Apr 01). Synthesis and labeling of RNA in vitro. Curr Protoc Mol Biol. Chapter 4, Unit4.15.
• 1. Ge J
  2. Yu YT
  (2013 Apr 01). RNA pseudouridylation: new insights into an old modification. Trends Biochem Sci. 38, 210-8.
• 1. Pryor EE
  2. Horanyi PS
  3. Clark KM
  4. Fedoriw N
  5. Connelly SM
  6. Koszelak-Rosenblum M
  7. Zhu G
  8. Malkowski MG
  9. Wiener MC
  10. Dumont ME
  (2013 Mar 29). Structure of the integral membrane protein CAAX protease Ste24p. Science. 339, 1600-4.
• 1. Wang J
  2. Li D
  3. Bambara RA
  4. Yang H
  5. Dykes C
  (2013 Mar 27). L74V increases the reverse transcriptase content of HIV-1 virions with non-nucleoside reverse transcriptase drug-resistant mutations L100I+K103N and K101E+G190S, which results in increased fitness. J Gen Virol. In press.
• 1. Lee SE
  2. Tartaglia MC
  3. Yener G
  4. Genç S
  5. Seeley WW
  6. Sanchez-Juan P
  7. Moreno F
  8. Mendez MF
  9. Klein E
  10. Rademakers R
  11. Munain AL
  12. Combarros O
  13. Kramer JH
  14. Kenet RO
  15. Boxer AL
  16. Geschwind MD
  17. Gorno-Tempini ML
  18. Karydas AM
  19. Rabinovici GD
  20. Coppola G
  21. Geschwind DH
  22. Miller BL
  (2013 Mar 25). Neurodegenerative Disease Phenotypes in Carriers of MAPT p.A152T, A Risk Factor for Frontotemporal Dementia Spectrum Disorders and Alzheimer Disease. Alzheimer Dis Assoc Disord. In press.
• 1. Yada K
  2. Nogami K
  3. Wakabayashi H
  4. Fay PJ
  5. Shima M
  (2013 Mar 07). The mild phenotype in severe hemophilia A with Arg1781His mutation is associated with enhanced binding affinity of factor VIII for factor X. Thromb Haemost. 109, .
• 1. Trcek T
  2. Sato H
  3. Singer RH
  4. Maquat LE
  (2013 Mar 01). Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev. 27, 541-51.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 28). Flap Endonuclease 1. Annu Rev Biochem. In press.
• 1. Kurosaki T
  2. Maquat LE
  (2013 Feb 26). Rules that govern UPF1 binding to mRNA 3' UTRs. Proc Natl Acad Sci U S A. 110, 3357-62.
• 1. Schmidt K
  2. Butler JS
  (2013 Feb 20). Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity. Wiley Interdiscip Rev RNA. 4, 217-31.
• 1. Tubbs JD
  2. Condon DE
  3. Kennedy SD
  4. Hauser M
  5. Bevilacqua PC
  6. Turner DH
  (2013 Feb 12). The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry. 52, 996-1010.
• 1. Martinez-Finley EJ
  2. Gavin CE
  3. Aschner M
  4. Gunter TE
  (2013 Feb 08). Manganese neurotoxicity and the role of reactive oxygen species. Free Radic Biol Med. In press.
• 1. Wang W
  2. Maucuer A
  3. Gupta A
  4. Manceau V
  5. Thickman KR
  6. Bauer WJ
  7. Kennedy SD
  8. Wedekind JE
  9. Green MR
  10. Kielkopf CL
  (2013 Feb 05). Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure. 21, 197-208.
• 1. Ermolenko DN
  2. Cornish PV
  3. Ha T
  4. Noller HF
  (2013 Feb 01). Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. RNA. 19, 158-66.
• 1. Preston MA
  2. D'Silva S
  3. Kon Y
  4. Phizicky EM
  (2013 Feb 01). tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae. RNA. 19, 243-56.
• 1. Takeyama M
  2. Wakabayashi H
  3. Fay PJ
  (2013 Feb 01). Contribution of factor VIII light-chain residues 2007-2016 to an activated protein C-interactive site. Thromb Haemost. 109, 187-98.
• 1. Elliott GO
  2. Murphy KJ
  3. Hayes JJ
  4. Thiriet C
  (2013 Feb 01). Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4. Nucleic Acids Res. 41, 2228-38.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 01). Okazaki fragment metabolism. Cold Spring Harb Perspect Biol. 5, .
• 1. Pieper U
  2. Schlessinger A
  3. Kloppmann E
  4. Chang GA
  5. Chou JJ
  6. Dumont ME
  7. Fox BG
  8. Fromme P
  9. Hendrickson WA
  10. Malkowski MG
  11. Rees DC
  12. Stokes DL
  13. Stowell MH
  14. Wiener MC
  15. Rost B
  16. Stroud RM
  17. Stevens RC
  18. Sali A
  (2013 Feb 01). Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol. 20, 135-8.
• 1. Park E
  2. Gleghorn ML
  3. Maquat LE
  (2013 Jan 08). Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc Natl Acad Sci U S A. 110, 405-12.
• 1. Gunter TE
  2. Gerstner B
  3. Gunter KK
  4. Malecki J
  5. Gelein R
  6. Valentine WM
  7. Aschner M
  8. Yule DI
  (2013 Jan 01). Manganese transport via the transferrin mechanism. Neurotoxicology. 34, 118-27.
• 1. Mathew E
  2. Ding FX
  3. Naider F
  4. Dumont ME
  (2013 Jan 01). Functional fusions of T4 lysozyme in the third intracellular loop of a G protein-coupled receptor identified by a random screening approach in yeast. Protein Eng Des Sel. 26, 59-71.
• 1. Marsh G
  2. Waugh RE
  (2013 Jan 01). Quantifying the mechanical properties of the endothelial glycocalyx with atomic force microscopy. J Vis Exp. In press.
• 1. Dean KM
  2. Grayhack EJ
  (2012 Dec 01). RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay. RNA. 18, 2335-44.
• 1. Muyan M
  2. Callahan LM
  3. Huang Y
  4. Lee AJ
  (2012 Dec 01). The ligand-mediated nuclear mobility and interaction with estrogen-responsive elements of estrogen receptors are subtype specific. J Mol Endocrinol. 49, 249-66.
• 1. Kennedy SD
  2. Kierzek R
  3. Turner DH
  (2012 Nov 20). Novel conformation of an RNA structural switch. Biochemistry. 51, 9257-9.
• 1. Pal S
  2. Fauchet PM
  3. Miller BL
  (2012 Nov 06). 1-D and 2-D photonic crystals as optical methods for amplifying biomolecular recognition. Anal Chem. 84, 8900-8.
• 1. Salter JD
  2. Lippa GM
  3. Belashov IA
  4. Wedekind JE
  (2012 Nov 06). Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry. 51, 8702-4.
• 1. Masoudi FA
  2. Go AS
  3. Magid DJ
  4. Cassidy-Bushrow AE
  5. Doris JM
  6. Fiocchi F
  7. Garcia-Montilla R
  8. Glenn KA
  9. Goldberg RJ
  10. Gupta N
  11. Gurwitz JH
  12. Hammill SC
  13. Hayes JJ
  14. Jackson N
  15. Kadish A
  16. Lauer M
  17. Miller AW
  18. Multerer D
  19. Peterson PN
  20. Reifler LM
  21. Reynolds K
  22. Saczynski JS
  23. Schuger C
  24. Sharma PP
  25. Smith DH
  26. Suits M
  27. Sung SH
  28. Varosy PD
  29. Vidaillet HJ
  30. Greenlee RT
  (2012 Nov 01). Longitudinal study of implantable cardioverter-defibrillators: methods and clinical characteristics of patients receiving implantable cardioverter-defibrillators for primary prevention in contemporary practice. Circ Cardiovasc Qual Outcomes. 5, e78-85.
• 1. Banáš P
  2. Sklenovský P
  3. Wedekind JE
  4. Šponer J
  5. Otyepka M
  (2012 Oct 25). Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B. 116, 12721-34.
• 1. Liberman JA
  2. Guo M
  3. Jenkins JL
  4. Krucinska J
  5. Chen Y
  6. Carey PR
  7. Wedekind JE
  (2012 Oct 17). A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. J Am Chem Soc. 134, 16933-6.
• 1. Schmidt K
  2. Xu Z
  3. Mathews DH
  4. Butler JS
  (2012 Oct 01). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA. 18, 1934-45.
• 1. Guy MP
  2. Podyma BM
  3. Preston MA
  4. Shaheen HH
  5. Krivos KL
  6. Limbach PA
  7. Hopper AK
  8. Phizicky EM
  (2012 Oct 01). Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA. 18, 1921-33.
• 1. Dewe JM
  2. Whipple JM
  3. Chernyakov I
  4. Jaramillo LN
  5. Phizicky EM
  (2012 Oct 01). The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. RNA. 18, 1886-96.
• 1. Gong C
  2. Popp MW
  3. Maquat LE
  (2012 Oct 01). Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes. Methods. 58, 88-93.