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D. Turner · SciRah

Researcher profile · Semantic Scholar

D. Turner

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D. Turner — researcher profile on SciRah

h-index: 52
Works: 228
Citations: 18K

Most-cited papers

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
D. Turner, D. Mathews
2009Nucleic Acids Res.570 citations Open access
Semantic Scholar
The contribution of pseudouridine to stabilities and structure of RNAs
E. Kierzek, Magdalena Małgowska, Jolanta Lisowiec, D. Turner +2 more
2013Nucleic Acids Research258 citations Open access
Semantic Scholar
Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
Ilyas Yildirim, H. A. Stern, S. Kennedy, J. D. Tubbs +1 more
2010Journal of Chemical Theory and Computation156 citations Open access
Semantic Scholar
Folding and finding RNA secondary structure.
D. Mathews, Walter N. Moss, D. Turner
2010Cold Spring Harbor Perspectives in Biology152 citations Open access
Semantic Scholar
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
Sandro Bottaro, G. Bussi, S. Kennedy, D. Turner +1 more
2018Science Advances119 citations Open access
Semantic Scholar
Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics
David E. Condon, S. Kennedy, Brendan C. Mort, R. Kierzek +2 more
2015Journal of Chemical Theory and Computation112 citations Open access
Semantic Scholar
Identification of potential conserved RNA secondary structure throughout influenza A coding regions.
Walter N. Moss, S. Priore, D. Turner
2011RNA: A publication of the RNA Society103 citations Open access
Semantic Scholar
Optical Melting Measurements of Nucleic Acid Thermodynamics
S. Schroeder, D. Turner
2009Methods in Enzymology101 citations Open access
Semantic Scholar
Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions
Ilyas Yildirim, H. A. Stern, J. D. Tubbs, S. Kennedy +1 more
2011Journal of Physical Chemistry B94 citations Open access
Semantic Scholar
Microarrays for identifying binding sites and probing structure of RNAs
R. Kierzek, D. Turner, E. Kierzek
2014Nucleic Acids Research88 citations Open access
Semantic Scholar
Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters
Jonathan L. Chen, Abigael L. Dishler, S. Kennedy, Ilyas Yildirim +3 more
2012Biochemistry88 citations Open access
Semantic Scholar
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
J. D. Tubbs, David E. Condon, S. Kennedy, Melanie Hauser +2 more
2013Biochemistry81 citations Open access
Semantic Scholar
Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs
Ilyas Yildirim, S. Kennedy, H. A. Stern, James M. Hart +2 more
2011Journal of Chemical Theory and Computation68 citations Open access
Semantic Scholar
Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts
Parin Sripakdeevong, Mirko Cevec, A. T. Chang, M. Erat +11 more
2014Nature Methods67 citations Open access
Semantic Scholar
In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs
L. Simon, Edoardo Morandi, A. Luganini, G. Gribaudo +4 more
2019Nucleic Acids Research59 citations Open access
Semantic Scholar
The determination of RNA folding nearest neighbor parameters.
Mirela Andronescu, A. Condon, D. Turner, D. Mathews
2014Methods in molecular biology58 citations
Semantic Scholar
NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon
James M. Hart, S. Kennedy, D. Mathews, D. Turner
2008Journal of the American Chemical Society49 citations Open access
Semantic Scholar
Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with Locked Nucleic Acids (LNA)
E. Kierzek, A. Pasternak, Karol Pasternak, Z. Gdaniec +3 more
2009Biochemistry44 citations Open access
Semantic Scholar
The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin
Walter N. Moss, Lumbini I. Dela-Moss, E. Kierzek, R. Kierzek +2 more
2012PLoS ONE43 citations Open access
Semantic Scholar
An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods
K. Réblová, Zora Strelcová, P. Kulhánek, Ivana Beššeová +5 more
2010Journal of Chemical Theory and Computation43 citations
Semantic Scholar
Influenza A Virus Coding Regions Exhibit Host-Specific Global Ordered RNA Structure
S. Priore, Walter N. Moss, D. Turner
2012PLoS ONE40 citations Open access
Semantic Scholar
RNA pseudoknots: folding and finding
Biao Liu, D. Mathews, D. Turner
2010F1000 Biology Reports39 citations Open access
Semantic Scholar
Facilitating RNA structure prediction with microarrays.
E. Kierzek, R. Kierzek, D. Turner, I. Catrina
2006Biochemistry39 citations Open access
Semantic Scholar
Secondary structures for 5′ regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints
E. Kierzek, Shawn M. Christensen, T. Eickbush, R. Kierzek +2 more
2009Journal of Molecular Biology38 citations Open access
Semantic Scholar
The influenza A segment 7 mRNA 3′ splice site pseudoknot/hairpin family
Walter N. Moss, Lumbini I. Dela-Moss, S. Priore, D. Turner
2012RNA Biology37 citations Open access
Semantic Scholar
Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs
Ilyas Yildirim, H. A. Stern, J. Šponer, N. Špačková +1 more
2009Journal of Chemical Theory and Computation37 citations Open access
Semantic Scholar
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
E. Kierzek, R. Kierzek, Walter N. Moss, Shawn M. Christensen +2 more
2008Nucleic Acids Research36 citations Open access
Semantic Scholar
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
N. B. Hammond, B. Tolbert, R. Kierzek, D. Turner +1 more
2010Biochemistry33 citations Open access
Semantic Scholar
A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes
A. Pasternak, E. Kierzek, Karol Pasternak, D. Turner +1 more
2007Nucleic Acids Research33 citations Open access
Semantic Scholar
Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus
Elzbieta Lenartowicz, Julita Kęsy, A. Ruszkowska, Marta Soszyńska-Jóźwiak +5 more
2016PLoS ONE32 citations Open access
Semantic Scholar
Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU)
David E. Condon, Ilyas Yildirim, S. Kennedy, Brendan C. Mort +2 more
2013Journal of Physical Chemistry B32 citations Open access
Semantic Scholar
Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture
T. Jiang, A. Nogales, Steven F. Baker, L. Martínez-Sobrido +1 more
2016PLoS ONE30 citations Open access
Semantic Scholar
Secondary Structure of a Conserved Domain in the Intron of Influenza A NS1 mRNA
S. Priore, E. Kierzek, R. Kierzek, J. Baman +3 more
2013PLoS ONE30 citations Open access
Semantic Scholar
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.
Gang Chen, S. Kennedy, Jing Qiao, T. Krugh +1 more
2006Biochemistry30 citations Open access
Semantic Scholar
Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters
Biao Liu, Joshua M. Diamond, D. Mathews, D. Turner
2010Biochemistry29 citations Open access
Semantic Scholar
A CA+ Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops
Gang Chen, S. Kennedy, D. Turner
2009Biochemistry29 citations Open access
Semantic Scholar
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits.
N. Shankar, S. Kennedy, Gang Chen, T. Krugh +1 more
2006Biochemistry28 citations Open access
Semantic Scholar
Predicting the kinetics of RNA oligonucleotides using Markov state models
Giovanni Pinamonti, Jianbo Zhao, David E. Condon, Fabian Paul +3 more
2016Journal of Chemical Theory and Computation27 citations Open access
Semantic Scholar
NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.
B. Tolbert, S. Kennedy, S. Schroeder, T. Krugh +1 more
2007Biochemistry27 citations Open access
Semantic Scholar
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.
Y. Lerman, S. Kennedy, N. Shankar, M. Parisien +2 more
2011RNA: A publication of the RNA Society25 citations Open access
Semantic Scholar
Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA
T. Jiang, S. Kennedy, Walter N. Moss, E. Kierzek +1 more
2014Biochemistry24 citations Open access
Semantic Scholar
Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes.
Claudio Morgado, D. Svozil, D. Turner, J. Šponer
2012Physical Chemistry, Chemical Physics - PCCP23 citations
Semantic Scholar
The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure.
A. Pasternak, E. Kierzek, Karol Pasternak, A. Fratczak +2 more
2008Biochemistry23 citations
Semantic Scholar
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects
Jeffrey Zuber, S. Schroeder, Hongying Sun, D. Turner +1 more
2022Nucleic Acids Research22 citations Open access
Semantic Scholar
Nuclear Magnetic Resonance of Single Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations.
Jianbo Zhao, S. Kennedy, K. D. Berger, D. Turner
2020Journal of Chemical Theory and Computation22 citations
Semantic Scholar
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model
A. Spasic, K. D. Berger, Jonathan L. Chen, Matthew G. Seetin +2 more
2018Nucleic Acids Research22 citations Open access
Semantic Scholar
Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.
Huixiang Li, Rui-ting Liang, D. Turner, L. Rothberg +1 more
2007RNA: A publication of the RNA Society21 citations Open access
Semantic Scholar
Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.
Shenghua Duan, D. Mathews, D. Turner
2006Biochemistry21 citations
Semantic Scholar
Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation
M. Gleghorn, Jianbo Zhao, D. Turner, L. Maquat
2016Nucleic Acids Research20 citations Open access
Semantic Scholar
The chemical synthesis of LNA-2-thiouridine and it’s influence on stability and selectivity of oligonucleotide binding to RNA
Marta Carlucci, E. Kierzek, Anna Marciniak, D. Turner +1 more
2009Biochemistry20 citations Open access
Semantic Scholar

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