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IDT Publications
A bibliography of research papers published by IDT scientists. Click on the reference and you will be redirected to the PubMed abstract. If available, you will be able to obtain a PDF download of the paper through the Pubmed site.
Chen AK, Behlke MA, Tsourkas A. 2008 Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA.
Nucleic Acids Res.
12
: 69
Doré-Savard L, Roussy G, Dansereau MA, Collingwood MA, Lennox KA, Rose SD, Beaudet N, Behlke MA, Sarret P. 2008 Central delivery of Dicer-substrate siRNA: a direct application for pain research.
Mol Ther.
7
: 1331-9
Owczarzy R, Tataurov AV, Wu Y, Manthey JA, McQuisten KA, Almabrazi HG, Pedersen KF, Lin Y, Garretson J, McEntaggart NO, Sailor CA, Dawson RB, Peek AS. 2008 IDT SciTools: a suite for analysis and design of nucleic acid oligomers.
Nucleic Acids Res.
36
: 163-9
Tataurov AV, You Y, Owczarzy R. 2008 Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids.
Biophys Chem.
3
: 66-70
Hildebrand MS, Newton SS, Gubbels SP, Sheffield AM, Kochhar A, de Silva MG, Dahl HH, Rose SD, Behlke MA, Smith RJ. 2008 Advances in molecular and cellular therapies for hearing loss.
Mol Ther.
2
: 224-36
Gantier, M.P., Tong, S., Behlke, M.A., Xu, D., Phipps, S., Foster, P.S., and Williams, B.R.G. 2008 TLR7 Is Involved in Sequence-Specific Sensing of Single-Stranded RNAs in Human Macrophages.
J Immunol.
4
: 2117-24
Owczarzy R, Moreira BG, You Y, Behlke MA, Walder JA. 2008 Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations.
Biochemistry.
19
: 5336-53
Zamanian-Daryoush M, Marques JT, Gantier MP, Behlke MA, John M, Rayman P, Finke J, Williams BR.. 2008 Determinants of cytokine induction by small interfering RNA in human peripheral blood mononuclear cells.
J Interferon Cytokine Res.
4
: 221-23
Devor EJ, Samollow PB. 2008 In vitro and in silico annotation of conserved and nonconserved microRNAs in the genome of the marsupial Monodelphis domestica.
J Hered.
1
: 66-72
Brown DW, Gunning KB, Henry DM, Awdeh ZL, Brinker JP, Tzipori S, Herrmann JE 2008 A DNA oligonucleotide microarray for detecting human astrovirus serotypes.
J Virol Methods
147
: 86-92
Chen AK, Behlke MA, Tsourkas A 2007 Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells.
Nucleic Acids Res.
35
: 105
Melton PE, Briceno I, Gomez A, Devor EJ, Bernal JE, Crawford MH. 2007 Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA.
American Journal of Physical Anthropology
133
: 753-770
Peek AS, Behlke MA. 2007 Design of active small interfering RNAs.
Current Opinion in Molecular Therapeutics
9
: 110-118
McQuisten KA, Peek AS. 2007 Identification of sequence motifs significantly associated with antisense activity.
BMC Bioinformatics
8
: 184
Peek AS. 2007 Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features.
BMC Bioinformatics
8
: 182
Amarzguioui M, Lundberg P, Cantin E, Hagstrom J, Behlke MA, Rossi JJ. 2006 Rational design and in vitro and in vivo delivery of Dicer substrate siRNA.
Nature Protocols
1
: 508-517
Robbins MA, Li M, Leung I, Li H, Boyer DV, Song Y, Behlke MA, Rossi JJ. 2006 Stable expression of shRNAs in human CD34(+) progenitor cells can avoid induction of interferon responses to siRNAs in vitro.
Nat Biotechnol.
5
: 566-71
Marques JT, Devosse T, Wang D, Zamanian-Daryoush M, Serbinowski P, Hartmann R, Fujita T, Behlke MA, Williams BR. 2006 A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells.
Nat Biotechnol.
5
: 559-65.
You Y, Moreira BG, Behlke MA, Owczarzy R 2006 Design of LNA probes that improve mismatch discrimination.
Nucleic Acids Res.
8
: 60.
Lennox KA, Sabel JL, Johnson MJ, Moreira BG, Fletcher CA, Rose SD, Behlke MA, Laikhter AL, Walder JA, Dagle JM. 2006 Characterization of Modified Antisense Oligonucleotides in Xenopus laevis Embryos.
Oligonucleotides
16
: 26-42.
Devor EJ. 2006 Primate MicroRNAs miR-220 and miR-492 Lie within Processed Pseudogenes.
J Hered.
97
: 186-90.
Zlojutro M, Rubicz R, Devor EJ, Spitsyn VA, Makarov SV, Wilson K, Crawford MH. 2006 Genetic structure of the Aleuts and Circumpolar populations based on mitochondrial DNA sequences: a synthesis.
Am J Phys Anthropol.
129
: 446-64.
Behlke MA. 2006 Progress towards in Vivo Use of siRNAs.
Mol Ther.
13
: 644-70.
Ramaswamy M, L Shi, SM Varga, S Barik, MA Behlke, and DC Look 2006 Respiratory syncytial virus nonstructural protein 2 specifically inhibits type I interferon signal transduction.
Virology
344
: 328-339.
Owczarzy R. 2005 Melting temperatures of nucleic acids: Discrepancies in analysis.
Biophys Chem.
117
: 207-215.
Eberhard S, Jain M, Im CS, Pollock S, Shrager J, Lin Y, Peek AS, Grossman AR 2005 Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii.
Curr Genet.
: 1-19.
Rose, SD, Kim, DH, Amarzguioui, M, Heidel, JD, Collingwood, MA, Davis, ME, Rossi, JJ, and Behlke, MA 2005 Functional polarity is introduced by Dicer processing of short substrate RNAs.
Nucleic Acids Res.
33
: 4140-56.
Soifer HS, A Zaragoza, M Peyvan, MA Behlke, and JJ Rossi 2005 A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon.
Nucleic Acids Res.
33
: 846-56.
Kim DH, MA Behlke, SD Rose, M-S Chang S Choi, and JJ Rossi 2005 Synthetic dsRNA dicer-substrates enhance RNAi potency and efficacy.
Nature Biotechnology
23
: 222-226
Moreira BG, Y You, MA Behlke, and R Owczarzy 2005 Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability.
Biochem Biophys Res Comm
327
: 473-484
Devor EJ, and K Moffat-Wilson 2004 An ancient RNase HI splice junction mutant preserved in a 19-million-year old genetic fossil in ape genomes.
Journal of Heredity
95
: 257-261
Hail ME, B Elliott, and A Anderson 2004 High-throughput analysis of oligonucleotides using automated electrospray ionization mass spectrometry.
American Biotechnology Laboratory
22
: 12-14
Montanelli L, JJJ van Durme, G Smits, M Bonomi, P Rodien, EJ Devor, K Moffat-Wilson, L Pardo, G Vassart, and S Costagliola 2004 Modulation of ligand selectivity associated with activation of the transmembrane region of the human follitropin receptor.
Molecular Endocrinology
18
: 2061-2073
Owczarzy R, Y You, B Moreira, JA Manthey, L Huang, MA Behlke, and JA Walder 2004 Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures.
Biochemistry
43
: 3537-3554
Devor EJ, and K Moffat-Wilson 2003 Molecular and temporal characteristics of human retropseuodgenes.
Human Biology
75
: 661-672
Owczarzy R, I Dunietz, MA Behlke, IM Klotz, and JA Walder 2003 Thermodynamic treatment of oligonucleotide duplex-simplex equilibria.
Proceedings of the National Academy of Science USA
100
: 14840-14845
Tsourkas A, MA Behlke, SD Rose, and G Bao 2003 Hybridization kinetics and thermodynamics of molecular beacons.
Nucleic Acids Research
31
: 1319-1330
Tsourkis A, MA Behlke, Y Xu, and G Bao 2003 Spectroscopic features of dual fluorescence/luminescence energy-transfer molecular beacons.
Analytical Chemistry
75
: 3697-3703
Tsourkas A, MA Behlke, and G Bao 2002 Structure-function relationships of shared stem and conventional molecular beacons.
Nucleic Acids Research
30
: 4208-4215
Tsourkis A, MA Behlke, and G Bao 2002 Hybridization of 2’-O-methyl and 2’-deoxy molecular beacons to RNA and DNA targets.
Nucleic Acids Research
30
: 5168-5174
Zhang L, Peek AS, Dunams D, Gaut BS 2002 Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).
Genetics
162
: 851-860
Devor EJ 2001 Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.
GenomeBiology
2
: 0006.1-0006.5
Devor EJ 2001 Molecular archeology of an SP100 splice variant revisted: dating the retrotranscription and Alu insertion events.
GenomeBiology
2
: 0040.1-0040.6
Park C, BR Keleman, TA Klink, R Sweeney, MA Behlke, SR Eubanks, and RT Raines 2001 Fast, facile, hypersensitive assays for ribonucleolytic activity.
Methods in Enzymology
341
: 81-94
Rose SD, GH Swift, MJ Peyton, RE Hammer, and RJ MacDonald 2001 The role of PTF1-P48 in pancreatic acinar gene expression.
Journal of Biological Chemistry
276
: 44018-44026
Behlke MA, SA Dames, WH McDonald, KL Gould, EJ Devor, and JA Walder 2000 Use of high specific activity StarFire oligonucleotide probes to visualize low-abundance pre-mRNA splicing intermediates in S. pombe.
Biotechniques
29
: 892-897
Keleman BR, TA Klink, MA Behlke, SR Eubanks, PA Leland, and RT Raines 1999 Hypersensitive substrate for ribonucleases.
Nucleic Acids Research
27
: 3696-3701
Conrad AH, MA Behlke, T Jaffredo, and GW Conrad 1998 Optimal lipofection reagent varies with the molecular modifications of the DNA.
Antisense & Nucleic Acid Drug Development
8
: 427-434
Devor EJ, RM Dill-Devor, HJ Magee, and R Waziri 1998 Serine hydroxymethyltransferase pseudogene, SHMT-ps1: A unique marker of the order Primates.
Journal of Experimental Zoology
282
: 150-156
Eder PS, RY Walder, and JA Walder 1993 Substrate specificity of human RNase H1 and its role in excision repair of ribose residues misincorporated in DNA.
Biochimie
75
: 123-126
Walder RY, JR Hays, and JA Walder 1993 Use of PCR primers containing a 3’-terminal ribose residue to prevent cross-contamination of amplified sequences.
Nucleic Acids Research
21
: 4339-4343
Dagle JM, ME Andracki, RJ DeVine, and JA Walder 1991 Physical properties of oligonucleotides containing phosphoramidite-modified internucleoside linkages.
Nucleic Acids Research
19
: 1805-1810
Eder PS, and JA Walder 1991 Ribonuclease H from K562 human erythroleulemia cells. Purification, characterization, and substrate specificity.
Journal of Biological Chemistry
266
: 6472-6479
Eder PS, RJ DeVine, JM Dagle, and JA Walder 1991 Substrate specificity and kinetics of degradation of antisense oligonucleotides by a 3’ exonuclease in plasma.
Antisense Research Developments
1
: 141-151
Dagle JM, DL Weeks, and JA Walder 1991 Pathways of degradation and mechanism of action of antisense oligonucleotides in Xenopus laevis embryos.
Antisense Research Developments
1
: 11-20
Dagle JM, JA Walder, and DL Weeks 1990 Targeted degradation of mRNA in Xenopus oocytes and embryos directed by modified oligonucleotides: studies of An2 and cyclin in embryogenesis.
Nucleic Acids Research
18
: 4751-4757
Walder RY, and JA Walder 1988 Role of RNase H in hybrid-arrested translation by antisense oligonucleotides.
Proceedings of the National Academy of Sciences USA
85
: 5011-5015