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Centers for Disease Control (CDC): “Visual OMP (version 4.2) software (DNA Software, Inc., Ann Arbor, MI) was used to design and simulate the performance of the O-group PCR primers and capture probes.” -- Fitzgerald,C., Collins,M., van Duyne,S., Mikoleit,M., Brown,T., Fields,P. (2007) “Multiplex, Bead-Based Suspension Array for Molecular Determination of Common Salmonella Serogroups”, Journal of Clinical Microbiology, 45, 3323-3334.
U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) / Boston University: “The microarray DNA probe design from candidate sequences was carried out using the commercial software oligonucleotide modeling platform (OMP) (available at http://www.dnasoftware.com), which implements a state-of-the-art hybridization model (SantaLucia and Hicks, 2004).” -- Tembe, W., Zavaljevski, N., Bode, E., Chase, C., Geyer, J., Wasieloski, L., Benson, G., Reifman, J. (2007) “Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays”, Bioinformatics, 23, 5-13.
U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID): “The specific primer and TaqMan minor groove binding (MGB) probe sequences were designed using Visual OMP version 4.1.0.0 for Windows (DNA Software).” -- Ulrich,M.P., Norwood,D.A., Christensen,D.R., Ulrich,R.L. (2006). “Using real time PCR to specifically detect Burkholderia mallei”, Journal of Medical Microbiology, 55, 551-559.
Harvard University: “We are grateful to [...] DNA Software for assistance with codon screening.” -- Gartner Z.J., Tse B.N., Grubina R., Doyon J.B., Snyder T.M., Liu D.R. (2004). “DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles”, Science, 305, 1601-1605.
Harvard University: “We thank DNA Software for assistance with screening coding and annealing sequences.” -- Kanan M.W., Rozenman M.M., Sakurai K., Snyder T.M., Liu D.R. (2004). “Reaction discovery enabled by DNA-templated synthesis and in vitro selection”, Nature, 431, 545-549.
Merck & Co. Inc./ Universitat de Barcelona / Los Alamos National Laboratory / Howard Hughes Medical Institute / University of California, Berkley: “... we obtain for the free energy of unfolding... excellent agreement with the result obtained using the Visual OMP from DNA software...” -- Collin,D., Ritort,F., Jarzynski,C., Smith,S.B., Tinoco,I.,Jr., Bustamante,C. (2005). “Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies”, Nature, 437, 231-234.
EraGen Biosciences Inc. / U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID): “Because the approach of mixing primer sets from separate assays was unsuccessful, we decided to construct new assays using new multiplex primer design software called Visual OMP... The new designs obtained... demonstrated similar limits of detection yet a noticeable improvement in sensitivity and specificity over the previously developed triplex assays... The current availability of RTx reagents and Visual OMP design software should allow others to compare multiplexed probe-based systems with the RTx probe-free system.” -- Moser,M.J., Christensen,D.R., Norwood,D., Prudent,J.R. (2006). “Multiplexed Detection of Antrax-Related Toxin Genes”, Journal of Molecular Diagnostics, 8, 89-96.
EraGen Biosciences Inc. / Emory University: “The same effects of mismatch types were predicted by simulations using the software Oligonucleotide Modeling Platform (OMP, DNA Software, Inc., Ann Arbor, MI) by Lee and co-workers...” -- Moser,M.J., Ruckstuhl,M., Larsen,C.A., Amanda, J.S., Kozlowski,M., Bassit,L., Sharma,P.L., Schinazi,R.F., Prudent,J.R. (2005). “Quantifying Mixed Populations of Drug-Resistant Human Immunodeficiency Virus Type 1”, Antimicrobial Agents and Chemotherapy, 49, 3334-3340.
EraGen Biosciences Inc. / Department of Pediatrics and Medicine / Wisconsin State Laboratory of Hygiene / University of Wisconsin: “…candidate primer sets were selected within these conserved sequences with computer software (Visual Oligonucleotide Modeling Platform; DNA Software, Inc.), according to the following criteria: appropriate melting temperature, minimal secondary-structure formation, minimal interactions with the other primers in multiplex settings, and no interaction with human sequences.” -- Wai-Ming Lee, Kris Grindle, Tressa Pappas, David J. Marshall, Michael J. Moser, Edward L. Beaty, Peter A. Shult, James R. Prudent, and James E. Gern. (2007). “High-Throughput, Sensitive, and Accurate Multiplex PCR-Microsphere Flow Cytometry System for Large-Scale Comprehensive Detection of Respiratory Viruses”, Journal of Clinical Microbiology, p. 2626–2634
University of Michigan /Kyushu University: “Melting temperature as a measure of hybridization stability is calculated using the nearest neighbor thermodynamics model (28) with licensed software Oligonucleotide Modeling Platform (OMP; http://www.dnasoftware.com). Observing that OMP calculations correlated with experimental Tm better than our in-house program containing publicly available parameters...” -- Lee,I., Ajay,S.S., Chen,H., Maruyama,A., Wang,N., McInnis,M.G., Athey,B.D. (2008). “Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)”, Nucleic Acids Research, 36, e27.
University of Michigan / Wayne State University: “Most hybridization Tm calculations were done using OMP software (DNA Software, Inc., Ann Arbor, MI; http://www.dna-software.com). The software simulates and predicts nucleic acid hybridization in solution and produces structural and thermodynamic parameters. OMP predicts nucleotide acid structures utilizing dynamic programming methods (30) and calculates their reactions in equilibrium based on nearest neighbor calculations, which determine `thermal' Tm using equation 2. OMP calculates `actual' Tm considering competing secondary structures of oligonucleotides... Nearest neighbor Tm calculations, especially using OMP, showed an excellent linear correlation with experimental Td for single-mismatched pairs....” -- Lee,I., Dombkowski,A.A., Athey,B.D. (2004). “Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray”, Nucleic Acids Research, 32, 681-690.
Michigan State University / University of Michigan: “The same effects of mismatch types were predicted by simulations using the software Oligonucleotide Modeling Platform (OMP, DNA Software, Inc., Ann Arbor, MI) by Lee and co-workers (43).” -- Wick,L.M., Rouillard,J.M., Whittam,T.S., Gulari,E., Tiedje,J.M., Hashsham,S.A. (2006). “On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes”, Nucleic Acids Research, 34, e26.
Medigenes Co. / KAIST (Korea Advanced Institute of Science and Technology) / Yonsei University College of Medicine / Harvard School of Dental Medicine / Yale University School of Medicine / CambridgeMED Co.: “Visual OMP [http://www.dnasoftware.com/Products/VisualOMP/index.htm] is a software for probe design, which was optimized to maximize the specificity of the probes. This program has been integrated in an engine for visualizing target and oligo structures, thermodynamics modeling, and built-in BLAST and ClustalW.” -- Yoo,S.M., Keum,K.C., Yoo,S.Y., Choi,J.Y., Chang,K.H., Yoo,N.C., Yoo,W.M., Kim,J.M., Lee,D., Lee,S.Y. (2004). “Development of DNA Microarray for Pathogen Detection”, Biotechnology and Bioprocess Engineering, 9, 93-99.
Providence Portland Medical Center: “... and Visual OMP software were used to design and simulate the performance of the primers and the probe.” -- Kohlhepp S.J., Hardick J., Gaydos C. (2005). “Chlamydia pneumoniae in Peripheral Blood Mononuclear Cells Isolated from Individuals Younger than 20 Years or Older than 60 Years”, Journal of Clinical Microbiology, 43, 3030.
Chung-Ho Memorial Hospital / Kaohsiung Medical University / Sung Hua Biotech Co., Ltd.: “Using a version of OMP (Oligonucleotide Modeling Platform, DNA Software, Ann Arbor, MI), DNA software tailored to the specifics of membrane-array assay, probe sequences for each target are designed and a single best candidate is selected.” -- Wang,J.Y., Yeh,C.S., Chen,Y.F., Wu,C.H., Hsieh,J.S., Huang,T.J., Huang, S.Y., Lin,S.R. (2006). “Development and evaluation of a colorimetric membrane-array method for the detection of circulating tumor cells in the peripheral blood of Taimanese patients with colorectal cancer”, International Journal of Molecular Medicine, 17, 737-747.
Kaohsiung Medical University Hospital / Kaohsiung Medical University / Tri-Service General Hospital, Taipei /Kaohsiung Municipal Hsiao-Kang Hospital: “Using a version of OMP (Oligonucleotide Modeling Platform, DNA Software, Ann Arbor, MI, USA), DNA software tailored to probe sequences for each target are designed and a single best candidate is selected...” -- Wang,J.Y., Wang,Y.H., Jao,S.W., Lu,C.Y., Kuo,C.H., Hu,H.M., Hsieh,J.S., Chong,I.W., Cheng,T.L., Lin,S.R. (2006). “Molecular mechanisms underlying the tumorigenesis of colorectal adenomas: Correlation to activated K-ras oncogene”, Oncology Reports, 16, 1245-1252.
Citations of DNA Software's Research
Portland Bioscience, Inc: Brewood GP, Rangineni Y, Fish DJ, et al. (2008)“Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes” Nucleic Acid Research, 36, 15, e98.
Universite Louis Pasteur: Kenfack CA, Piemont E, Ben Gaied N, et al. (2008) “Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes” Journal of Physical Chemistry, 112, 32.
University of Missouri: Chen SJ (2008) “Conformational statistics, folding kinetics, and ion electrostatics” Annual Review of Biophysics, 37, 197-214.
California Institute of Technology: Lin MM, Meinhold L, Shorokhov D, et al. (2008) “Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes” Physical Chemistry Chemical Physics, 10, 29, 4227-4239.
Los Alamos National Laboratory: Gans JD, Wolinsky M. (2008) “Improved assay-dependent searching of nucleic acid sequence databases” Nucleic Acid Research, 36, 12, e74.
Universität Bayreuth: Naiser T, Ehler O, Kayser J, et al. (2008) “Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges” BMC Biotechnology, 8, 48.
Naval Research Laboratory: Malanoski AP, Lin B, Stenger DA. (2008) “A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays” Nucleic Acid Research, 36, 10, 3194-3201.
Syntrix Biosystems, Inc.: Morgan JR, Lyon RP, Maeda DY, et al. (2008) “Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity” Nucleic Acid Research, 36, 11, 3522-3530.
University of Tartu and Estonian Biocentre: Andreson R, Mols T, Remm M. (2008) “Predicting failure rate of PCR in large genomes” Nucleic Acid Research, 36, 11, e66
SUNY Geneseo: Macula AJ, Schliep A, Bishop MA, et al. (2008) “New, improved, and practical k-stem sequence similarity measures for probe design” Journal of Computational Biology, 15, 5, 525-534.
University of Missouri: Tan ZJ, Chen SJ. (2008) “Salt dependence of nucleic acid hairpin stability” Biophysical Journal, 95, 2, 738-752.
Konan University: Nakano S, Wu L, Oka H, et al. (2008) “Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media” Molecular Biosystems, 4, 6, 579-588.
Tsinghua University: Xue XC, Liu F, Ou-Yang ZC. (2008) “A kinetic model of transcription initiation by RNA polymerase” Journal of Molecular Biology, 387, 3, 520-529.
US Army Medical Research and Materiel Command: Satya RV, Zavaljevski N, Kumar K, et al. (2008) “A high-throughput pipeline for designing microarray-based pathogen diagnostic assays” BMC Bioinformatics, 9, 185.
Temple University: Yang KS, Stanley RJ. (2008) “The extent of DNA deformation in DNA photolyase-Substrate complexes: A solution state fluorescence study” Photochemistry and Photobiology, 84, 3, 741-749.
Integrated DNA Technologies: Owczarzy R, Moreira BG, You Y, et al. (2008) “Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations” Biochemistry, 47, 19, 5336-5353.
ARO Volcani Center: Koltai H., Weingarten-Baror C. (2008) “Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction”, Nucleic Acids Research, 7, 2395-2405.
Centre National de la Recherche Scientifique: Fiche JB, Fuchs J, Buhot A, et al. (2008) “Point mutation detection by surface plasmon resonance imaging coupled with a temperature scan method in a model system”, Analytical Chemistry, 4, 1049-1057.
University United Methodist Church: Montgomery J., Wittwer C.T., Palais R., et al. (2007) “Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis”, Nature Protocols, 1, 59-66.
University of Massachusetts: Zhou Y, Navaroli D.M., Enuameh M.S., et al. (2007) “Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism”, Proceedings of the National Academy of Sciences of the United States of America, 25, 10352-10357.
The State University of New Jersey: Volker J., Klump H.H., Breslauer K.J. (2007) “The energetic of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)(3)C-5]”, Biopolymers, 86 (2), 136-147.
Biophysical Journal, 92 (10): 3615-3632 MAY 10 2007, 104 (17), 7199-7204.
Ritsumeikan Asia Pacific University: Rose, J.A., Deaton, R.J., Hagiya, M., Suyama, A. (2007) “Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems”, IEEE Transactions on Nanobioscience, 6, 18-27.
University of Natural Resources and Applied Life Sciences, Vienna, Austria: Kreil, D.P., Russell, R.R., Russell, S. (2006) “Microarray oligonucleotide probes”, Methods in Enzymology, 410: 73-98.
CEA (Commissariat à l'énergie atomique): Fiche, J.B., Buhot, A., Calemczuk, R., Livache, T. (2007) “Temperature effects on DNA chip experiments from surface plasmon resonance imaging: Isotherms and melting curves”, Biophysical Journal, 92, 935-946.
U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) / Boston University: Tembe, W., Zavaljevski, N., Bode, E., Chase, C., Geyer, J., Wasieloski, L., Benson, G., Reifman, J. (2007) “Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays”, Bioinformatics, 23, 5-13.
CEA (Commissariat à l'énergie atomique) / Russian Academy of Sciences: Halperin, A., Buhot, A., Zhulina, E.B. (2006) “Hybridization at a surface: The role of spacers in DNA microarrays”, Langmuir, 22, 11290-11304.
University of Leeds: West, D.K., Olmsted, P.D., Paci, E. (2006) “Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality”, Journal of Chemical Physics, 125, 204910.
Stanford University: Thiyagarajan, S., Karhanek, M., Akhras, M. (2006) “PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens”, BMC Bioinformatics, 7, 500.
Texas A&M University: Kosmider, B., Wells, R.D. (2006) “Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli”, Nucleic Acids Research, 34, 5369-5382.
Portland State University: Horne, M.T., Fish, D.J., Benight, A.S. (2006) “Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions”, Biophysical Journal, 91, 4133-4153.
Cornell University: Yuan, C.L., Rhoades, E., Lou, X.W., Archer, L.A. (2006) “Spontaneous sharp bending of DNA: role of melting bubbles”, Nucleic Acids Research, 34, 4554-4560.
Rutgers, The State University of New Jersey: Pan, S., Sun, X.J., Lee, J.K.
(2006) “DNA stability in the gas versus solution phases: A systematic study of thirty-one duplexes with varying length, sequence, and charge level”, Journal of the American Society for Mass Spectrometry, 17, 1383-1395.
University of Rochester / Polish Academy of Sciences: Kierzek, E., Mathews, D.H., Ciesielska, A. (2006) “Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2 '-O-methyl RNA and RNA oligonucleotides”, Nucleic Acids Research, 34, 3609-3614
Temple University: Yang, K.S., Stanley, R.J. (2006) “Differential distortion of substrate occurs when it binds to DNA photolyase: A 2-aminopurine study”, Biochemistry, 45, 11239-11245.
University of Cambridge: Russell, S. (2006) “Learning to fly - getting the best out of microarrays”, Molecular Biosystems, 2, 402-405.
University of Toronto: Tikhomirova, A., Beletskaya, I.V., Chalikian, T.V. (2006) ”Stability of DNA duplexes containing GG, CC, AA, and TT mismatches”, Biochemistry, 45, 10563-10571.
Russian Academy of Sciences / Max Planck Institute for Biophysical Chemistry / National Cancer Institute NIH: Shchyolkina, A.K., Kaluzhny, D.N., Arndt-Jovin, D.J., Jovin, T.M., Zhurkin, V.B. (2006) “Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine”, Nucleic Acids Research, 34, 3239-3245.
New York University: Seeman, N.C. (2005) “The challenge of structural control on the nanoscale: bottom-up self-assembly of nucleic acids in 3D”, International Journal of Nanotechnology, 2, 348-370.
Stanford University: Lee, A.H.F., Kool, E.T. (2006) “Exploring the limits of DNA size: Naphtho-homologated DNA bases and pairs”, Journal of the American Chemical Society, 128, 9219-9230.
Rutgers, The State University of New Jersey: Pan, S., Sun, X.J., Lee, J.K. (2006) “Stability of complementary and mismatched DNA duplexes: Comparison and contrast in gas versus solution phases”, International Journal of Mass Spectrometry, 253, 238-248.
University of New Mexico: Sager, J., Stefanovic, D. (2006) “Designing nucleotide sequences for computation: A survey of constraints”, Lecture Notes in Computer Science, 3892, 275-289.
Seoul National University: Zhang, B.T., Jang, H.Y. (2006) “Molecular learning of wDNF formulae”, Lecture Notes in Computer Science, 3892, 427-437.
University of Missouri: Tan, Z.J., Chen, S.J. (2006) “Ion-mediated nucleic acid helix-helix interactions”, Biophysical Journal, 91, 518-536.
Tata Institute of Fundamental Research: Murugan, R. “Effect of external fluctuations on the affinity-specificity negative correlation in DNA-probe interactions”, Physical Review E, 73, 051915.
CEA (Commissariat à l'énergie atomique) / Russian Academy of Sciences: Halperin, A., Buhot, A., Zhulina, E.B. (2006) “On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions”, Journal of Physics: Condensed Matter, 18, S463-S490.
California Institute of Technology: Vikalo, H., Hassibi, B., Hassibi, A. (2006) “A statistical model for microarrays, optimal estimation algorithms, and limits of performance”, IEEE Transactions on Signal Processing, 54, 2444-2455.
Russian Academy of Sciences / Novosibirsk State University: Dyrkheeva, N.S., Lomzov, A.A., Pyshnyi, D.V., Khodyreva, S.N., Lavrik, O.I. (2006) “Efficiency of exonucleolytic action of apurinic/apyrimidinic endonuclease 1 towards matched and mismatched dNMP at the 3 ' terminus of different oligomeric DNA structures correlates with thermal stability of DNA duplexes”, Biochimica et Biophysica Acta - Proteins & Proteomics, 1764, 699-706.
Kyushu University / bResearch Institute of Biomolecule Metrology Co., Ltd: Asakawa, T., Nishi, K., Mizuno, R., Yoneda, K., Okada, T., Hayashi, K. (2006) “Build-to-order nanostructures using DNA self-assembly”, Thin Solid Films, 509, 85-93.
Integrated DNA Technologies: You, Y., Moreira, B.G., Behlke, M.A., Owczarzy, R. (2006) “Design of LNA probes that improve mismatch discrimination”, Nucleic Acid Research, 34, e60.
University of Tartu / BioData Ltd. / Estonian Biocentre: Andreson, R., Reppo, E., Kaplinski, L., Remm, M. (2006) ”GENOMEMASKER package for designing unique genomic PCR primers”
BMC BIOINFORMATICS 7: Art. No. 172 MAR 27 2006
Ludwig-Maximilians-Universität München: Neher, R.A., Gerland, U. (2006) “Intermediate phase in DNA melting”, Physical Review E, 73, 030902.
Academy of Sciences of the Czech Republic / Parc Científic de Barcelona / Universitat de Barcelona: Sponer, J., Jurecka, P., Marchan, I., Luque, F.J., Orozco, M., Hobza, P. (2006) “Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps”, Chemistry- A European Journal,
CHEMISTRY-A EUROPEAN JOURNAL 12 (10): 2854-2865 MAR 20 2006
Russian Academy of Sciences / Novosibirsk State University: Pyshnyi, D.V., Lomzov, A.A., Pyshnaya, I.A., Ivanova, E.M. (2006) “Hybridization of the bridged oligonucleotides with DNA: Thermodynamic and kinetic studies”, Journal of Biomolecular Structure & Dynamics, 23, 567-579.
Boston University: Liang, X.G., Kuhn, H., Frank-Kamenetskii, M.D. (2006) “Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes”, Biophysical Journal, 90, 2877-2889.
Michigan State University / University of Michigan: Wick,L.M., Rouillard,J.M., Whittam,T.S., Gulari,E., Tiedje,J.M., Hashsham,S.A. (2006). “On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes”, Nucleic Acids Research, 34, e26.
University of Missouri-Columbia: Cao, S., Chen, S.J. Free energy landscapes of RNA/RNA complexes: With applications to snRNA complexes in spliceosomes
JOURNAL OF MOLECULAR BIOLOGY 357 (1): 292-312 MAR 17 2006
Harvard Medical School / Duke University / Washington University: Zhang, K., Zhu, J., Shendure, J., Porreca, G.J., Aach, J.D., Mitra, R.D., Church, G.M. (2006) “Long-range polony haplotyping of individual human chromosome molecules”, Nature Genetics, 38, 382-387.
Vanderbilt University: Guengerich, F.P. (2006) “Interactions of carcinogen-bound DNA with individual DNA polymerases”, Chemical Reviews, 106, 420-452.
Boston University: Yakovchuk, P., Protozanova, E., Frank-Kamenetskii, M.D. (2006) “Base-stacking and base-pairing contributions into thermal stability of the DNA double helix”, Nucleic Acids Research, 34, 564-574.
University of Missouri: Tan, Z.J., Chen, S.J. (2006) “Nucleic acid helix stability: Effects of salt concentration, cation valence and size, and chain length”, Biophysical Journal, 90, 1175-1190
Indiana University: Mikulecky, P.J., Feig, A.L. Heat capacity changes associated with DNA duplex formation: Salt- and sequence-dependent effects
BIOCHEMISTRY 45 (2): 604-616 JAN 17 2006
Applied Biosystems: Koehler, R.T., Peyret, N. (2005) “Effects of DNA secondary structure on oligonucleotide probe binding efficiency”, Computational Biology and Chemistry, 29, 393-397.
Wayne State University: Watkins, N.E., Jr., SantaLucia, J., Jr. (2005) “Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes”, Nucleic Acids Research, 33, 6258-6267.
Institute of Genomics and Integrative Biology: Chavali, S., Mahajan, A., Tabassum, R., Maiti, S., Bharadwaj, D. (2005) “Oligonucleotide properties determination and primer designing: a critical examination of predictions”, Bioinformatics, 21, 3918-3925.
University of Rochester: Yildirim, I., Turner, D.H. (2005) “RNA challenges for computational chemists”, Biochemistry, 44, 13225-13234.
University of Rochester / Polish Academy of Sciences: Kierzek, E., Ciesielska, A., Pasternak, K., Mathews, D.H., Turner, D.H., Kierzek, R. (2005) “The influence of locked nucleic acid residues on the thermodynamic properties of 2 '-O-methyl RNA/RNA heteroduplexes”, Nucleic Acids Research, 33, 5082-5093.
Uppsala University: Stenberg, J., Nilsson, M., Landegren, U. (2005) “ProbeMaker: an extensible framework for design of sets of oligonucleotide probes”, BMC Bioinformatics, 6, 229.
Osaka University: Kawai, K., Yoshida, H., Sugimoto, A., Fujitsuka, M., Majima, T. (2005) “Kinetics of transient end-to-end contact of single-stranded DNAs”, Journal of the American Chemical Society, 127, 13232-13237.
University of British Columbia / University of Wisconsin-Madison: Tulpan, D., Andronescu, M., Chang, S.B., Shortreed, M.R., Condon, A., Hoos, H.H., Smith, L.M. (2005) ”Thermodynamically based DNA strand design”, Nucleic Acids Research, 33, 4951-4964.
Merck & Co. Inc./ Universitat de Barcelona / Los Alamos National Laboratory / Howard Hughes Medical Institute / University of California, Berkley: Collin,D., Ritort,F., Jarzynski,C., Smith,S.B., Tinoco,I.,Jr., Bustamante,C. (2005). “Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies”, Nature, 437, 231-234.
Université de Montréal: Hauth, A.M., Maier, U.G., Lang, B.F. (2005) “The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region”, Nucleic Acids Research, 33, 4433-4442.
Applied Biosystems: Koehler, R.T., Peyret, N. (2005) “Thermodynamic properties of DNA sequences: characteristic values for the human genome”, Bioinformatics, 21, 3333-3339.
CEA (Commissariat à l'énergie atomique) / Institute of Macromolecular Compounds of the Russian Academy of Sciences: Halperin, A., Buhot, A., Zhulina, E.B. (2005) “Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines”, Biophysical Journal, 89, 796-811.
University of Florida: Benner, S.A., Sismour, A.M. (2005) “Synthetic biology”, Nature Reviews Genetics, 6, 533-543.
Mount Sinai School of Medicine / New England Biolabs, Inc.: Townson, S.A., Samuelson, J.C., Xu, S.Y., Aggarwal, A.K. (2005) “Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence”, Structure, 13, 791-801.
Wesleyen University: Coman, D., Russu, I.M. (2005) “Base pair opening in three DNA-unwinding elements”, Journal of Biological Chemistry, 280, 20216-20221.
University of Cologne: Leber, M., Kaderali, L., Schonhuth, A., Schrader, R. (2005) “A fractional programming approach to efficient DNA melting temperature calculation”, Bioinformatics, 21, 2375-2382.
LMU Munich: Simmel, F.C., Dittmer, W.U. (2005) “DNA nanodevices”, Small, 1, 284-299.
Wayne State University: Zauner, K.P. (2005) “Molecular information technology” Critical Reviews in Solid State and Materials Sciences, 30, 33-69
Seoul National University: Shin, S.Y., Lee, I.H., Kim, D., Zhang, B.T. (2005) “Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing”, IEEE Transactions on Evolutionary Computation, 9, 143-158.
Uppsala University: Isaksson, J., Chattopadhyaya, J. (2005) “A uniform mechanism correlating dangling-end stabilization and stacking geometry”, Biochemistry, 44, 5390-5401.
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