Cited by 13,404RNA and protein synthesis mechanismsProtein Structure and DynamicsDNA and Nucleic Acid Chemistry

The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.

Mfold web server for nucleic acid folding and hybridization prediction

Open access

Zuker, M.·2003·Nucleic Acids Research

Open this paper in CoChat — free account Open PDF

Abstract

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gkg595

Cites

40 of 40 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

A comprehensive set of sequence analysis programs for the VAX
Devereux, J., Haeberli, P. E., & Smithies, O. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.1part1.387 · Cited by 14,222
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Self-citation
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
Zuker, M., & Stiegler, P. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.133 · Cited by 3,604
Self-citation
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.4.1460 · Cited by 2,791
Improved Estimation of Secondary Structure in Ribonucleic Acids
Tinoco, I., Borer, P. N., Dengler, B., Levine, M., Uhlenbeck, O. C., Crothers, D. M., & Gralla, J. D. (1973) · Nature New Biology · doi:10.1038/newbio246040a0 · Cited by 2,270
On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 1,998
Self-citation
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
Zuker, M., Mathews, D. H., & Turner, D. H. (1999) · Springer eBooks · doi:10.1007/978-94-011-4485-8_2 · Cited by 1,139
Self-citation
Improved predictions of secondary structures for RNA.
Jaeger, J. A., Turner, D. H., & Zuker, M. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.20.7706 · Cited by 817
Self-citation
Stability of ribonucleic acid double-stranded helices
Borer, P. N., Dengler, B., Tinoco, I., & Uhlenbeck, O. C. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90357-x · Cited by 762

Show all 40 references

Research works printed but not linked: 2

Waterman,M.S. (1978) Secondary structure of single-stranded nucleic acids. In Rota, G.-C. (ed.), Studies in Foundations and Combinatorics number 1 in Advances in Mathematics, Supplementary Studies. Academic Press, NY, pp. 167-212.
Sankoff,D., Kruskal,J.B., Mainville,S. and Cedergren,R.J. (1983) Fast algorithms to determine RNA secondary structures containing multiple loops. chapter 3. In Sankoff,D. and Kruskal,J.B. (eds), Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley Reading, MA, pp. 93-120.

Sorted by citations

Items 701–800 of 1,049

Rational Design of “Turn‐On” Allosteric DNAzyme Catalytic Beacons for Aqueous Mercury Ions with Ultrahigh Sensitivity and Selectivity
Liu, J., & Lu, Y. (2007) · Angewandte Chemie · doi:10.1002/ange.200702006 · Cited by 156
Altered expression profiles of microRNAs during TPA-induced differentiation of HL-60 cells
Kasashima, K., Nakamura, Y., & Kozu, T. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.07.130 · Cited by 155
Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms
Zhang, Z., Qi, S., Tang, N., Zhang, X., Chen, S., Zhu, P., Ma, L., Cheng, J., Xu, Y., Lu, M., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004553 · Cited by 160
Structure Determinants for Accurate Processing of miR172a in Arabidopsis thaliana
Werner, S., Wollmann, H., Schneeberger, K., & Weigel, D. (2009) · Current Biology · doi:10.1016/j.cub.2009.10.073 · Cited by 155
BCL-2 Translation Is Mediated via Internal Ribosome Entry during Cell Stress
Sherrill, K. W., Byrd, M. P., Eden, M. E. V., & Lloyd, R. E. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402727200 · Cited by 155
Genetic switchboard for synthetic biology applications
Callura, J. M., Cantor, C. R., & Collins, J. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203808109 · Cited by 155
MicroRNA-Mediated Down-Regulation of PRDM1/Blimp-1 in Hodgkin/Reed-Sternberg Cells: A Potential Pathogenetic Lesion in Hodgkin Lymphomas
Nie, K., Gomez, M. F., Landgraf, P., García, J. F., Liu, Y., Tan, L. H. C., Chadburn, A., Tuschl, T., Knowles, D. M., & Tam, W. (2008) · American Journal Of Pathology · doi:10.2353/ajpath.2008.080009 · Cited by 155
Cucumber mosaic virus suppressor 2b binds to AGO4‐related small RNAs and impairs AGO4 activities
Hamera, S., Song, X., Su, L., Chen, X., & Fang, R. (2011) · The Plant Journal · doi:10.1111/j.1365-313x.2011.04774.x · Cited by 155
On virus growth and form
Zandi, R., Dragnea, B. G., Travesset, A., & Podgornik, R. (2020) · Physics Reports · doi:10.1016/j.physrep.2019.12.005 · Cited by 154
A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA
Wingfield, L. K., Kotta‐Loizou, I., Özkan-Kotiloğlu, S., Gunning, A. P., & Coutts, R. H. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419225112 · Cited by 154
Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs
Dominguez, C., Fisette, J., Chabot, B., & Allain, F. H. ‐. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1814 · Cited by 165
Rational evolution of Cd 2+ -specific DNAzymes with phosphorothioate modified cleavage junction and Cd 2+ sensing
Huang, P. J., & Liu, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv519 · Cited by 153
Internal guide RNA interactions interfere with Cas9-mediated cleavage
Thyme, S. B., Akhmetova, L., Montague, T. G., Valen, E., & Schier, A. F. (2016) · Nature Communications · doi:10.1038/ncomms11750 · Cited by 154
Molecular characterization of a new serotype of duck hepatitis virus
Tseng, C.-H., & Tsai, H. (2007) · Virus Research · doi:10.1016/j.virusres.2007.01.012 · Cited by 154
Molecular analysis of duck hepatitis virus type 1 reveals a novel lineage close to the genus Parechovirus in the family Picornaviridae
Kim, M. C., Kwon, Y., Joh, S.-J., Lindberg, A., Kwon, J.-H., Kim, J., & Kim, S.-J. (2006) · Journal of General Virology · doi:10.1099/vir.0.81804-0 · Cited by 154
A Nanosensor for Transmembrane Capture and Identification of Single Nucleic Acid Molecules
Nakane, J., Wiggin, M., & Marziali, A. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.040212 · Cited by 154
Screening and Initial Binding Assessment of Fumonisin B1 Aptamers
McKeague, M., Bradley, C. R., Girolamo, A. D., Visconti, A., Miller, J. D., & DeRosa, M. C. (2010) · International Journal of Molecular Sciences · doi:10.3390/ijms11124864 · Cited by 153
The role of the precursor structure in the biogenesis of microRNA
Staręga‐Rosłan, J., Kościańska, E., Kozłowski, P., & Krzyżosiak, W. J. (2011) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-011-0726-2 · Cited by 158
Cyclin D1 and c-myc Internal Ribosome Entry Site (IRES)-dependent Translation Is Regulated by AKT Activity and Enhanced by Rapamycin through a p38 MAPK- and ERK-dependent Pathway
Shi, Y., Sharma, A., Wu, H., Lichtenstein, A. K., & Gera, J. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m407874200 · Cited by 153
Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species.
Böck, C., Krienitz, L., & Pröschold, T. (2011) · Fottea · doi:10.5507/fot.2011.028 · Cited by 153
Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification
Sharanowski, B. J., Dowling, A. P. G., & Sharkey, M. J. (2011) · Systematic Entomology · doi:10.1111/j.1365-3113.2011.00580.x · Cited by 153
PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease
Boele, J., Persson, H., Shin, J. W., Ishizu, Y., Newie, I., Søkilde, R., Hawkins, S. M., Coarfa, C., Ikeda, K., Takayama, K., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317751111 · Cited by 158
Candidate gene association studies: a comprehensive guide to useful in silicotools
Patnala, R., Clements, J. A., & Batra, J. (2013) · BMC Genetics · doi:10.1186/1471-2156-14-39 · Cited by 154
The ubiquitous hammerhead ribozyme
Hammann, C., Lupták, A., Perreault, J., & de la Peña, M. (2012) · RNA · doi:10.1261/rna.031401.111 · Cited by 157
Firefly genomes illuminate parallel origins of bioluminescence in beetles
Fallon, T. R., Lower, S. E., Chang, C.-H., Bessho‐Uehara, M., Martin, G. J., Bewick, A. J., Behringer, M. G., Debat, H., Wong, I., Day, J. C., et al. (2018) · eLife · doi:10.7554/elife.36495 · Cited by 153
Alu elements within human mRNAs are probable microRNA targets
Smalheiser, N. R., & Torvik, V. I. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.08.007 · Cited by 157
5′-Terminal Deletions Occur in Coxsackievirus B3 during Replication in Murine Hearts and Cardiac Myocyte Cultures and Correlate with Encapsidation of Negative-Strand Viral RNA
Kim, K.-S., Tracy, S., Tapprich, W. E., Bailey, J. M., Lee, C.-K., Kim, K., Barry, W. H., & Chapman, N. M. (2005) · Journal of Virology · doi:10.1128/jvi.79.11.7024-7041.2005 · Cited by 153
Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules
Wang, Y., Li, P., Cao, X., Wang, X., Zhang, A., & Li, X. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.11.140 · Cited by 152
Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L
Yi, D., & Kim, K. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035872 · Cited by 152
ADAR2-editing activity inhibits glioblastoma growth through the modulation of the CDC14B/Skp2/p21/p27 axis
Galeano, F., Rossetti, C., Tomaselli, S., Cifaldi, L., Lezzerini, M., Pezzullo, M., Boldrini, R., Massimi, L., Rocco, C. M. D., Locatelli, F., et al. (2012) · Oncogene · doi:10.1038/onc.2012.125 · Cited by 152
A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression.
Ausländer, S., Ketzer, P., & Hartig, J. (2010) · Molecular Biosystems · doi:10.1039/b923076a · Cited by 154
A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti–hepatitis C target
Wang, S., Min, Y., Wang, J.-Q., Liu, C., Fu, B., Wu, F., Wu, L., Qiao, Z., Song, Y., Xu, G.-H., et al. (2016) · Science Advances · doi:10.1126/sciadv.1501535 · Cited by 156
A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing
Hefferon, T. W., Groman, J. D., Yurk, C. E., & Cutting, G. R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400182101 · Cited by 152
Production and processing of aptamer microarrays
Collett, J. R., Cho, E. J., & Ellington, A. D. (2005) · Methods · doi:10.1016/j.ymeth.2005.05.009 · Cited by 152
RNA Recognition and Cleavage by the SARS Coronavirus Endoribonuclease
Bhardwaj, K., Sun, J., Holzenburg, A., Guarino, L. A., & Kao, C. C. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.06.021 · Cited by 151
The polyphasic analysis of two native Raphidiopsis isolates supports the unification of the genera Raphidiopsis and Cylindrospermopsis (Nostocales, Cyanobacteria)
Aguilera, A., Berrendero, E., Kaštovský, J., Echenique, R. O., & Salerno, G. L. (2018) · Phycologia · doi:10.2216/17-2.1 · Cited by 151
RNA Structure and Cellular Applications of Fluorescent Light‐Up Aptamers
Neubacher, S., & Hennig, S. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201806482 · Cited by 159
Assessment of Cas12a‐mediated gene editing efficiency in plants
Bernabé‐Orts, J. M., Casas‐Rodrigo, I., Minguet, E. G., Landolfi, V., García‐Carpintero, V., Gianoglio, S., Vázquez‐Vilar, M., Granell, A., & Orzáez, D. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13113 · Cited by 148
Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples
Darienko, T., Gustavs, L., Eggert, A., Wolf, W., & Pröschold, T. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127838 · Cited by 156
RNA-RNA and RNA-protein interactions in coronavirus replication and transcription
Sola, I., Mateos‐Gómez, P. A., Almazán, F., Zúñiga, S., & Enjuanes, L. (2011) · RNA Biology · doi:10.4161/rna.8.2.14991 · Cited by 152
Substrate-Specific Kinetics of Dicer-Catalyzed RNA Processing
Chakravarthy, S., Sternberg, S. H., Kellenberger, C. A., & Doudna, J. A. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.09.030 · Cited by 150
Interaction between the Cellular Protein eEF1A and the 3′-Terminal Stem-Loop of West Nile Virus Genomic RNA Facilitates Viral Minus-Strand RNA Synthesis
Davis, W. G., Blackwell, J. L., Shi, P., & Brinton, M. A. (2007) · Journal of Virology · doi:10.1128/jvi.00531-07 · Cited by 150
Selection of aptamers against Ara h 1 protein for FO-SPR biosensing of peanut allergens in food matrices
Tran, T. D., Knez, K., Janssen, K. P. F., Pollet, J. B. K., Spasić, D., & Lammertyn, J. (2012) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2012.12.022 · Cited by 150
Identification and characterization of miRNAs expressed in the bovine ovary
Hossain, M. M., Ghanem, N., Hoelker, M., Rings, F., Phatsara, C., Tholen, E., Schellander, K., & Tesfaye, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-443 · Cited by 156
Innovative engineering and sensing strategies for aptamer-based small-molecule detection
Alkhamis, O., Canoura, J., Yu, H., Liu, Y., & Xiao, Y. (2019) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2019.115699 · Cited by 150
Artificial Intelligence in Aptamer–Target Binding Prediction
Chen, Z., Hu, L., Zhang, B., Lü, A., Wang, Y., Yu, Y., & Zhang, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073605 · Cited by 150
Culture Isolation and Culture-Independent Clone Libraries Reveal New MarineSynechococcusEcotypes with Distinctive Light and N Physiologies
Ahlgren, N. A., & Rocap, G. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.00358-06 · Cited by 150
Pure multiple RNA secondary structure alignments: a progressive profile approach
Hochsmann, M., Voß, B., & Giegerich, R. (2004) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2004.11 · Cited by 150
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets
Barenboim, M., Zoltick, B. J., Guo, Y., & Weinberger, D. R. (2010) · Human Mutation · doi:10.1002/humu.21349 · Cited by 150
Conservation and divergence of microRNAs in Populus
Barakat, A., Wall, P. K., DiLoreto, S., dePamphilis, C. W., & Carlson, J. E. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-481 · Cited by 149
Computational approaches to RNA structure prediction, analysis, and design
Laing, C., & Tamar Schlick, A. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.015 · Cited by 154
Auto‐regulation of the circadian slave oscillator component At GRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation
Schöning, J. C., Streitner, C., Page, D. R., Hennig, S., Uchida, K., Wolf, E., Furuya, M., & Staiger, D. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03302.x · Cited by 149
Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection
Barreda-García, S., Miranda‐Castro, R., de-los-Santos-Álvarez, N., Miranda-Ordieres, A. J., & Lobo-Castañón, M. J. (2017) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-017-0620-3 · Cited by 149
A SARS‐CoV‐2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD‐Independent Mechanism**
Schmitz, A., Weber, A., Bayin, M., Breuers, S., Fieberg, V., Famulok, M., & Mayer, G. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202100316 · Cited by 152
Functional Analysis of luxS in the Probiotic Strain Lactobacillus rhamnosus GG Reveals a Central Metabolic Role Important for Growth and Biofilm Formation
Lebeer, S., Keersmaecker, S. C. J. D., Verhoeven, T. L. A., Fadda, A. A., Kathleen Marchal, D., & Vanderleyden, J. (2006) · Journal of Bacteriology · doi:10.1128/jb.01394-06 · Cited by 149
Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria
Rot, C., Goldfarb, I., Ilan, M., & Huchon, D. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-71 · Cited by 149
How RNA Unfolds and Refolds
Li, P. T. X., Vieregg, J., & Tinoco, I. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.061206.174353 · Cited by 149
Rare Autosomal Recessive Cardiac Valvular Form of Ehlers-Danlos Syndrome Results from Mutations in the COL1A2 Gene That Activate the Nonsense-Mediated RNA Decay Pathway
Schwarze, U., Hata, R.-I., McKusick, V. A., Shinkai, H., Hoyme, H. E., Pyeritz, R. E., & Byers, P. H. (2004) · The American Journal of Human Genetics · doi:10.1086/420794 · Cited by 180
Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas
Ibrahim, F., Rymarquis, L. A., Kim, E., Becker, J., Balassa, E., Green, P. J., & Cerutti, H. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912632107 · Cited by 144
Aptamer-based molecular recognition for biosensor development
Zhou, J., Battig, M. R., & Wang, Y. (2010) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-010-3987-y · Cited by 148
The sequence, structure and evolutionary features of HOTAIR in mammals
He, S., Liu, S., & Zhu, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-102 · Cited by 148
qPCR-Based Methods for Expression Analysis of miRNAs
Forero, D. A., González‐Giraldo, Y., Castro‐Vega, L. J., & Barreto, G. E. (2019) · BioTechniques · doi:10.2144/btn-2019-0065 · Cited by 154
Guidelines for Antisense Oligonucleotide Design and Insight Into Splice-modulating Mechanisms
Aartsma-Rus, A. M., van Vliet, L., Hirschi, M., Janson, A. A. M., Heemskerk, H., de Winter, C. L., de Kimpe, S. J., van Deutekom, J. C. T., Hoen, P. A. C. ’., & van Ommen, G. B. (2008) · Molecular Therapy · doi:10.1038/mt.2008.205 · Cited by 147
Structural basis for broad DNA-specificity in integron recombination
Macdonald, D. J., Demarre, G., Bouvier, M., Mazel, D., & Gopaul, D. N. (2006) · Nature · doi:10.1038/nature04643 · Cited by 148
First Snapshots of the HIV-1 RNA Structure in Infected Cells and in Virions
Paillart, J., Dettenhofer, M., Yu, X.-F., Ehresmann, C., Ehresmann, B., & Marquet, R. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m408294200 · Cited by 158
SIRT1 interacts with p73 and suppresses p73‐dependent transcriptional activity
Dai, J. M., Wang, Z. Y., Sun, D. C., Lin, R. X., & Wang, S. Q. (2006) · Journal of Cellular Physiology · doi:10.1002/jcp.20831 · Cited by 157
Epirubicin loaded super paramagnetic iron oxide nanoparticle-aptamer bioconjugate for combined colon cancer therapy and imaging in vivo
Jalalian, S. H., Taghdisi, S. M., Hamedani, N. S., Moosavian, S. A., Lavaee, P., Zandkarimi, M., Ghows, N., Jaafari, M. R., Naghibi, S., Danesh, N. M., et al. (2013) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2013.06.015 · Cited by 147
Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction
Navarro, B., Pantaleo, V., Gisel, A., Moxon, S., Dalmay, T., Bisztray, G., Serio, F. D., & Burgyán, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007686 · Cited by 149
A flow cytometry-based screen for synthetic riboswitches
Lynch, S. A., & Gallivan, J. P. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn924 · Cited by 152
Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean
Ahlgren, N. A., & Rocap, G. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00213 · Cited by 152
Pseudo-nitzschia pungens (Bacillariophyceae): A cosmopolitan diatom species?
Casteleyn, G., Chepurnov, V. A., Leliaert, F., Mann, D. G., Bates, S. S., Lundholm, N., Rhodes, L. L., Sabbe, K., & Vyverman, W. (2007) · Harmful Algae · doi:10.1016/j.hal.2007.08.004 · Cited by 146
Targeting the PD-1/PD-L1 Immune Evasion Axis With DNA Aptamers as a Novel Therapeutic Strategy for the Treatment of Disseminated Cancers
Prodeus, A., Abdul‐Wahid, A., Fischer, N. W., Huang, E. H. ‐., Cydzik, M., & Gariépy, J. (2015) · Molecular Therapy — Nucleic Acids · doi:10.1038/mtna.2015.11 · Cited by 148
Force Unfolding Kinetics of RNA Using Optical Tweezers. I. Effects of Experimental Variables on Measured Results
Wen, J., Mañosas, M., Li, P. T. X., Smith, S. B., Bustamante, C., Ritort, F., & Tinoco, I. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.094052 · Cited by 146
RNA aptamer-based sensitive detection of SARS coronavirus nucleocapsid protein
Ahn, D., Jeon, I.-J., Kim, J. D., Song, M.-S., Han, S.-R., Lee, S., Jung, H., & Oh, J. (2009) · The Analyst · doi:10.1039/b906788d · Cited by 146
R2DT is a framework for predicting and visualising RNA secondary structure using templates
Sweeney, B., Hoksza, D., Nawrocki, E. P., Ribas, C. E., Madeira, F., Cannone, J. J., Gutell, R. R., Maddala, A., Meade, C. D., Williams, L. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23555-5 · Cited by 146
A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more
Rivas, E., Lang, R., & Eddy, S. R. (2012) · RNA · doi:10.1261/rna.030049.111 · Cited by 145
MicroRNA-125a Inhibits Autophagy Activation and Antimicrobial Responses during Mycobacterial Infection
Kim, J. K., Yuk, J., Kim, S. Y., Kim, T. S., Jin, H. S., Yang, C., & Jo, E. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1402557 · Cited by 149
Structured mRNAs Regulate Translation Initiation by Binding to the Platform of the Ribosome
Marzi, S., Myasnikov, A. G., Serganov, A., Ehresmann, C., Romby, P., Yusupov, M., & Klaholz, B. P. (2007) · Cell · doi:10.1016/j.cell.2007.07.008 · Cited by 155
Type II-C CRISPR-Cas9 Biology, Mechanism, and Application
Mir, A., Edraki, A., Lee, J., & Sontheimer, E. J. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00855 · Cited by 155
circDCUN1D4 suppresses tumor metastasis and glycolysis in lung adenocarcinoma by stabilizing TXNIP expression
Liang, Y., Wang, H., Chen, B., Mao, Q., Xia, W., Zhang, T., Song, X., Zhang, Z., Xu, L., Dong, G., et al. (2020) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2020.11.012 · Cited by 149
Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments
Bailey, S. F., Morales, L. A. A., & Kassen, R. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab141 · Cited by 144
Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation
Xu, F., Liu, Q., Chen, L., Kuang, J., Walk, T. C., Wang, J., & Liao, H. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-66 · Cited by 144
Switchable self-protected attractions in DNA-functionalized colloids
Leunissen, M. E., Dreyfus, R., Cheong, F. C., Grier, D. G., Sha, R., Seeman, N. C., & Chaikin, P. M. (2009) · Nature Materials · doi:10.1038/nmat2471 · Cited by 144
Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer targeted to the top of the terminal 3′ stem–loop structure
Holden, K. L., Stein, D. A., Pierson, T. C., Ahmed, A. A., Clyde, K., Iversen, P. L., & Harris, E. (2005) · Virology · doi:10.1016/j.virol.2005.08.034 · Cited by 144
The microRNAs of Epstein–Barr Virus are expressed at dramatically differing levels among cell lines
Pratt, Z. L., Kuzembayeva, M., Sengupta, S., & Sugden, B. (2009) · Virology · doi:10.1016/j.virol.2009.01.006 · Cited by 143
Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
Xu, Q., Liu, Y., Zhu, A., Wu, X., Ye, J., Yu, K., Guo, W., & Deng, X. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-246 · Cited by 143
MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots
Xia, R., Meyers, B. C., Liu, Z., Beers, E. P., Ye, S., & Liu, Z. (2013) · The Plant Cell · doi:10.1105/tpc.113.110957 · Cited by 143
Utility of 16S-23S ITS sequence and secondary structure for recognition of intrageneric and intergeneric limits within cyanobacterial taxa: Leptolyngbya corticola sp. nov. (Pseudanabaenaceae, Cyanobacteria)
Johansen, J. R., Kováčik, Ľ., Casamatta, D. A., Iková, K. F., & Kaštovský, J. (2011) · Nova Hedwigia · doi:10.1127/0029-5035/2011/0092-0283 · Cited by 145
siRNA Delivery with Chitosan: Influence of Chitosan Molecular Weight, Degree of Deacetylation, and Amine to Phosphate Ratio on in Vitro Silencing Efficiency, Hemocompatibility, Biodistribution, and in Vivo Efficacy
Alameh, M., Lavertu, M., Tran‐Khanh, N., Chang, C., Lesage, F., Bail, M., Darras, V., Chevrier, A., & Buschmann, M. D. (2017) · Biomacromolecules · doi:10.1021/acs.biomac.7b01297 · Cited by 142
A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants
Chen, J., Férec, C., & Cooper, D. N. (2006) · Human Genetics · doi:10.1007/s00439-006-0218-x · Cited by 143
Screening and Improvement of an Anti-VEGF DNA Aptamer
Nonaka, Y., Sode, K., & Ikebukuro, K. (2010) · Molecules · doi:10.3390/molecules15010215 · Cited by 142
Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA
Kang, M., Peterson, R. D., & Feigon, J. F. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.019 · Cited by 146
Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation
Hubé, F., Velasco, G., Rollin, J., Furling, D., & Francastel, C. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq833 · Cited by 142
Evidence for a microRNA expansion in the bilaterian ancestor
Prochnik, S. E., Rokhsar, D. S., & Aboobaker, A. A. (2006) · Development Genes and Evolution · doi:10.1007/s00427-006-0116-1 · Cited by 142
Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing
Cuperus, J. T., Montgomery, T. A., Fahlgren, N., Burke, R. T., Townsend, T. M., Sullivan, C. M., & Carrington, J. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913203107 · Cited by 142
Antisense oligonucleotides targeting translation inhibitory elements in 5′ UTRs can selectively increase protein levels
Liang, X., Sun, H., Shen, W., Wang, S., Yao, J., Migawa, M. T., Bui, H., Damle, S. S., Riney, S., Graham, M. J., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx632 · Cited by 144
RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes
Abatemarco, J., Sarhan, M. F., Wagner, J. M., Lin, J., Liu, L., Hassouneh, W., Yuan, S., Alper, H. S., & Abate, A. R. (2017) · Nature Communications · doi:10.1038/s41467-017-00425-7 · Cited by 142
Switching the activity of Cas12a using guide RNA strand displacement circuits
Oesinghaus, L., & Simmel, F. C. (2019) · Nature Communications · doi:10.1038/s41467-019-09953-w · Cited by 142
Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags
Qiu, C. X., Xie, F. L., Zhu, Y., Guo, K., Huang, S. Q., Nie, L., & Yang, Z. M. (2007) · Gene · doi:10.1016/j.gene.2007.01.034 · Cited by 140
New subtype of salmonid alphavirus (SAV), Togaviridae, from Atlantic salmon Salmo salar and rainbow trout Oncorhynchus mykiss in Norway
Hodneland, K., Bratland, A., Christie, K. E., Endresen, C., & Nylund, A. (2005) · Diseases of Aquatic Organisms · doi:10.3354/dao066113 · Cited by 141

Authors: Zuker, M.
Affiliations: Rensselaer Polytechnic Institute (US)
Corresponding author: Zuker, M.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2003-07-01
Volume: 31
Issue: 13
Pages: 3406-3415
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkg595
PMC: PMC169194
OpenAlex: W2141157874
Cited by: 13,404
References: 40
Citations by year: 2026: 320 · 2025: 487 · 2024: 535 · 2023: 536 · 2022: 575 · 2021: 620 · 2020: 615 · 2019: 625 · 2018: 596 · 2017: 653 · 2016: 634 · 2015: 672 · 2014: 681 · 2013: 716 · 2012: 686
FWCI: 151.48
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Nucleic Acids Research (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (GM54250, R01GM054250)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: RNA secondary structure prediction, single-stranded nucleic acids, web application, graphical user interface
MeSH terms: Base Sequence, Computer Graphics, DNA, DNA, Single-Stranded, Models, Molecular, Nucleic Acid Conformation, Nucleic Acid Denaturation, Nucleic Acid Hybridization, RNA, Software, Thermodynamics, User-Computer Interface, Internet, Databases, Nucleic Acid

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Mfold web server for nucleic acid folding and hybridization prediction

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks