Mfold web server for nucleic acid folding and hybridization prediction

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

On Finding All Suboptimal Foldings of an RNA Molecule

Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 2,023 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Estimation of Secondary Structure in Ribonucleic Acids

Tinoco, I., Uhlenbeck, O. C., & Levine, M. (1971) · Nature · doi:10.1038/230362a0 · Cited by 686 · see citing works

Thermodynamics and NMR of Internal G·T Mismatches in DNA

Allawi, H. T., & SantaLucia, J. (1997) · Biochemistry · doi:10.1021/bi962590c · Cited by 623 · see citing works

Fast algorithm for predicting the secondary structure of single-stranded RNA.

Nussinov, R., & Jacobson, A. B. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.11.6309 · Cited by 607 · see citing works

Algorithms for Loop Matchings

Nussinov, R., Pieczenik, G., Griggs, J. R., & Kleitman, D. J. (1978) · SIAM Journal on Applied Mathematics · doi:10.1137/0135006 · Cited by 587 · see citing works

Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A·A, C·C, G·G, and T·T Mismatches

Peyret, N., Seneviratne, P. A., Allawi, H. T., & SantaLucia, J. (1999) · Biochemistry · doi:10.1021/bi9825091 · Cited by 570 · see citing works

Nomenclature for incompletely specified bases in nucleic acid sequences: rcommendations 1984

Cornish-Bowden, A. (1985) · Nucleic Acids Research · doi:10.1093/nar/13.9.3021 · Cited by 548 · see citing works

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., & Zuker, M. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.20.9218 · Cited by 466 · see citing works

Globin mRNA Sequences: Analysis of Base Pairing and Evolutionary ImplicationsPreprint

Salser, W. A. (1978) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1978.042.01.099 · Cited by 403 · see citing works

[20] Computer prediction of RNA structure

Zuker, M. (1989) · Methods in Enzymology · doi:10.1016/0076-6879(89)80106-5 · Cited by 388 · see citing works

[17] Predicting optimal and suboptimal secondary structure for RNA

Jaeger, J. A., Turner, D. H., & Zuker, M. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83019-6 · Cited by 382 · see citing works

SECONDARY STRUCTURE IN RIBONUCLEIC ACIDS

Doty, P. M., Boedtker, H., Fresco, J. R., Haselkorn, R., & Litt, M. J. (1959) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.45.4.482 · Cited by 366 · see citing works

Thermodynamic parameters for DNA sequences with dangling ends.

Bommarito, S., Peyret, N., & SantaLucia, J. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.9.1929 · Cited by 332 · see citing works

RNA secondary structure: a complete mathematical analysis

Waterman, M. S., & Smith, T. F. (1978) · Mathematical Biosciences · doi:10.1016/0025-5564(78)90099-8 · Cited by 270 · see citing works

Some Molecular Details of the Secondary Structure of Ribonucleic Acid

Fresco, J. R., Alberts, B., & Doty, P. M. (1960) · Nature · doi:10.1038/188098a0 · Cited by 256 · see citing works

Nearest-Neighbor Thermodynamics of Internal A·C Mismatches in DNA: Sequence Dependence and pH Effects

Allawi, H. T., & SantaLucia, J. (1998) · Biochemistry · doi:10.1021/bi9803729 · Cited by 255 · see citing works

Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA

Allawi, H. T., & SantaLucia, J. (1998) · Biochemistry · doi:10.1021/bi9724873 · Cited by 241 · see citing works

Thermodynamics of internal C.T mismatches in DNA.

Allawi, H., & SantaLucia, J. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.11.2694 · Cited by 237 · see citing works

Prediction of hybridization and melting for double-stranded nucleic acids.

Dimitrov, R., & Zuker, M. (2004) · Biophysical Journal · doi:10.1529/biophysj.103.020743 · Cited by 223 · see citing works

Prediction of RNA Secondary Structure by Energy Minimization

Zuker, M. (1994) · Humana Press eBooks · doi:10.1385/0-89603-276-0:267 · Cited by 201 · see citing works

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips

Fotin, A., Drobyshev, A. L., Proudnikov, D., Perov, A. N., & Mirzabekov, A. D. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.6.1515 · Cited by 195 · see citing works

Using reliability information to annotate RNA secondary structures

Zuker, M., & Jacobson, A. B. (1998) · RNA · doi:10.1017/s1355838298980116 · Cited by 174 · see citing works

OligoArray: genome-scale oligonucleotide design for microarrays

Rouillard, J., Herbert, C. J., & Zuker, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.3.486 · Cited by 162 · see citing works

Stability of RNA hairpin loops: A6-Cm-U6

Uhlenbeck, O. C., Borer, P. N., Dengler, B., & Tinoco, I. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90095-8 · Cited by 161 · see citing works

RNA Secondary Structure Prediction

Mathews, D. H., Turner, D. H., & Zuker, M. (2007) · Current Protocols in Nucleic Acid Chemistry · doi:10.1002/0471142700.nc1102s28 · Cited by 153 · see citing works

RNAML: A standard syntax for exchanging RNA information

Waugh, A., Gendron, P., Altman, R. B., Brown, J. W., Case, D. A., Gautheret, D., Harvey, S. C., Leontis, N. B., Westbrook, J., Westhof, É., et al. (2002) · RNA · doi:10.1017/s1355838202028017 · Cited by 102 · see citing works

‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA

Zuker, M., & Jacobson, A. B. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.14.2791 · Cited by 101 · see citing works

Prediction of RNA Secondary Structure

DeLisi, C., & Crothers, D. M. (1971) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.68.11.2682 · Cited by 81 · see citing works

Prediction of nucleic acid hybridization : Parameters and Algorithms

Peyret, N. (2000) · Human Biology · Cited by 77 · see citing works

An improved algorithm for nucleic acid secondary structure display

Bruccoleri, R. E., & Heinrich, G. (1988) · Computer applications in the biosciences · doi:10.1093/bioinformatics/4.1.167 · Cited by 72 · see citing works

RNA Secondary Structure Prediction

Mathews, D. H., Turner, D. H., & Watson, R. M. (2016) · Current Protocols in Nucleic Acid Chemistry · doi:10.1002/cpnc.19 · Cited by 48 · see citing works

The HCV Life Cycle: In vitro Tissue Culture Systems and Therapeutic Targets

Gerold, G., & Pietschmann, T. (2014) · Digestive Diseases · doi:10.1159/000360830 · Cited by 4,854 · see citing works

Human MicroRNA Targets

John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796 · see citing works

A unified classification system for eukaryotic transposable elements

Wicker, T., Sabot, F., Hua‐Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A. J., Leroy, P., Morgante, M., Panaud, O., et al. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2165 · Cited by 3,021 · see citing works

Efficient genome editing in zebrafish using a CRISPR-Cas system

Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works

Asymmetry in the Assembly of the RNAi Enzyme Complex

Schwarz, D. S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., & Zamore, P. D. (2003) · Cell · doi:10.1016/s0092-8674(03)00759-1 · Cited by 2,323 · see citing works

In vivo genome editing using Staphylococcus aureus Cas9

Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687 · see citing works

Fast and effective prediction of microRNA/target duplexes

REHMSMEIER, M., STEFFEN, P., HÖCHSMANN, M., & GIEGERICH, R. (2004) · RNA · doi:10.1261/rna.5248604 · Cited by 2,560 · see citing works

Functional Nucleic Acid Sensors

Liu, J., Cao, Z. C., & Lu, Y. (2009) · Chemical Reviews · doi:10.1021/cr030183i · Cited by 2,188 · see citing works

Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis[W]

Sunkar, R., & Zhu, J. (2004) · The Plant Cell · doi:10.1105/tpc.104.022830 · Cited by 1,936 · see citing works

Control of leaf morphogenesis by microRNAs

Palatnik, J. F., Allen, E. M., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., & Weigel, D. (2003) · Nature · doi:10.1038/nature01958 · Cited by 1,833 · see citing works

Dynamic DNA nanotechnology using strand-displacement reactions

Zhang, D. Y., & Seelig, G. (2011) · Nature Chemistry · doi:10.1038/nchem.957 · Cited by 1,785 · see citing works

A pancreatic islet-specific microRNA regulates insulin secretion

Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., MacDonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P., et al. (2004) · Nature · doi:10.1038/nature03076 · Cited by 2,102 · see citing works

Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches

Beermann, J., Piccoli, M.-T., Viereck, J., & Thum, T. (2016) · Physiological Reviews · doi:10.1152/physrev.00041.2015 · Cited by 1,727 · see citing works

Specificity of microRNA target selection in translational repressionPreprint

Doench, J. G., & Sharp, P. A. (2004) · Genes & Development · doi:10.1101/gad.1184404 · Cited by 1,642 · see citing works

The evolution of gene regulation by transcription factors and microRNAs

Chen, K., & Rajewsky, N. (2007) · Nature Reviews Genetics · doi:10.1038/nrg1990 · Cited by 1,547 · see citing works

miR-145 and miR-143 regulate smooth muscle cell fate and plasticity

Cordes, K. R., Sheehy, N. T., White, M. P., Berry, E. C., Morton, S. U., Muth, A. N., Lee, T.-H., Miano, J. M., Ivey, K. N., & Srivastava, D. (2009) · Nature · doi:10.1038/nature08195 · Cited by 1,585 · see citing works

Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis

Zhao, Y. B., Samal, E., & Srivastava, D. P. (2005) · Nature · doi:10.1038/nature03817 · Cited by 1,556 · see citing works

Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex

Han, J., Lee, Y., Yeom, K., Nam, J., Heo, I., Rhee, J., Sohn, S. Y., Cho, Y., Zhang, B.-T., & Kim, V. N. (2006) · Cell · doi:10.1016/j.cell.2006.03.043 · Cited by 1,552 · see citing works

The developmental transcriptome of Drosophila melanogaster

Graveley, B. R., Brooks, A. N., Carlson, J. W., Duff, M. O., Landolin, J. M., Yang, L. C., Artieri, C. G., van Baren, M. J., Boley, N. P., Booth, B. W., et al. (2010) · Nature · doi:10.1038/nature09715 · Cited by 1,487 · see citing works

Specific effects of microRNAs on the plant transcriptome

Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M., & Weigel, D. (2005) · Developmental Cell · doi:10.1016/j.devcel.2005.01.018 · Cited by 1,467 · see citing works

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

Zhang, D. Y., & Winfree, E. (2009) · Journal of the American Chemical Society · doi:10.1021/ja906987s · Cited by 1,447 · see citing works

SELEX—A (r)evolutionary method to generate high-affinity nucleic acid ligands

Stoltenburg, R., Reinemann, C., & Strehlitz, B. (2007) · Biomolecular Engineering · doi:10.1016/j.bioeng.2007.06.001 · Cited by 1,432 · see citing works

The current state and future directions of RNAi-based therapeutics

Setten, R. L., Rossi, J. J., & Han, S.-P. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0017-4 · Cited by 1,443 · see citing works

Codon bias and heterologous protein expression

Gustafsson, C., Govindarajan, S., & Minshull, J. (2004) · Trends in Biotechnology · doi:10.1016/j.tibtech.2004.04.006 · Cited by 1,330 · see citing works

RNA Mimics of Green Fluorescent Protein

Paige, J. S., Wu, K., & Jaffrey, S. R. (2011) · Science · doi:10.1126/science.1207339 · Cited by 1,353 · see citing works

Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis

Schwab, R., Ossowski, S., Riester, M., Warthmann, N., & Weigel, D. (2006) · The Plant Cell · doi:10.1105/tpc.105.039834 · Cited by 1,348 · see citing works

OligoCalc: an online oligonucleotide properties calculator

Kibbe, W. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm234 · Cited by 1,300 · see citing works

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

Gong, C., & Maquat, L. E. (2011) · Nature · doi:10.1038/nature09701 · Cited by 1,261 · see citing works

Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Zhang, D. Y., Turberfield, A. J., Yurke, B., & Winfree, E. (2007) · Science · doi:10.1126/science.1148532 · Cited by 1,245 · see citing works

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Станиславович, М. Л., Joung, J., Konermann, S., Severinov, K., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.008 · Cited by 1,221 · see citing works

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-7 · Cited by 1,199 · see citing works

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.132 · Cited by 1,193 · see citing works

Specific expression of long noncoding RNAs in the mouse brain

Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706729105 · Cited by 1,103 · see citing works

Preparation of aptamer-linked gold nanoparticle purple aggregates for colorimetric sensing of analytes

Liu, J., & Lu, Y. (2006) · Nature Protocols · doi:10.1038/nprot.2006.38 · Cited by 1,126 · see citing works

microRNA target predictions in animals

Rajewsky, N. (2006) · Nature Genetics · doi:10.1038/ng1798 · Cited by 1,092 · see citing works

mRNA is an endogenous ligand for toll-like receptor 3

Karikó, K., Ni, H., Capodici, J., Lamphier, M., & Weissman, D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310175200 · Cited by 1,062 · see citing works

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

Collin, D., Ritort, F., Jarzynski, C., Smith, S. B., Tinoco, I., & Bustamante, C. (2005) · Nature · doi:10.1038/nature04061 · Cited by 1,051 · see citing works

UNAFold

Markham, N. R., & Zuker, M. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-429-6_1 · Cited by 1,026 · see citing works

A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron

Shih, W. M., Quispe, J. D., & Joyce, G. F. (2004) · Nature · doi:10.1038/nature02307 · Cited by 989 · see citing works

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Leppek, K., Das, R., & Barna, M. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.103 · Cited by 949 · see citing works

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz, M., Siprashvili, Z., Chu, C., Webster, D., Zehnder, A., Qu, K., Lee, C. S., Flockhart, R., Groff, A., Chow, J. M., et al. (2012) · Nature · doi:10.1038/nature11661 · Cited by 920 · see citing works

The colorectal microRNAome

Cummins, J. M., He, Y., Leary, R. J., Pagliarini, R. A., Diaz, L. A., Sjöblom, T., Barad, O., Bentwich, Z., Szafranska, A. E., Labourier, E., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511155103 · Cited by 927 · see citing works

A primer to scaffolded DNA origami

Castro, C. E., Kilchherr, F., Kim, D., Lin-Shiao, E., Wauer, T., Wortmann, P., Bathe, M., & Dietz, H. (2011) · Nature Methods · doi:10.1038/nmeth.1570 · Cited by 926 · see citing works

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

Liu, B., Sun, L., Liu, Q., Gong, C., Yao, Y., Lv, X., Lin, L., Yao, H., Su, F., Li, D., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.02.004 · Cited by 906 · see citing works

RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III–transcribed RNA intermediate

Ablasser, A., Bauernfeind, F. G., Hartmann, G., Latz, E., Fitzgerald, K. A., & Hornung, V. (2009) · Nature Immunology · doi:10.1038/ni.1779 · Cited by 892 · see citing works

Machine learning in bioinformatics

Larrañaga, P., Calvo, B., Santana, R., Bielza, C., Galdiano, J., Inza, I., Lozano, J. A., Armañanzas, R., Santafé, G., Pérez, A., et al. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbk007 · Cited by 867 · see citing works

Control of Root Cap Formation by MicroRNA-Targeted Auxin Response Factors in Arabidopsis

Wang, J., Wang, L.-J., Mao, Y., Cai, W., Xue, H., & Chen, X. (2005) · The Plant Cell · doi:10.1105/tpc.105.033076 · Cited by 855 · see citing works

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

Rouskin, S., Zubradt, M. M., Stefan Washietl, A., Kellis, M., & Weissman, J. S. (2013) · Nature · doi:10.1038/nature12894 · Cited by 860 · see citing works

Human Catechol- <i>O</i> -Methyltransferase Haplotypes Modulate Protein Expression by Altering mRNA Secondary Structure

Nackley, A. G., Shabalina, S. A., Tchivileva, I. E., Satterfield, K., Korchynskyi, O., Makarov, S. S., Maixner, W., & Diatchenko, L. (2006) · Science · doi:10.1126/science.1131262 · Cited by 848 · see citing works

The RNA modification database, RNAMDB: 2011 update

Cantara, W. A., Crain, P. F., Rozenski, J., McCloskey, J. A., Harris, K. A., Zhang, X., Vendeix, F. A. P., Fabris, D., & Agris, P. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1028 · Cited by 822 · see citing works

Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution

Filonov, G. S., Moon, J. D., Svensen, N., & Jaffrey, S. R. (2014) · Journal of the American Chemical Society · doi:10.1021/ja508478x · Cited by 780 · see citing works

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Chiang, H. R., Schoenfeld, L. W., Ruby, J. G., Auyeung, V. C., Spies, N., Baek, D., Johnston, W. K., Russ, C., Luo, S., Babiarz, J. E., et al. (2010) · Genes &amp; Development · doi:10.1101/gad.1884710 · Cited by 732 · see citing works

Microarray analysis of microRNA expression in the developing mammalian brain

Miska, E. A., Alvarez-Saavedra, E., Townsend, M., Yoshii, A., Šestan, N., Rakic, P., Constantine-Paton, M., & Horvitz, H. R. (2004) · Genome Biology · doi:10.1186/gb-2004-5-9-r68 · Cited by 651 · see citing works

Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing

Jackson, A. L., Burchard, J., Leake, D., Reynolds, A., Schelter, J. M., Guo, J., Johnson, J. M., Lim, L. P., Karpilow, J. M., Nichols, K. E., et al. (2006) · RNA · doi:10.1261/rna.30706 · Cited by 790 · see citing works

Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus

Horvath, P., Romero, D. A., Coûté-Monvoisin, A.-C., Richards, M., Deveau, H., Moineau, S., Boyaval, P., Fremaux, C., & Barrangou, R. (2007) · Journal of Bacteriology · doi:10.1128/jb.01415-07 · Cited by 775 · see citing works

Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity

Du, W. W., Fang, L., Yang, W., Wu, N., Awan, F. M., Yang, Z., & Yang, B. B. (2016) · Cell Death and Differentiation · doi:10.1038/cdd.2016.133 · Cited by 777 · see citing works

A practical approach to RT-qPCR—Publishing data that conform to the MIQE guidelines

Taylor, S., Wakem, M., Dijkman, G., Alsarraj, M., & Nguyen, M. (2010) · Methods · doi:10.1016/j.ymeth.2010.01.005 · Cited by 776 · see citing works

A Synthetic DNA Walker for Molecular Transport

Shin, J., & Pierce, N. A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja047543j · Cited by 774 · see citing works

Analysis of Thermal Melting Curves

Mergny, J., & Lacroix, L. (2003) · Oligonucleotides · doi:10.1089/154545703322860825 · Cited by 772 · see citing works

Structural imprints in vivo decode RNA regulatory mechanisms

Spitale, R. C., Flynn, R. A., Zhang, Q. C., Crisalli, P., Lee, B., Jung, J., Kuchelmeister, H. Y., Batista, P. J., Torre, E. A., Kool, E. T., et al. (2015) · Nature · doi:10.1038/nature14263 · Cited by 745 · see citing works

Arabidopsis microRNA167controls patterns ofARF6andARF8expression, and regulates both female and male reproduction

Wu, M., Tian, Q., & Reed, J. W. (2006) · Development · doi:10.1242/dev.02602 · Cited by 768 · see citing works

Ecological Genomics of Marine Picocyanobacteria

Scanlan, D. J., Ostrowski, M. D., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I. T., & Partensky, F. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00035-08 · Cited by 739 · see citing works

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

Grimson, A., Srivastava, M., Fahey, B., Woodcroft, B. J., Chiang, H. R., King, N., Degnan, B. M., Rokhsar, D. S., & Bartel, D. P. (2008) · Nature · doi:10.1038/nature07415 · Cited by 725 · see citing works

Synthetic genetic polymers capable of heredity and evolution

Pinheiro, V. B., Taylor, A. I., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J. C., Wengel, J., Peak-Chew, S.-Y., McLaughlin, S. H., et al. (2012) · Science · doi:10.1126/science.1217622 · Cited by 730 · see citing works

Conservation and divergence of plant microRNA genes

Zhang, B., Pan, X., Cannon, C. H., Cobb, G. P., & Anderson, T. A. (2006) · The Plant Journal · doi:10.1111/j.1365-313x.2006.02697.x · Cited by 717 · see citing works

The emerging field of RNA nanotechnology

Guo, P. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.231 · Cited by 722 · see citing works

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

Wilusz, J. E., Freier, S. M., & Spector, D. L. (2008) · Cell · doi:10.1016/j.cell.2008.10.012 · Cited by 721 · see citing works

MEG3 noncoding RNA: a tumor suppressor

Zhou, Y., Zhang, X., & Klibanski, A. (2012) · Journal of Molecular Endocrinology · doi:10.1530/jme-12-0008 · Cited by 717 · see citing works

Plant microRNA: A small regulatory molecule with big impact

Zhang, B., Pan, X., Cobb, G. P., & Anderson, T. A. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.10.036 · Cited by 705 · see citing works

Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686 · see citing works

Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686 · see citing works

Gene silencing in plants using artificial microRNAs and other small RNAs

Ossowski, S., Schwab, R., & Weigel, D. (2008) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03328.x · Cited by 679 · see citing works

Selection of reliable reference genes for gene expression studies in peach using real-time PCR

Tong, Z., Gao, Z., Wang, F., Zhou, J. C., & Zhang, Z. (2009) · BMC Molecular Biology · doi:10.1186/1471-2199-10-71 · Cited by 665 · see citing works

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

Fazal, F. M., Han, S., Parker, K. R., Kaewsapsak, P., Xu, J., Boettiger, A. N., Chang, H. Y., & Ting, A. Y. (2019) · Cell · doi:10.1016/j.cell.2019.05.027 · Cited by 648 · see citing works

Regulation of p53 Translation and Induction after DNA Damage by Ribosomal Protein L26 and Nucleolin

Takagi, M., Absalon, M. J., McLure, K. G., & Kastan, M. B. (2005) · Cell · doi:10.1016/j.cell.2005.07.034 · Cited by 656 · see citing works

Splicing mutations in human genetic disorders: Examples, detection, and confirmation

Anna, A., & Monika, G. (2018) · Journal of Applied Genetics · doi:10.1007/s13353-018-0444-7 · Cited by 657 · see citing works

Activation of p53 by MEG3 Non-coding RNA

Zhou, Y., Zhong, Y., Wang, Y., Zhang, X., Batista, D. L., Gejman, R., Ansell, P. J., Zhao, J. C., Weng, C., & Klibanski, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702029200 · Cited by 654 · see citing works

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

Li, J., Macdonald, J., & von Stetten, F. (2018) · The Analyst · doi:10.1039/c8an01621f · Cited by 648 · see citing works

Molecular Engineering of DNA: Molecular Beacons

Wang, K., Tang, Z., Yang, C. J., Kim, Y., Fang, X., Li, W., Wu, Y., Medley, C. D., Cao, Z. C., Li, J., et al. (2008) · Angewandte Chemie International Edition · doi:10.1002/anie.200800370 · Cited by 640 · see citing works

A Novel Gene, erm (41), Confers Inducible Macrolide Resistance to Clinical Isolates of Mycobacterium abscessus but Is Absent from Mycobacterium chelonae

Nash, K. A., Brown‐Elliott, B. A., & Wallace, R. J. (2009) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01275-08 · Cited by 639 · see citing works

Accelerated Color Change of Gold Nanoparticles Assembled by DNAzymes for Simple and Fast Colorimetric Pb2+ Detection

Liu, J., & Lu, Y. (2004) · Journal of the American Chemical Society · doi:10.1021/ja046628h · Cited by 635 · see citing works

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

Turner, D. H., & Mathews, D. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp892 · Cited by 575 · see citing works

SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells

Sullivan, C. S., Grundhoff, A. T., Tevethia, S. S., Pipas, J. M., & Ganem, D. (2005) · Nature · doi:10.1038/nature03576 · Cited by 625 · see citing works

CONTRAfold: RNA secondary structure prediction without physics-based models

Do, C., Woods, D. A., & Batzoglou, S. (2006) · Intelligent Systems in Molecular Biology · doi:10.1093/bioinformatics/btl246 · Cited by 623 · see citing works

MicroRNA regulation of plant innate immune receptors

Li, F., Pignatta, D., Bendix, C., Brunkard, J. O., Cohn, M. M., Tung, J., Sun, H.-Y., Kumar, P., & Baker, B. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118282109 · Cited by 619 · see citing works

The Balance between the MIR164A and CUC2 Genes Controls Leaf Margin Serration in Arabidopsis

Nikovics, K., Blein, T., Peaucelle, A., Ishida, T., Morin, H., Aida, M., & Laufs, P. (2006) · The Plant Cell · doi:10.1105/tpc.106.045617 · Cited by 612 · see citing works

An Aptamer–Doxorubicin Physical Conjugate as a Novel Targeted Drug‐Delivery Platform

Bagalkot, V., Farokhzad, O. C., Langer, R., & Jon, S. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200602251 · Cited by 614 · see citing works

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 584 · see citing works

Differential Uptake of Functionalized Polystyrene Nanoparticles by Human Macrophages and a Monocytic Cell Line

Lunov, O., Syrovets, T., Loos, C., Beil, J., Delacher, M., Tron, K., Nienhaus, G. U., Musyanovych, A., Mailänder, V., Landfester, K., et al. (2011) · ACS Nano · doi:10.1021/nn2000756 · Cited by 599 · see citing works

Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsis

Lu, S., Sun, Y., Shi, R., Clark, C. M., Li, L., & Chiang, V. L. (2005) · The Plant Cell · doi:10.1105/tpc.105.033456 · Cited by 597 · see citing works

Targeting RNA structures with small molecules

Childs‐Disney, J. L., Yang, X., Gibaut, Q. M. R., Tong, Y., Batey, R., & Disney, M. D. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00521-4 · Cited by 599 · see citing works

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 International Edition · doi:10.1002/anie.200702006 · Cited by 596 · see citing works

HTLV-I basic leucine zipper factor gene mRNA supports proliferation of adult T cell leukemia cells

Satou, Y., Yasunaga, J., Yoshida, M., & Matsuoka, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507631103 · Cited by 594 · see citing works

Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells

Cai, X., Lu, S., Zhang, Z., Gonzalez, C. M., Damania, B., & Cullen, B. R. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408192102 · Cited by 586 · see citing works

Genetic variants of miRNA sequences and non–small cell lung cancer survival

Hu, Z., Chen, J., Tian, T., Zhou, X., Gu, H., Xu, L., Zeng, Y., Miao, R., Jin, G., Ma, H., et al. (2008) · Journal of Clinical Investigation · doi:10.1172/jci34934 · Cited by 586 · see citing works

New CRISPR–Cas systems from uncultivated microbes

Burstein, D. E., Harrington, L. B., Strutt, S. C., Probst, A. J., Anantharaman, K., Thomas, B. C., Doudna, J. A., & Banfield, J. F. (2016) · Nature · doi:10.1038/nature21059 · Cited by 574 · see citing works

Structure of the Yeast Mitochondrial Large Ribosomal Subunit

Amunts, A., Brown, A., Bai, X., Llacer, J. L., Hussain, T., Emsley, P., Long, F., Murshudov, G. N., Scheres, S. H. W., & Ramakrishnan, V. (2014) · Science · doi:10.1126/science.1249410 · Cited by 580 · see citing works

A transfer-RNA-derived small RNA regulates ribosome biogenesis

Kim, H. K., Fuchs, G., Wang, S., Wei, W., Zhang, Y., Park, H., Roy‐Chaudhuri, B., Li, P., Xu, J., Chu, K. C., et al. (2017) · Nature · doi:10.1038/nature25005 · Cited by 579 · see citing works

Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testesPreprint

Watanabe, T., Takeda, A., Tsukiyama, T., Mise, K., Okuno, T., Sasaki, H., Minami, N., & Imai, H. (2006) · Genes & Development · doi:10.1101/gad.1425706 · Cited by 577 · see citing works

Nucleic Acid Based Molecular Devices

Krishnan, Y., & Simmel, F. C. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.200907223 · Cited by 572 · see citing works

CENTROIDFOLD: a web server for RNA secondary structure prediction

Sato, K., Hamada, M., Asai, K., & Mitsuyama, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp367 · Cited by 334 · see citing works

HyperFold

Bindewald, E., & Shapiro, B. A. (2022) · CRC Press eBooks · doi:10.1201/9781003001560-18

Modeling RNA secondary structure

Gray, S. G. (2001) · Genome biology · doi:10.1186/gb-2001-2-8-reports2007 · Cited by 5 · see citing works

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

Xu, X., Zhao, P., & Chen, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0107504 · Cited by 179 · see citing works

RNAstructure: web servers for RNA secondary structure prediction and analysis

Bellaousov, S., Reuter, J. S., Seetin, M. G., & Mathews, D. H. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt290 · Cited by 434 · see citing works