Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine

Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Pérez Marc, G., Moreira, E. D., Zerbini, C., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2034577 · Cited by 14,592

Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine

Baden, L. R., El Sahly, H. M., Essink, B., Kotloff, K., Frey, S., Novak, R., Diemert, D., Spector, S. A., Rouphael, N., Creech, C. B., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2035389 · Cited by 10,119

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566

Characteristics of SARS-CoV-2 and COVID-19

Hu, B., Guo, H., Zhou, P., & Shi, Z.-L. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00459-7 · Cited by 5,291

ViennaRNA Package 2.0

Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098

An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs

Kozak, M. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.20.8125 · Cited by 5,090

mRNA vaccines — a new era in vaccinology

Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.243 · Cited by 4,667

The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

Sharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992

The scanning model for translation: an update.

Kozak, M. (1989) · The Journal of Cell Biology · doi:10.1083/jcb.108.2.229 · Cited by 3,485

Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA

Karikó, K., Buckstein, M., Ni, H., & Weissman, D. (2005) · Immunity · doi:10.1016/j.immuni.2005.06.008 · Cited by 2,728

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

Sahin, U., Derhovanessian, E., Miller, M., Kloke, B.-P., Simon, P., Löwer, M., Bukur, V., Tadmor, A. D., Luxemburger, U., Schrörs, B., et al. (2017) · Nature · doi:10.1038/nature23003 · Cited by 2,488

mRNA-based therapeutics--developing a new class of drugs

Sahin, U., Karikó, K., & Türeci, Ö. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4278 · Cited by 2,474

5'-Triphosphate RNA Is the Ligand for RIG-I

Hornung, V., Ellegast, J., Kim, S., Brzózka, K., Jung, A., Kato, H., Poeck, H., Akira, S., Conzelmann, K.-K., Schlee, M., et al. (2006) · Science · doi:10.1126/science.1132505 · Cited by 2,474

The Architecture of SARS-CoV-2 Transcriptome

Kim, D., Lee, J.-Y., Yang, J.-S., Kim, J. W., Kim, V. N., & Chang, H. (2020) · Cell · doi:10.1016/j.cell.2020.04.011 · Cited by 2,123

RNAstructure: software for RNA secondary structure prediction and analysis

Reuter, J. S., & Mathews, D. H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-129 · Cited by 2,018

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

Karikó, K., Muramatsu, H., Welsh, F. A., Ludwig, J., Kato, H., Akira, S., & Weissman, D. (2008) · Molecular Therapy · doi:10.1038/mt.2008.200 · Cited by 1,930

cocor: A Comprehensive Solution for the Statistical Comparison of Correlations

Diedenhofen, B., & Musch, J. (2015) · PLOS ONE · doi:10.1371/journal.pone.0121945 · Cited by 1,919

SARS-CoV-2 mRNA Vaccine Design Enabled by Prototype Pathogen Preparedness

Corbett, K. S., Edwards, D. K., Leist, S. R., Abiona, O. M., Boyoglu-Barnum, S., Gillespie, R. A., Himansu, S., Schäfer, A., Ziwawo, C. T., DiPiazza, A. T., et al. (2020) · Nature · doi:10.1038/s41586-020-2622-0 · Cited by 1,615

Engineered Luciferase Reporter from a Deep Sea Shrimp Utilizing a Novel Imidazopyrazinone Substrate

Hall, M. P., Unch, J., Binkowski, B. F., Valley, M. P., Butler, B. L., Wood, M. G., Otto, P., Zimmerman, K., Vidugiris, G. J. A., Machleidt, T., et al. (2012) · ACS Chemical Biology · doi:10.1021/cb3002478 · Cited by 1,588

A unifying model for mTORC1-mediated regulation of mRNA translation

Thoreen, C. C., Chantranupong, L., Keys, H. R., Wang, T., Gray, N. S., & Sabatini, D. M. (2012) · Nature · doi:10.1038/nature11083 · Cited by 1,477

The translational landscape of mTOR signalling steers cancer initiation and metastasis

Hsieh, A. C., Liu, Y., Edlind, M. P., Ingolia, N. T., Janes, M. R., Sher, A., Shi, E. Y., Stumpf, C. R., Christensen, C., Bonham, M. J., et al. (2012) · Nature · doi:10.1038/nature10912 · Cited by 1,313

The highways and byways of mRNA decay

Garneau, N. L., Wilusz, J., & Wilusz, C. J. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2104 · Cited by 1,294

From unwinding to clamping — the DEAD box RNA helicase family

Linder, P., & Jankowsky, E. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3154 · Cited by 1,177

Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery

Kowalski, P. S., Rudra, A., Miao, L., & Anderson, D. G. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2019.02.012 · Cited by 1,127

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

Codon optimality, bias and usage in translation and mRNA decay

Hanson, G., & Coller, J. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.91 · Cited by 825

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2014) · Nature · doi:10.1038/nature12756 · Cited by 775

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

Anderson, B. R., Muramatsu, H., Nallagatla, S. R., Bevilacqua, P. C., Sansing, L. H., Weissman, D., & Karikó, K. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq347 · Cited by 682

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E., & Weeks, K. M. (2014) · Nature Methods · doi:10.1038/nmeth.3029 · Cited by 675

Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group

Li, Y., & Breaker, R. R. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990592p · Cited by 587

NanoLuc: A Small Luciferase Is Brightening Up the Field of Bioluminescence

England, C. G., Ehlerding, E. B., & Cai, W. (2016) · Bioconjugate Chemistry · doi:10.1021/acs.bioconjchem.6b00112 · Cited by 585

mRNA structure regulates protein expression through changes in functional half-life

Mauger, D. M., Cabral, B. J., Presnyak, V., Su, S. V., Reid, D. W., Goodman, B., Link, K., Khatwani, N., Reynders, J., Moore, M. J., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1908052116 · Cited by 555

What Are 3′ UTRs Doing?

Mayr, C. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034728 · Cited by 519

Addressing the Cold Reality of mRNA Vaccine Stability

Crommelin, D. J. A., Anchordoquy, T. J., Volkin, D. B., Jiskoot, W., & Mastrobattista, E. (2021) · Journal of Pharmaceutical Sciences · doi:10.1016/j.xphs.2020.12.006 · Cited by 517

Sequence-engineered mRNA without chemical nucleoside modifications enables an effective protein therapy in large animals

Thess, A., Grund, S., Mui, B. L., Hope, M. J., Baumhof, P., Fotin-Mleczek, M., & Schlake, T. (2015) · Molecular Therapy · doi:10.1038/mt.2015.103 · Cited by 513

mRNA Helicase Activity of the Ribosome

Takyar, S. S., Hickerson, R. P., & Noller, H. F. (2005) · Cell · doi:10.1016/j.cell.2004.11.042 · Cited by 508

Ribosome collisions trigger general stress responses to regulate cell fate

Wu, C. C.-C., Peterson, A. F., Zinshteyn, B., Regot, S., & Green, R. (2020) · Cell · doi:10.1016/j.cell.2020.06.006 · Cited by 503

The promise of mRNA vaccines: a biotech and industrial perspective

Jackson, N. A. C., Kester, K. E., Casimiro, D., Gurunathan, S., & DeRosa, F. (2020) · npj Vaccines · doi:10.1038/s41541-020-0159-8 · Cited by 498

A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tailsPreprint

Wilusz, J. E., JnBaptiste, C. K., Lu, L. Y., Kuhn, C., Joshua‐Tor, L., & Sharp, P. A. (2012) · Genes & Development · doi:10.1101/gad.204438.112 · Cited by 487

Rate-Limiting Steps in Yeast Protein Translation

Shah, P., Ding, Y., Niemczyk, M., Kudla, G., & Plotkin, J. B. (2013) · Cell · doi:10.1016/j.cell.2013.05.049 · Cited by 463

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

Zubradt, M., Gupta, P., Persad, S., Lambowitz, A. M., Weissman, J. S., & Rouskin, S. (2016) · Nature Methods · doi:10.1038/nmeth.4057 · Cited by 457

Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

Sample, P. J., Wang, B., Reid, D. W., Presnyak, V., McFadyen, I. J., Morris, D. R., & Seelig, G. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0164-5 · Cited by 442

The challenge and prospect of mRNA therapeutics landscape

Weng, Y., Li, C., Yang, T., Hu, B., Zhang, M., Guo, S., Xiao, H., Liang, X.-J., & Huang, Y. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107534 · Cited by 417

Stabilization of RNA stacking by pseudouridine

Davis, D. R. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.24.5020 · Cited by 399

Improving mRNA-Based Therapeutic Gene Delivery by Expression-Augmenting 3′ UTRs Identified by Cellular Library Screening

Orlandini von Niessen, A. G., Poleganov, M. A., Rechner, C., Plaschke, A., Kranz, L. M., Fesser, S., Diken, M., Löwer, M., Vallazza, B., Beissert, T., et al. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2018.12.011 · Cited by 365

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

Matoulkova, E., Michalova, E., Vojtesek, B., & Hrstka, R. (2012) · RNA Biology · doi:10.4161/rna.20231 · Cited by 357

Multi-epitope vaccines: a promising strategy against tumors and viral infections

Zhang, L. (2017) · Cellular and Molecular Immunology · doi:10.1038/cmi.2017.92 · Cited by 352

Control of mammalian translation by mRNA structure near caps

Babendure, J. R., Babendure, J. L., Ding, J.-H., & Tsien, R. Y. (2006) · RNA · doi:10.1261/rna.2309906 · Cited by 339

In-Line Probing Analysis of Riboswitches

Regulski, E. E., & Breaker, R. R. (2008) · Methods In Molecular Biology™ · doi:10.1007/978-1-59745-033-1_4 · Cited by 338

The ribosome uses two active mechanisms to unwind messenger RNA during translation

Qu, X., Wen, J., Lancaster, L., Noller, H. F., Bustamante, C., & Tinoco, I. (2011) · Nature · doi:10.1038/nature10126 · Cited by 327

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

Xue, S., Tian, S., Fujii, K., Kladwang, W., Das, R., & Barna, M. (2014) · Nature · doi:10.1038/nature14010 · Cited by 319

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

Huston, N. C., Wan, H., Strine, M. S., Tavares, R. D. C. A., Wilen, C. B., & Pyle, A. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.041 · Cited by 311

RNA design rules from a massive open laboratory

Lee, J., Kladwang, W., Lee, M. J., Cantu, D., Azizyan, M., Kim, H., Limpaecher, A., Gaikwad, S. M., Yoon, S., Treuille, A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313039111 · Cited by 303

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

Manfredonia, I., Nithin, C., Ponce-Salvatierra, A., Ghosh, P., Wirecki, T. K., Marinus, T., Ogando, N. S., Snijder, E. J., van Hemert, M. J., Bujnicki, J. M., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1053 · Cited by 283

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

Lan, T. C. T., Allan, M. F., Malsick, L. E., Woo, J. Z., Zhu, C., Zhang, F., Khandwala, S., Nyeo, S. S. Y., Sun, Y., Guo, J. U., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28603-2 · Cited by 267

The contribution of pseudouridine to stabilities and structure of RNAs

Kierzek, E., Malgowska, M., Lisowiec, J., Turner, D. H., Gdaniec, Z., & Kierzek, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1330 · Cited by 264

Decoding mRNA translatability and stability from the 5′ UTR

Jia, L., Mao, Y., Ji, Q., Dersh, D., Yewdell, J. W., & Qian, S.-B. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0465-x · Cited by 248

Multiple roles of the coding sequence 5′ end in gene expression regulation

Tuller, T., & Zur, H. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1313 · Cited by 206

3′ Cap-Independent Translation Enhancers of Plant Viruses

Simon, A. E., & Miller, W. A. (2013) · Annual Review of Microbiology · doi:10.1146/annurev-micro-092412-155609 · Cited by 204

Theoretical basis for stabilizing messenger RNA through secondary structure design

Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197

Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

Juszkiewicz, S., Slodkowicz, G., Lin, Z., Freire-Pritchett, P., Peak‐Chew, S., & Hegde, R. S. (2020) · eLife · doi:10.7554/elife.60038 · Cited by 170

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

Hickey, K. L., Dickson, K., Cogan, J. Z., Replogle, J. M., Schoof, M., D’Orazio, K. N., Sinha, N. K., Hussmann, J. A., Jost, M., Frost, A. S., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.007 · Cited by 162

High-throughput 5’ UTR engineering for enhanced protein production in non-viral gene therapies

Cao, J., Novoa, E. M., Zhang, Z., Chen, W. C. W., Liu, D., Choi, G. C. G., Wong, A. S. L., Wehrspaun, C., Kellis, M., & Lu, T. K. (2021) · Nature Communications · doi:10.1038/s41467-021-24436-7 · Cited by 159

Leveraging mRNA Sequences and Nanoparticles to Deliver SARS‐CoV‐2 Antigens In Vivo

Zeng, C., Hou, X., Yan, J., Zhang, C., Li, W., Zhao, W., Du, S., & Dong, Y. (2020) · Advanced Materials · doi:10.1002/adma.202004452 · Cited by 152

The 5'-leader of tobacco mosaic virus promotes translation through enhanced recruitment of eIF4F

Gallie, D. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf457 · Cited by 149

Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner

Nallagatla, S. R., & Bevilacqua, P. C. (2008) · RNA · doi:10.1261/rna.1007408 · Cited by 143

Predicting the sizes of large RNA molecules

Yoffe, A. M., Prinsen, P., Gopal, A., Knobler, C. M., Gelbart, W. M., & Ben-Shaul, A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808089105 · Cited by 140

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

Wu, X., & Bartel, D. P. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx323 · Cited by 140

The tobacco etch viral 5′ leader and poly(A) tail are functionally synergistic regulators of translation

Gallie, D., Tanguay, R. L., & Leathers, V. L. (1995) · Gene · doi:10.1016/0378-1119(95)00521-7 · Cited by 125

Massively parallel functional annotation of 3′ untranslated regions

Zhao, W., Pollack, J. L., Blagev, D. P., Zaitlen, N., McManus, M. T., & Erle, D. J. (2014) · Nature Biotechnology · doi:10.1038/nbt.2851 · Cited by 125

Enhancement of dengue virus translation: role of the 3′ untranslated region and the terminal 3′ stem-loop domain

Holden, K. L., & Harris, E. (2004) · Virology · doi:10.1016/j.virol.2004.08.004 · Cited by 121

A Dengue Virus Serotype 1 mRNA-LNP Vaccine Elicits Protective Immune Responses

Wollner, C. J., Richner, M., Hassert, M., Pinto, A. K., Brien, J. D., & Richner, J. M. (2021) · Journal of Virology · doi:10.1128/jvi.02482-20 · Cited by 120

Control of Translation by the 5′- and 3′-Terminal Regions of the Dengue Virus Genome

Chiu, W.-W., Kinney, R. M., & Dreher, T. W. (2005) · Journal of Virology · doi:10.1128/jvi.79.13.8303-8315.2005 · Cited by 118

Single-cell mRNA transfection studies: Delivery, kinetics and statistics by numbers

Leonhardt, C., Schwake, G., Stögbauer, T. R., Rappl, S., Kuhr, J.-T., Ligon, T. S., & Rädler, J. O. (2014) · Nanomedicine: Nanotechnology, Biology and Medicine · doi:10.1016/j.nano.2013.11.008 · Cited by 117

Sindbis Virus Usurps the Cellular HuR Protein to Stabilize Its Transcripts and Promote Productive Infections in Mammalian and Mosquito Cells

Sokoloski, K. J., Dickson, A., Chaskey, E. L., Garneau, N. L., Wilusz, C. J., & Wilusz, J. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.07.003 · Cited by 116

Optimization of mRNA untranslated regions for improved expression of therapeutic mRNA

Asrani, K. H., Farelli, J. D., Stahley, M. R., Miller, R. L., Cheng, C. J., Subramanian, R. R., & Brown, J. M. (2018) · RNA Biology · doi:10.1080/15476286.2018.1450054 · Cited by 115

Ciphers and Executioners: How 3′-Untranslated Regions Determine the Fate of Messenger RNAs

Mayya, V. K., & Duchaîne, T. F. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00006 · Cited by 113

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

Incarnato, D., Morandi, E., Simon, L. M., & Oliviero, S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky486 · Cited by 104

Features in the 5′ non-coding sequences of rabbit α and β-globin mRNAs that affect translational efficiency

Kozak, M. (1994) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80019-1 · Cited by 101

3′ Cap-independent translation enhancers of positive-strand RNA plant viruses

Nicholson, B. L., & White, K. A. (2011) · Current Opinion in Virology · doi:10.1016/j.coviro.2011.10.002 · Cited by 100

Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors

Shirokikh, N. E., & Spirin, A. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804940105 · Cited by 98

The 3′ Untranslated Region of Sindbis Virus Represses Deadenylation of Viral Transcripts in Mosquito and Mammalian Cells

Garneau, N. L., Sokoloski, K. J., Opyrchal, M., Neff, C. P., Wilusz, C. J., & Wilusz, J. (2007) · Journal of Virology · doi:10.1128/jvi.01205-07 · Cited by 80

In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing

Osuna, B. A., Howard, C. J., Subheksha, K. C., Frost, A. S., & Weinberg, D. E. (2017) · eLife · doi:10.7554/elife.27949 · Cited by 73

Consistent global structures of complex RNA states through multidimensional chemical mapping

Cheng, C. Y., Chou, F., Kladwang, W., Tian, S., Cordero, P., & Das, R. (2015) · eLife · doi:10.7554/elife.07600 · Cited by 72

The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence

Kaukinen, U. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.2.468 · Cited by 69

The effect of secondary structure on cleavage of the phosphodiester bonds of RNA

Mikkola, S., Kaukinen, U., & Lönnberg, H. (2001) · Cell Biochemistry and Biophysics · doi:10.1385/cbb:34:1:95 · Cited by 67

Penalized Regression with Ordinal Predictors

Gertheiss, J., & Tutz, G. (2009) · International Statistical Review · doi:10.1111/j.1751-5823.2009.00088.x · Cited by 66

Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol

Seetin, M. G., Kladwang, W., Bida, J. P., & Das, R. (2014) · Methods in Molecular Biology · doi:10.1007/978-1-62703-667-2_6 · Cited by 63

Arginase I mRNA therapy – a novel approach to rescue arginase 1 enzyme deficiency

Asrani, K. H., Cheng, L., Cheng, C. J., & Subramanian, R. R. (2018) · RNA Biology · doi:10.1080/15476286.2018.1475178 · Cited by 58

Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments

Leppek, K., Fujii, K., Quade, N., Susanto, T. T., Boehringer, D., Lenarčič, T., Xue, S., Genuth, N. R., Ban, N., & Barna, M. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.10.023 · Cited by 56

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

Liu, D. (2019) · PeerJ · doi:10.7717/peerj.8275 · Cited by 54

Untranslated Regions of FbRbcS1 mRNA Mediate Bundle Sheath Cell-specific Gene Expression in Leaves of a C4 Plant

Patel, M., Siegel, A. J., & Berry, J. O. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m604162200 · Cited by 53

Standardization of RNA Chemical Mapping Experiments

Kladwang, W., Mann, T. H., Becka, A. J., Tian, S., Kim, H., Yoon, S., & Das, R. (2014) · Biochemistry · doi:10.1021/bi5003426 · Cited by 53

Identification of a grpE Heat-shock Gene Homolog in the Archeon Methanosarcina mazie

de Macario, E. C., Dugan, C. B., & Macario, A. J. L. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1422 · Cited by 48

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

Manfredonia, I., & Incarnato, D. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200670 · Cited by 48

Human cellular CYBA UTR sequences increase mRNA translation without affecting the half-life of recombinant RNA transcripts

Ferizi, M., Aneja, M. K., Balmayor, E. R., Badieyan, Z. S., Mykhaylyk, O., Rudolph, C., & Plank, C. (2016) · Scientific Reports · doi:10.1038/srep39149 · Cited by 46

Optimization of 5′ Untranslated Region of Modified mRNA for Use in Cardiac or Hepatic Ischemic Injury

Sultana, N., Hadas, Y., Sharkar, M. T. K., Kaur, K., Magadum, A., Kurian, A. A., Hossain, N., Alburquerque, B., Ahmed, S. M. M., Chepurko, E., et al. (2020) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2020.03.019 · Cited by 45

Systematic use of synthetic 5′-UTR RNA structures to tune protein translation improves yield and quality of complex proteins in mammalian cell factories

Eisenhut, P., Mebrahtu, A., Moradi Barzadd, M., Thalén, N., Klanert, G., Weinguny, M., Sandegren, A., Su, C., Hatton, D., Borth, N., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa847 · Cited by 38

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure

Terai, G., Kamegai, S., & Asai, K. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv678 · Cited by 36

Natural Selection and Algorithmic Design of mRNA

Cohen, B., & Skiena, S. (2003) · Journal of Computational Biology · doi:10.1089/10665270360688101 · Cited by 35

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

Kim, H., Cordero, P., Das, R., & Yoon, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt501 · Cited by 31

Leveraging mRNAs sequences to express SARS-CoV-2 antigens in vivoPreprint

Zeng, C., Hou, X., Yan, J., Zhang, C., Li, W., Zhao, W., Du, S., & Dong, Y. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.01.019877 · Cited by 29

The 3′ Untranslated Region of the Rabies Virus Glycoprotein mRNA Specifically Interacts with Cellular PCBP2 Protein and Promotes Transcript Stability

Palusa, S. G., Ndaluka, C., Bowen, R. A., Wilusz, C. J., & Wilusz, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033561 · Cited by 26

Updates to the RNA mapping database (RMDB), version 2

Yesselman, J. D., Tian, S., Liu, X., Shi, L., Li, J. B., & Das, R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx873 · Cited by 23

Selection of mRNA 5′-untranslated region sequence with high translation efficiency through ribosome display

Mie, M., Shimizu, S., Takahashi, F., & Kobatake, E. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.05.173 · Cited by 11

LinearDesign: Efficient Algorithms for Optimized mRNA Sequence DesignPreprint

Zhang, H., Zhang, L., Li, Z., Liu, K., Liu, B., Mathews, D. H., & Huang, L. (2020) · arXiv (Cornell University) · Cited by 8

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring

Wang, H., Yu, Y., Liu, T., Pan, Y., Yan, S., & Wang, Y. (2015) · SpringerPlus · doi:10.1186/s40064-015-0973-z · Cited by 7

A mRNA-LNP vaccine against Dengue Virus elicits robust, serotype-specific immunity

Wollner, C. J., Richner, M., Hassert, M. A., Pinto, A. K., Brien, J. D., & Richner, J. M. (2021) · doi:10.1101/2021.01.05.425517 · Cited by 6

mRNA-based therapeutics: powerful and versatile tools to combat diseases

Qin, S., Tang, X., Chen, Y., Chen, K., Fan, N., Xiao, W., Zheng, Q., Li, G., Teng, Y., Wu, M., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01007-w · Cited by 852

Nanodelivery of nucleic acids

Mendes, B. B., Conniot, J., Avital, A., Yao, D., Jiang, X., Zhou, X., Sharf-Pauker, N., Xiao, Y., Adir, O., Liang, H., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00104-y · Cited by 719

The landscape of mRNA nanomedicine

Huang, X., Kong, N., Zhang, X., Cao, Y., Langer, R., & Tao, W. (2022) · Nature Medicine · doi:10.1038/s41591-022-02061-1 · Cited by 511

Algorithm for optimized mRNA design improves stability and immunogenicity

Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Jiang, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06127-z · Cited by 531

mRNA vaccines for infectious diseases — advances, challenges and opportunities

Pardi, N., & Krammer, F. (2024) · Nature Reviews Drug Discovery · doi:10.1038/s41573-024-01042-y · Cited by 252

mRNAid, an open-source platform for therapeutic mRNA design and optimization strategies

Vostrosablin, N., Lim, S., Gopal, P., Brazdilova, K., Parajuli, S., Wei, X., Gromek, A., Příhoda, D., Spale, M., Muždalo, A., et al. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae028 · Cited by 30

Fine-scale structural information substantially improves mRNA therapeutic stability prediction

Yi, S., Ali, S. E., Jadeja, Y., Davis, J. W., & Metkar, M. (2026) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2026.102960 · Cited by 1

Theoretical basis for stabilizing messenger RNA through secondary structure design

Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197

A tool for optimizing messenger RNA sequence

Blakney, A. K. (2023) · Nature · doi:10.1038/d41586-023-01745-z · Cited by 7

RNA stability enhancers for durable base-modified mRNA therapeutics

Jung, S.-J., Seo, J. J., Lee, S., Hyun, S.-I., Lee, J.-E., Lee, S., Lee, Y., Chang, H., Lee, H., Kim, J.-H., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02891-7 · Cited by 26