Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853 · see citing works

The Vienna RNA Websuite

Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R., & Hofacker, I. L. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn188 · Cited by 2,717 · see citing works

Correlation of mRNA and protein in complex biological samples

Maier, T., Güell, M., & Serrano, L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.036 · Cited by 1,802 · see citing works

Comparing protein abundance and mRNA expression levels on a genomic scale

Greenbaum, D. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-117 · Cited by 1,692 · see citing works

Synonymous but not the same: the causes and consequences of codon bias

Plotkin, J. B., & Kudla, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2899 · Cited by 1,677 · see citing works

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

Mathews, D. H., Disney, M. D., Childs‐Disney, J. L., Schroeder, S. J., Zuker, M., & Turner, D. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401799101 · Cited by 1,609 · see citing works

Coding-Sequence Determinants of Gene Expression in <i>Escherichia coli</i>

Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458 · see citing works

The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution

Shem, A. B., de Loubresse, N. G., Melnikov, S. V., Jenner, L. B., Yusupova, G. Z., & Yusupov, M. (2011) · Science · doi:10.1126/science.1212642 · Cited by 1,114 · see citing works

Ribosome Structure and the Mechanism of Translation

Ramakrishnan, V. (2002) · Cell · doi:10.1016/s0092-8674(02)00619-0 · Cited by 932 · see citing works

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

Tuller, T., Carmi, A., Vestsigian, K., Navon, S., Dorfan, Y., Zaborske, J., Pan, T., Dahan, O., Furman, I., & Pilpel, Y. (2010) · Cell · doi:10.1016/j.cell.2010.03.031 · Cited by 874 · see citing works

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

Chan, P. P., & Lowe, T. M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn787 · Cited by 867 · 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

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 · see citing works

Genome-wide measurement of RNA secondary structure in yeast

Kertesz, M., Wan, Y., Mazor, E., Rinn, J. L., Nutter, R. C., Chang, H. Y., & Segal, E. (2010) · Nature · doi:10.1038/nature09322 · Cited by 765 · see citing works

Solving the riddle of codon usage preferences: a test for translational selection

dos Reis, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh834 · Cited by 745 · see citing works

Single-RNA counting reveals alternative modes of gene expression in yeast

Zenklusen, D., Larson, D. R., & Singer, R. H. (2008) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.1514 · Cited by 684 · see citing works

Genome-wide analysis of mRNA translation profiles in <i>Saccharomyces</i> <i>cerevisiae</i>

Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O., & Herschlag, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0635171100 · Cited by 663 · see citing works

Translation efficiency is determined by both codon bias and folding energy

Tuller, T., Waldman, Y. Y., Kupiec, M., & Ruppin, E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909910107 · Cited by 584 · see citing works

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Pedersen, J. S., Bejerano, G., Siepel, A. C., Rosenbloom, K. R., Lindblad‐Toh, K., Lander, E. S., Kent, J., Miller, W., & Haussler, D. H. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020033 · Cited by 515 · see citing works

The Elongation, Termination, and Recycling Phases of Translation in EukaryotesPreprint

Dever, T. E., & Green, R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a013706 · Cited by 507 · see citing works

The Mechanism of Eukaryotic Translation Initiation: New Insights and ChallengesPreprint

Hinnebusch, A. G., & Lorsch, J. R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a011544 · Cited by 506 · see citing works

Determinants of translation efficiency and accuracy

Gingold, H., & Pilpel, Y. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.14 · Cited by 488 · see citing works

Paxdb, a database of protein abundance averages across all three domains of life

Wang, M., Weiss, M., Simonovic, M., Haertinger, G., Schrimpf, S. P., Hengartner, M. O., & von Mering, C. (2012) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.o111.014704 · Cited by 466 · cited 2× · see citing works

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 · see citing works

A mechanistic overview of translation initiation in eukaryotes

Aitken, C. E., & Lorsch, J. R. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2303 · Cited by 419 · see citing works

Translation drives mRNA quality control

Shoemaker, C. J., & Green, R. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2301 · Cited by 397 · see citing works

Variation and genetic control of protein abundance in humans

Wu, L., Candille, S. I., Choi, Y., Xie, D., Jiang, L., Li-Pook-Than, J., Tang, H., & Snyder, M. (2013) · Nature · doi:10.1038/nature12223 · Cited by 364 · see citing works

A Role for Codon Order in Translation Dynamics

Cannarozzi, G., Schraudolph, N. N., Faty, M., von Rohr, P., Friberg, M. T., Roth, A. C., Gonnet, P., Gonnet, G., & Barral, Y. (2010) · Cell · doi:10.1016/j.cell.2010.02.036 · Cited by 354 · see citing works

Translational control by changes in poly(A) tail length: recycling mRNAs

Weill, L., Belloc, E., Bava, F.-A., & Méndez, R. (2012) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.2311 · Cited by 328 · see citing works

Rate-limiting steps in RNA chain initiation.

McClure, W. R. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.10.5634 · Cited by 308 · see citing works

Following translation by single ribosomes one codon at a time

Wen, J.-D., Lancaster, L., Hodges, C., Zeri, A., Yoshimura, S., Noller, H., Bustamante, C., & Tinoco, I. (2008) · Nature · doi:10.1038/nature06716 · Cited by 292 · see citing works

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

Shabalina, S. A., Spiridonov, N. A., & Kashina, A. S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1205 · Cited by 287 · see citing works

Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast

Dvir, S., Velten, L., Sharon, E., Zeevi, D., Carey, L. B., Weinberger, A., & Segal, E. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222534110 · Cited by 246 · see citing works

Eukaryotic Initiation Factor 6 is rate-limiting in translation, growth and transformation

Gandin, V., Miluzio, A., Barbieri, A., Beugnet, A., Kiyokawa, H., Marchisio, P., & Biffo, S. (2008) · Nature · doi:10.1038/nature07267 · Cited by 235 · see citing works

Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

Wang, T., Cui, Y., Jin, J., Guo, J., Wang, G., Yin, X., He, Q., & Zhang, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt178 · Cited by 209 · see citing works

Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial GenesPreprint

Katz, L., & Burge, C. B. (2003) · Genome Research · doi:10.1101/gr.1257503 · Cited by 204 · see citing works

Composite effects of gene determinants on the translation speed and density of ribosomes

Tuller, T., Veksler‐Lublinsky, I., Gazit, N., Kupiec, M., Ruppin, E., & Ziv-Ukelson, M. (2011) · Genome biology · doi:10.1186/gb-2011-12-11-r110 · Cited by 191 · see citing works

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

Reuveni, S., Meilijson, I., Kupiec, M., Ruppin, E., & Tuller, T. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002127 · Cited by 182 · see citing works

Dynamics of translation by single ribosomes through mRNA secondary structures

Chen, C., Zhang, H., Broitman, S. L., Reiche, M., Farrell, I., Cooperman, B. S., & Goldman, Y. E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2544 · Cited by 147 · see citing works

Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme

Agashe, D., Martinez-Gomez, N. C., Drummond, D. A., & Marx, C. J. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss273 · Cited by 145 · see citing works

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

Zhang, J., & Ferré-D’Amaré, A. R. (2013) · Nature · doi:10.1038/nature12440 · Cited by 143 · see citing works

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

Zheng, Q., Ryvkin, P., Li, F., Dragomir, I. C., Valladares, O., Yang, J., Cao, K., Wang, L., & Gregory, B. D. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001141 · Cited by 135 · see citing works

Global Analysis of RNA Secondary Structure in Two Metazoans

Li, F., Zheng, Q., Ryvkin, P., Dragomir, I. C., Desai, Y. B., Aiyer, S., Valladares, O., Yang, J., Bambina, S., Sabin, L. R., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2011.10.002 · Cited by 133 · see citing works

Determination of in vivo RNA structure in low-abundance transcripts

Kwok, C. K., Ding, Y., Tang, Y., Assmann, S. M., & Bevilacqua, P. C. (2013) · Nature Communications · doi:10.1038/ncomms3971 · Cited by 123 · see citing works

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

Ciandrini, L., Stansfield, I., & Romano, M. C. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002866 · Cited by 117 · see citing works

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

Park, C., Chen, X., Yang, J., & Zhang, J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218066110 · Cited by 113 · see citing works

The development of bactericidal yeast strains by expressing thePediococcus acidilactici pediocin gene (pedA) inSaccharomyces cerevisiae

Schoeman, H., Vivier, M. A., du Toit, M., Dicks, L. M. T., & Pretorius, I. S. (1999) · Yeast · doi:10.1002/(sici)1097-0061(19990615)15:8 · Cited by 112 · see citing works

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs

Meyer, I. M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki923 · Cited by 102 · see citing works

Riboswitch-mediated control of gene expression in eukaryotes

Wachter, A. (2010) · RNA Biology · doi:10.4161/rna.7.1.10489 · Cited by 100 · see citing works

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

Zur, H., & Tuller, T. (2012) · EMBO Reports · doi:10.1038/embor.2011.262 · Cited by 95 · see citing works

An in vivo control map for the eukaryotic mRNA translation machinery

Firczuk, H., Kannambath, S., Pahle, J., Claydon, A. J., Beynon, R. J., Duncan, J. N., Westerhoff, H. V., Mendes, P., & McCarthy, J. E. G. (2013) · Molecular Systems Biology · doi:10.1038/msb.2012.73 · Cited by 93 · see citing works

A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3

Locker, N., Chamond, N., & Sargueil, B. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1118 · Cited by 92 · see citing works

mRNA pseudoknot structures can act as ribosomal roadblocks

Tholstrup, J., Oddershede, L. B., & Sørensen, M. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr686 · Cited by 74 · see citing works

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

Gingold, H., Dahan, O., & Pilpel, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks772 · Cited by 68 · see citing works

The genetic code as expressed through relationships between mRNA structure and protein function

Mauger, D., Siegfried, N. A., & Weeks, K. M. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.03.002 · Cited by 58 · see citing works

Codon usage variability determines the correlation between proteome and transcriptome fold changes

Olivares‐Hernández, R., Bordel, S., & Nielsen, J. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-33 · Cited by 42 · see citing works

Distributed control for recruitment, scanning and subunit joining steps of translation initiation

Sangthong, P., Hughes, J. M. X., & McCarthy, J. E. G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm283 · Cited by 12 · see citing works

Number Variation of High Stability Regions Is Correlated with Gene Functions

Mao, Y., Li, Q., Wang, W., Liang, P., & Tao, S. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt020 · Cited by 8 · see citing works

IgG Subclasses and Allotypes: From Structure to Effector Functions

Vidarsson, G., Dekkers, G., & Rispens, T. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00520 · Cited by 2,667 · see citing works

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

Guillén‐Boixet, J., Kopach, A., Holehouse, A. S., Wittmann, S., Jahnel, M., Schlüßler, R., Kim, K., Trussina, I. R. E. A., Wang, J., Matějů, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.049 · Cited by 869 · see citing works

The dawn of mRNA vaccines: the COVID-19 case

Verbeke, R., Lentacker, I., De Smedt, S. C., & Dewitte, H. (2021) · Journal of Controlled Release · doi:10.1016/j.jconrel.2021.03.043 · Cited by 504 · see citing works

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua, P. C., Ritchey, L. E., Su, Z. Z., & Assmann, S. M. (2016) · Annual Review of Genetics · doi:10.1146/annurev-genet-120215-035034 · Cited by 222 · see citing works

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 · see citing works

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Riba, A., Di Nanni, N., Mittal, N., Arhné, E., Schmidt, A., & Zavolan, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817299116 · Cited by 209 · see citing works

Role of mRNA structure in the control of protein folding

Faure, G., Ogurtsov, A. Y., Shabalina, S. A., & Koonin, E. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw671 · Cited by 134 · see citing works

RNA Droplets

Rhine, K., Vidaurre, V., & Myong, S. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-052118-115508 · Cited by 130 · see citing works

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Gorochowski, T. E., Ignatova, Z., Bovenberg, R. A. L., & Roubos, J. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv199 · Cited by 125 · see citing works

The landscape of eukaryotic mRNPs

Khong, A., & Parker, R. (2019) · RNA · doi:10.1261/rna.073601.119 · Cited by 93 · see citing works

RPLP1 and RPLP2 Are Essential Flavivirus Host Factors That Promote Early Viral Protein Accumulation

Campos, R. K., Wong, B., Xie, X., Lu, Y.-F., Shi, P., Pompon, J., García-Blanco, M. A., & Bradrick, S. S. (2017) · Journal of Virology · doi:10.1128/jvi.01706-16 · Cited by 77 · see citing works

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Zur, H., & Tuller, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw764 · Cited by 73 · see citing works

Synonymous codon usage regulates translation initiation

Barrington, C. L., Galindo, G., Koch, A. L., Horton, E. R., Morrison, E. J., Tisa, S., Stasevich, T. J., & Rissland, O. S. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113413 · Cited by 58 · see citing works

Cell-Free Translation Is More Variable than Transcription

Chizzolini, F., Forlin, M., Martín, N. Y., Berloffa, G., Cecchi, D., & Mansy, S. S. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00250 · Cited by 55 · see citing works

Nucleotides upstream of the Kozak sequence strongly influence gene expression in the yeast S. cerevisiae

Li, J., Liang, Q., Song, W., & Marchisio, M. A. (2017) · Journal of Biological Engineering · doi:10.1186/s13036-017-0068-1 · Cited by 49 · see citing works

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution

Fang, H., Huang, Y.-F., Radhakrishnan, A., Siepel, A. C., Lyon, G. J., & Schatz, M. C. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.007 · Cited by 48 · see citing works

Fine-tuning the expression of pathway gene in yeast using a regulatory library formed by fusing a synthetic minimal promoter with different Kozak variants

Xu, L., Liu, P., Dai, Z., Fan, F., & Zhang, X. (2021) · Microbial Cell Factories · doi:10.1186/s12934-021-01641-z · Cited by 46 · see citing works

Widespread non-modular overlapping codes in the coding regions*

Bergman, S., & Tuller, T. (2020) · Physical Biology · doi:10.1088/1478-3975/ab7083 · Cited by 37 · see citing works

Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks

Wang, J., Zhang, T., Zhang, Y., Tan, W. T., Wen, M., Shen, Y., Lambert, F. R. P., Huber, R. G., & Wan, Y. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.09.027 · Cited by 37 · see citing works

Synonymous codons, ribosome speed, and eukaryotic gene expression regulation

Tarrant, D., & von der Haar, T. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1684-2 · Cited by 37 · see citing works

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population

Gaither, J., Lammi, G., Li, J., Gordon, D. M., Kuck, H. C., Kelly, B., Fitch, J., & White, P. (2021) · GigaScience · doi:10.1093/gigascience/giab023 · Cited by 35 · see citing works

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage

Trotta, E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2692-4 · Cited by 31 · see citing works

Optimization of inside and outside factors to improve recombinant protein yield in plant

Habibi, P., Prado, G. S., Pelegrini, P. B., Hefferon, K. L., Soccol, C. R., & Grossi‐de‐Sá, M. F. (2017) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-017-1240-5 · Cited by 33 · see citing works

Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum

Bhartiya, D., Chawla, V., Ghosh, S., Shankar, R., & Kumar, N. (2016) · Genomics · doi:10.1016/j.ygeno.2016.10.004 · Cited by 32 · see citing works

Codon optimization, promoter and expression system selection that achieved high-level production of Yarrowia lipolytica lipase in Pichia pastoris

Zhou, W., Yang, J., Mao, L., & Miao, L. (2014) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2014.10.007 · Cited by 30 · see citing works

Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation

Xiao, M., Zhang, B., Li, Y., Gao, Q., Sun, W., & Chen, W. (2016) · Molecular Systems Biology · doi:10.15252/msb.20167375 · Cited by 27 · see citing works

RNA structure profiling at single-cell resolution reveals new determinants of cell identity

Wang, J., Zhang, Y., Zhang, T., Tan, W. T., Lambert, F. R. P., Darmawan, J., Huber, R. G., & Wan, Y. (2024) · Nature Methods · doi:10.1038/s41592-023-02128-y · Cited by 27 · see citing works

The optimization of mRNA expression level by its intrinsic properties—Insights from codon usage pattern and structural stability of mRNA

Victor, M. P., Acharya, D., Begum, T., & Ghosh, T. C. (2018) · Genomics · doi:10.1016/j.ygeno.2018.08.009 · Cited by 27 · see citing works

Global 5′-UTR RNA structure regulates translation of a SERPINA1 mRNA

Grayeski, P. J., Weidmann, C. A., Kumar, J., Lackey, L., Mustoe, A. M., Busan, S., Laederach, A., & Weeks, K. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac739 · Cited by 26 · see citing works

LncPep: A Resource of Translational Evidences for lncRNAs

Liu, T., Wu, J., Wu, Y., Hu, W., Fang, Z., Wang, Z., Jiang, C., & Li, S. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.795084 · Cited by 25 · see citing works

Engineering the 5′ UTR-Mediated Regulation of Protein Abundance in Yeast Using Nucleotide Sequence Activity Relationships

Ding, W., Cheng, J., Guo, D. H., Mao, L., Li, J., Lu, L., Zhang, Y., Yang, J., & Jiang, H. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00127 · Cited by 23 · see citing works

RNA Structure: Past, Future, and Gene Therapy Applications

Haseltine, W. A., Hazel, K., & Patarca, R. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms26010110 · Cited by 22 · see citing works

A transformation clustering algorithm and its application in polyribosomes structural profiling

Jiang, W., Wagner, J., Du, W., Plitzko, J. M., Baumeister, W. P., Beck, F., & Guo, Q. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac547 · Cited by 21 · see citing works

RNA search engines empower the bacterial intranet

Dendooven, T., & Luisi, B. F. (2017) · Biochemical Society Transactions · doi:10.1042/bst20160373 · Cited by 20 · see citing works

Design of Adjacent Transcriptional Regions to Tune Gene Expression and Facilitate Circuit Construction

Wu, F., Zhang, Q., & Wang, X. (2018) · Cell Systems · doi:10.1016/j.cels.2018.01.010 · Cited by 19 · see citing works

Proximity Ligation Assays for In Situ Detection of Innate Immune Activation: Focus on In Vitro-Transcribed mRNA

Blanchard, E. L., Loomis, K. H., Bhosle, S. M., Vanover, D. A., Baumhof, P., Pitard, B., Zurla, C., & Santangelo, P. J. (2018) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2018.11.002 · Cited by 19 · see citing works

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Clauer, P. R., Nou, A., Toth, T., Yu, Q., Chemla, Y., Boo, A., Yoon, K. S., & Voigt, C. A. (2026) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00687 · Cited by 20 · see citing works

Massively parallel gene expression variation measurement of a synonymous codon library

Schmitz, A., & Zhang, F. (2021) · BMC Genomics · doi:10.1186/s12864-021-07462-z · Cited by 16 · see citing works

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times

Sharma, A. K., Ahmed, N., & O’Brien, E. P. (2018) · Physical review. E · doi:10.1103/physreve.97.022409 · Cited by 18 · see citing works

Global importance of RNA secondary structures in protein-coding sequences

Fricke, M., Gerst, R., Ibrahim, B., Niepmann, M., & Marz, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty678 · Cited by 18 · see citing works

A novel silk fibroin protein–based fusion system for enhancing the expression of nanobodies in Escherichia coli

Yu, J., Guo, Y., Gu, Y., Fan, X., Li, F., Song, H., Nian, R., & Liu, W. (2022) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-022-11857-7 · Cited by 16 · see citing works

Ribosome inactivation regulates translation elongation in neurons

Popper, B., Bürkle, M., Ciccopiedi, G., Marchioretto, M., Forné, I., Imhof, A., Straub, T., Viero, G., Götz, M., & Schieweck, R. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.105648 · Cited by 15 · see citing works

The combined influence of codon composition and tRNA copy number regulates translational efficiency by influencing synonymous nucleotide substitution

Victor, M. P., Acharya, D., Chakraborty, S., & Ghosh, T. C. (2020) · Gene · doi:10.1016/j.gene.2020.144640 · Cited by 14 · see citing works

Codon usage bias in 5′ terminal coding sequences reveals distinct enrichment of gene functions

Liu, H., Rahman, S. U., Mao, Y., Xu, X., & Tao, S. (2017) · Genomics · doi:10.1016/j.ygeno.2017.07.008 · Cited by 14 · see citing works

The molecular choreography of protein synthesis: translational control, regulation, and pathways

Chen, J., Choi, J., O’Leary, S. E., Prabhakar, A., Petrov, A. N., Grosely, R., Puglisi, E. V., & Puglisi, J. D. (2016) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583516000056 · Cited by 13 · see citing works

The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum

Alvarez, D. R., Ospina, A., Barwell, T., Zheng, B., Dey, A., Li, C. V., Basu, S., Shi, X. M., Kadri, S., & Chakrabarti, K. (2021) · RNA Biology · doi:10.1080/15476286.2021.1926747 · Cited by 12 · see citing works

The importance of codon–anticodon interactions in translation elongation

Saint-Léger, A., & de Pouplana, L. R. (2015) · Biochimie · doi:10.1016/j.biochi.2015.04.013 · Cited by 12 · see citing works

Full-length ribosome density prediction by a multi-input and multi-output model

Tian, T., Li, S., Peng, L., Zhao, D. Y., & Zeng, J. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008842 · Cited by 12 · see citing works

Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life

Gebert, D., Jehn, J., & Rosenkranz, D. (2019) · Open Biology · doi:10.1098/rsob.190020 · Cited by 12 · see citing works

The KLF14 Variant is Associated with Type 2 Diabetes and HbA1C Level

Shahvazian, E., Mahmoudi, M. B., Yazd, E. F., Gharibi, S., Moghimi, B., HosseinNia, P., & Mirzaei, M. (2021) · Biochemical Genetics · doi:10.1007/s10528-020-10015-w · Cited by 10 · see citing works

Readthrough-induced misincorporated amino acid ratios guide mutant-specific therapeutic approaches for two CFTR nonsense mutations

Premchandar, A., Ming, R., Baiad, A. A., Fonte, D. F. D., Xu, H., Faubert, D., Veit, G., & Lukács, G. L. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2024.1389586 · Cited by 8 · see citing works

Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks

Yu, H., Meng, W., Mao, Y., Zhang, Y., Sun, Q., & Tao, S. (2019) · RNA Biology · doi:10.1080/15476286.2019.1612692 · Cited by 8 · see citing works

GCN sensitive protein translation in yeast

Barr, W., Sheth, R. B., Kwon, J. B., Cho, J., Glickman, J. W., Hart, F., Chatterji, O. K., Scopino, K., Voelkel‐Meiman, K., Krizanc, D., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0233197 · Cited by 8 · see citing works

High-level secretory expression of Aspergillus exo-inulinase and its use in the preparation of fructose syrup from inulin

Chen, G.-J., Yang, J., Peng, X.-B., & He, J. (2016) · Journal of Molecular Catalysis B Enzymatic · doi:10.1016/j.molcatb.2017.09.001 · Cited by 7 · see citing works

Harnessing Synthetic Riboswitches for Tunable Gene Regulation in Mammalian Cells

Khadake, R. M., Arora, V., Gupta, P., & Rode, A. B. (2025) · ChemBioChem · doi:10.1002/cbic.202401015 · Cited by 5 · see citing works

Utilizing 5′ UTR Engineering Enables Fine-Tuning of Multiple Genes within Operons to Balance Metabolic Flux in Bacillus subtilis

You, J., Wang, Y., Wang, K., Du, Y., Zhang, X., Zhang, X., Yang, T., Pan, X., & Rao, Z. (2024) · Biology · doi:10.3390/biology13040277 · Cited by 5 · see citing works

Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding

Gutman, T., & Tuller, T. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012685 · Cited by 5 · see citing works

VeloPro: A pipeline integrating Ribo‐seq and AlphaFold deciphers association patterns between translation velocity and protein structure features

Bian, B., Kumagai, T., & Saitō, Y. (2023) · iMeta · doi:10.1002/imt2.148 · Cited by 5 · see citing works

Formulation of the protein synthesis rate with sequence information

Xia, W., & Lei, J. (2017) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2018023 · Cited by 5 · see citing works

The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage

Babaylova, E. S., Gopanenko, A. V., Tupikin, A. E., Kabilov, M. R., & Malygin, A. A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1013 · Cited by 4 · see citing works

In vivo RNA structure influences the translation and stability of plant long non-coding RNAs

Dong, Q., Yang, B., Sun, W., Liang, J., Xing, Q., Ren, L., Li, Y., Ding, Y., & Zhang, H. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101575 · Cited by 4 · see citing works

Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures

Yu, G., Zhu, H.-B., Chen, X.-S., & Yang, J.-R. (2018) · bioRxiv · doi:10.1016/j.gpb.2019.11.013 · Cited by 3 · see citing works

TIR predictor and optimizer: Web‐tools for accurate prediction of translation initiation rate and precision gene design in Saccharomyces cerevisiae

Chakarborty, S., Irshad, I. U., Mahima, M., & Sharma, A. K. (2024) · Biotechnology Journal · doi:10.1002/biot.202400081 · Cited by 3 · see citing works

A Single Point Mutation, Asn16→Lys, Dictates the Temperature-Sensitivity of the Reovirus tsG453 Mutant

Glover, K. K. M., Sutherland, D. M., Dermody, T. S., & Coombs, K. M. (2021) · Viruses · doi:10.3390/v13020289 · Cited by 3 · see citing works

P-bodies act as dynamic control hubs for RNA processing and storage

Feng, M. W., Mossanen-Parsi, A., Stonys, V., Hubbard, S. J., Ashe, M., & Grant, C. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.111273 · Cited by 3 · see citing works

Efficient Prediction Model of mRNA End-to-End Distance and Conformation: Three-Dimensional RNA Illustration Program (TRIP)

Ma, J., & Tsuboi, T. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3766-1_13 · Cited by 2 · see citing works

Genome-wide analysis of codon usage bias in Ascovirus: Insights into viral evolution and host adaptation

Dizman, Y. A. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107892 · Cited by 2 · see citing works

Probing Single Chaperone Substrates

Wruck, F., Avellaneda, M. J., Naqvi, M. M., Koers, E. J., Till, K., Gross, L., Moayed, F., Roland, A., Heling, L. W. H. J., Mashaghi, A., et al. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00278 · Cited by 2 · see citing works

Isoform-specific translational control is evolutionarily conserved in primatesPreprint

Draper, J. M., Philipp, J., Neeb, Z., Thomas, R. C., Katzman, S. J., Salama, S. R., Haussler, D. H., & Sanford, J. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.21.537863 · Cited by 2 · see citing works

Recombinant production, purification and characterization of vessel dilator in E. coli

Abbasian, M., Seyedi, H. A. E., Tabatabaei, B. E. S., Arab‐Bafrani, Z., Mofid, M. R., & Zareie, R. (2016) · Protein Expression and Purification · doi:10.1016/j.pep.2016.09.010 · Cited by 1 · see citing works

Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae

Wienecke, A., Barry, M. L., & Pollard, D. A. (2023) · Genetics · doi:10.1093/genetics/iyad113 · Cited by 1 · see citing works

The differential subcellular localization of soybean transcripts, an additional regulatory mechanism of gene activity

Tennant, S., Amézquita, E. J., Li, Y., Smith, B. E., Subramanyam, S. S. M. V., Cervantes-Pérez, S. A., Thibivilliers, S., Bhattacharya, S., Kläver, J., & Libault, M. (2025) · Genome biology · doi:10.1186/s13059-025-03920-z · Cited by 1 · see citing works

Multiscale modeling guided potency assessment of mRNA-lipid nanoparticles

Yang, Y., Qiu, Y., Wang, K., Liu, Y., Sanyal, G., Whitford, P. C., Rouhanifard, S. H., & Xie, W. (2026) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2026.102965 · Cited by 1 · see citing works

Fingerprints of a message: integrating positional information on the transcriptome

Dassi, E., & Quattrone, A. (2014) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2014.00039 · Cited by 1 · see citing works

Revisiting SARS-CoV-2: Evolution, polymorphism and compatibility with human tRNA pool in a lineage over a month

Victor, M. P., Das, R., & Ghos, T. C. (2023) · Indian Journal of Applied Microbiology · doi:10.46798/ijam.2023.v25i02.2 · Cited by 1 · see citing works

Enhancing mycophenolic acid production in Penicillium brevicompactum through Kozak-optimized 2A peptide multi-gene expression system

Wu, J., Hu, T., Lin, L., Yan, Y., Li, T., Wei, W., & Wei, D. (2025) · Fungal Biology · doi:10.1016/j.funbio.2025.101568 · Cited by 1 · see citing works

Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genesPreprint

van den Berg, A. A., & Depken, M. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/065268 · Cited by 1 · see citing works

Do Gamma Rays of Cancer Radiotherapy Effect on the Sequence of Collagenase Gene?

Mousa, A., Ali, S. E., Elhadary, A., Awwad, M., & Ghonemy, O. (2016) · International Journal of Advanced Research · doi:10.21474/ijar01/1243

Ribosome Processivity and Co-translational Protein Folding

Thommen, M. (2017) · doi:10.53846/goediss-6242

Modulating protein translation through proposed mRNA-rRNA base pairing

Barr, W. A. (2019) · doi:10.14418/wes01.2.231

An in-silico study on SARS-CoV-2: Its compatibility with human tRNA pool, and the polymorphism arising in a single lineage over a monthPreprint

Victor, M. P., Das, R., & Ghosh, T. C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.23.217083

Additional file 1 of Fine-tuning the expression of pathway gene in yeast using a regulatory library formed by fusing a synthetic minimal promoter with different Kozak variants

Xu, L., Liu, P., Dai, Z., Fan, F., & Zhang, X. (2021) · Figshare · doi:10.6084/m9.figshare.15071449

Additional file 1 of Massively parallel gene expression variation measurement of a synonymous codon library

Schmitz, A., & Zhang, F. (2021) · Figshare · doi:10.6084/m9.figshare.14151221

Soluble Expression of Recombinant Human Mitsugumin 53 in Escherichia coli NiCo21(DE3)

Dewi, K. S., Tasia, W., Agustiyanti, D. F., Hariyatun, H., Wisnuwardhani, P. H., Rubiyana, Y., Arifa, N., Purba, H. H., Forentin, ⁠. M., Utami, R. A., et al. (2026) · The Protein Journal · doi:10.1007/s10930-026-10319-7

Regulation of mRNA translation during the inflammatory response in murine macrophages

Blin, J. (2020) · theses.fr (ABES) · doi:10.70675/9eed69d2z2c72z4b4dz8603zdc632396f487

Etude des principes d’assemblage et de maturation des kinases de la famille des PIKKs chez Schizosaccharomyces pombe

Toullec, D. (2020) · theses.fr (ABES) · doi:10.70675/a7933611z0027z41dfz8436za664ba25bd4a

circRET-mediated regulation of RET influences enteric neural crest cell development in Hirschsprung disease

Yan, Y., Wang, J., Zhao, F., & Wang, Y. (2026) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00041.2026

Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome

Subramanian, K., Waugh, N., Shanks, C., & Hendrix, D. A. (2026) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1014501 · Cited by 1 · see citing works

BFPSM: A biological language model-based framework for pathogenic synonymous mutation prediction

Chen, H., Yang, S., Ye, C., Wang, C., Xia, J., & Cheng, N. (2026) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2026.109432

Meeting report: 3rd Codon Usage Conference: Function, Mechanism and Evolution

Palazzo, A. F. (2026) · Biochemistry and Cell Biology · doi:10.1139/bcb-2026-0275

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Gorochowski, T. E., Ignatova, Z., Bovenberg, R. A. L., & Roubos, J. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv199 · Cited by 125 · see citing works

Dynamics of translation by single ribosomes through mRNA secondary structures

Chen, C., Zhang, H., Broitman, S. L., Reiche, M., Farrell, I., Cooperman, B. S., & Goldman, Y. E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2544 · Cited by 147 · see citing works

Downstream mRNA Secondary Structure, Not Codon Elongation Supply, Coordinates Co-Translational Protein Folding Across the Human Ribosomal Exit TunnelPreprint

Hassan, M. S. U., Jabeen, I., & Kiani, Y. S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.27.753847

Control of Translation by mRNA Secondary Structure in Escherichia coli

de Smit, M. H., & DUIN, J. V. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1714 · Cited by 200 · see citing works

Deciphering the role of RNA structure in translation efficiency

Lin, J., Chen, Y., Zhang, Y., Lin, H., & Ouyang, Z. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-05037-7 · Cited by 19 · see citing works