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Ribosome reinitiation can explain length-dependent translation of messenger RNA

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Ribosome slowdown triggers codon‐mediated mRNA decay independently of ribosome quality control

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5'UTR mutations of ENG cause hereditary hemorrhagic telangiectasia

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Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning

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5'-UTR SNP of FGF13 causes translational defect and intellectual disability

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A nascent peptide code for translational control of mRNA stability in human cells

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Using protein-per-mRNA differences among human tissues in codon optimization

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Quantitative profiling of human translation initiation reveals elements that potently regulate endogenous and therapeutically modified mRNAs

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Current limitations in predicting mRNA translation with deep learning models

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Translation elongation as a rate-limiting step of protein production

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Translation arrest as a protein quality control system for aberrant translation of the 3′‐UTR in mammalian cells

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Riboformer: a deep learning framework for predicting context-dependent translation dynamics

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mRNA-LM: full-length integrated SLM for mRNA analysis

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A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

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NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development

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The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation

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Translation efficiency covariation identifies conserved coordination patterns across cell types

Liu, Y., Rao, S., Hoskins, I., Geng, M., Zhao, Q., Chacko, J., Ghatpande, V., Qi, K., Persyn, L., Wang, J., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02718-5 · Cited by 15 · see citing works

Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease

Rey, A. D., Pozo‐Valero, M. D., Bouckaert, M., Wood, K., den Broeck, F. V., Varela, M. D., Thomas, H. B., Heetvelde, M. V., Bruyne, M. D., de Sompele, S. V., et al. (2024) · Genome Medicine · doi:10.1186/s13073-023-01277-1 · Cited by 14 · see citing works

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

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Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders

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Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates

Ahmed, N., Friedrich, U. A., Sormanni, P., Ciryam, P., Altman, N., Bukau, B., Krämer, G., & O’Brien, E. P. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.10.030 · Cited by 11 · see citing works

Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activationPreprint

Mercier, B. C., Labaronne, E., Cluet, D., Guiguettaz, L., Fontrodona, N., Bicknell, A. A., Corbin, A., Wencker, M., Aubé, F., Modolo, L., et al. (2024) · Genome Research · doi:10.1101/gr.277863.123 · Cited by 11 · see citing works

Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiationPreprint

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Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control

Chen, K. Y., Park, H., & Subramaniam, A. R. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae285 · Cited by 6 · see citing works

Influence of nascent polypeptide positive charges on translation dynamics

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How DNA encodes the start of transcription

Wang, J., & Agarwal, V. (2024) · Science · doi:10.1126/science.adp0869 · Cited by 3 · see citing works

RiboNN: A deep learning model to predict translation efficiency from mRNA sequence

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Classical machine learning models to predict TE

Persyn, L., Liu, Y., & Cenik, C. (2025) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.15360966 · Cited by 1 · see citing works

Current Analytical Strategies for mRNA-Based Therapeutics

Camperi, J., Chatla, K., Freund, E. C., Galan, C., Lippold, S., & Guilbaud, A. (2025) · Molecules · doi:10.3390/molecules30071629 · Cited by 43 · see citing works

Regulation of gene expression by alternative polyadenylation in health and disease

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Not so cold! Improving the thermostability of mRNA vaccines

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mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset

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Translation efficiency covariation identifies conserved coordination patterns across cell types

Liu, Y., Rao, S., Hoskins, I., Geng, M., Zhao, Q., Chacko, J., Ghatpande, V., Qi, K., Persyn, L., Wang, J., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02718-5 · Cited by 15 · see citing works

Long-read RNA sequencing reveals allele-specific N 6 -methyladenosine modificationsPreprint

Park, D., & Cenik, C. (2024) · Genome Research · doi:10.1101/gr.279270.124 · Cited by 13 · see citing works

The Fluidic Connectome in Brain Disease: Integrating Aquaporin-4 Polarity with Multisystem Pathways in Neurodegeneration

Brehar, F.-M., Costea, D., Tătaru, C. P., Rădoi, M. P., Ciurea, A. V., Munteanu, O., & Tulin, A. D. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262311536 · Cited by 10 · see citing works

Translational buffering tunes gene expression in mice and humans

Rao, S., Le, A. Y., Persyn, L., & Cenik, C. (2026) · Genome biology · doi:10.1186/s13059-026-04010-4 · Cited by 9 · see citing works

The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture

Vázquez, N., Lee, C., Valenzuela, I., Phan, T. P., Derderian, C., Chávez, M., Mooney, N. A., Demeter, J., Aziz‐Zanjani, M. O., Cuscó, I., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61005-8 · Cited by 8 · see citing works

Artificial intelligence in precision mRNA therapeutics: Towards genomic language models and multi-agent virtual humans

Tan, T., Diao, Y., Yu, X., Chen, L., & Fang, H. (2026) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2025.12.044 · Cited by 7 · see citing works

Polysomal Profiling Coupled to Allele-Specific Proteomics Reveals an EIF4H TranSNP Allele Possessing Higher mRNA Translation Potential

Hamadou, M. H., Alunno, L., Peroni, D., Pancher, M., Mazza, F., Venturelli, T., Belli, R., Dassi, E., Romanel, A., & Inga, A. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101535 · Cited by 3 · see citing works

Interplay between codon usage and ribosome heterogeneity: A new layer of translational regulation

Dahal, U., Bansal, A., Dahal, A. R., Aryal, M. R., & Khanal, B. (2025) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2025.152971 · Cited by 3 · see citing works

Mechanometabolism instructs hematopoietic stem cell specification

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mRNABench: A curated benchmark for mature mRNA property and function predictionPreprint

Shi, R., Dalal, T., Fradkin, P., Koyyalagunta, D., Chhabria, S., Jung, A., Tam, C. L., Ceyhan, D., Lin, J., Laverty, K. U., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.05.662870 · Cited by 3 · see citing works

Programming human cell type-specific gene expression via an atlas of AI-designed enhancersPreprint

Castillo-Hair, S. M., Yin, C., VandenBosch, L. S., Cherry, T. J., Meuleman, W. R. A., & Seelig, G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.679565 · Cited by 4 · see citing works

mRNA vaccines in cancer immunotherapy: current progress and perspectives in solid tumors and hematologic malignancies

Qiao, N., Chen, J., Liu, Y., Chen, Z. J., & Chen, S. J. (2026) · MedScience · doi:10.1007/s11684-026-1210-6 · Cited by 2 · see citing works

FlashRNA: An Efficient Model for Regulatory GenomicsPreprint

Jung, A., Zhu, H., Gao, A. J., Li, R., Slobodyanyuk, M., Chu, V., Lim, D., Lee, L. J., Celaj, A., & Frey, B. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.14.682350 · Cited by 2 · see citing works

Spatiotemporal multi-omics atlas of the aging neuromuscular junctionPreprint

Amoretti, S., Negro, S., Lauria, F., Tebaldi, T., Zanetti, G., Pirazzini, M., Mann, M., Murgia, M., Viero, G., & Rigoni, M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.27.690955 · Cited by 2 · see citing works

System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural developmentPreprint

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Deep learning model for predicting mRNA half-life based on 3′UTR sequences

Jin, X., Wang, W., Wang, A., Zhang, Y., Mao, Y., & Zhang, D. (2026) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2026.153691 · Cited by 1 · see citing works

Decoding the language of messenger RNA

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Molecular and structural remodeling of stress granules in slowly and rapidly progressive Alzheimer’s diseasePreprint

Saleem, T., Schmitz, M., Zafar, S., Correia, S., Fernandez, L. C. F., Fischer, A.-L., Thomas, C., Goebel, S., Möbius, W., Younas, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.20.665556 · Cited by 1 · see citing works

Ultra-parallel ribosome profiling platform with RNA-dependent RNA amplificationPreprint

Shichino, Y., Mito, M., Kinugasa, Y., Wakigawa, T., Yamashita, A., Mishima, Y., Imai, Y., & Iwasaki, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.06.668979 · Cited by 1 · see citing works

Enigma: An Efficient Model for Deciphering Regulatory GenomicsPreprint

Jung, A., Zhu, H., Li, R., Gao, A. J., Lau, T., Chu, V. S., Lim, D., Cole, C. B., Lee, L. J., Celaj, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.18.694875 · Cited by 1 · see citing works

Di-codon organization links tRNA modifications to cancer cell proteome compositionPreprint

Moghaddam, K. H., Timpone, C., Gowda, L. N., Tutuka, C. A., Risbridger, G. P., Steele, J. R., Schittenhelm, R. B., Kusnadi, E. P., Furic, L., & Larsson, O. S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.10.710911 · Cited by 1 · see citing works

5′ untranslated regions tune Toxoplasma translationPreprint

Peters, M. L., Shukla, A., Gotthold, Z. A., McCormick, D. M., Xiang, K., Bartel, D. P., & Lourido, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.14.664749

Topological and functional characterization of human translation efficiency covariation network

Qi, K., & Cenik, C. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf583

GC3 codons enhance protein production in diverse GC- and AT-rich plant speciesPreprint

Kaufman, I. D., Wu, H.-Y. L., & Hsu, P. Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.25.690434 · Cited by 1 · see citing works

Decoding UTRs by applying explainable AI to a genomic foundation modelPreprint

Brase, L., Creamer, D. R., Shapovalova, Y., Ashe, M., Ashe, H. L., & Rattray, M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.04.692303

Robust Functionality and Regulation of Selectively Expressed RNA as AAV Vectors and In Vitro Transcribed Molecules

Rastfeld, F., Hersch, N., Dreissen, G., Manoharan, H., Wagner, L., Lövenich, L., Barczak, E., Büning, H., Merkel, R., & Hoffmann, B. (2025) · Pharmaceutics · doi:10.3390/pharmaceutics17121595

Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia

Khadra, E., Iqbal, Z., Gall, M. L., Clary, G., Levavasseur, F., Tuerdi, Z., Dussiau, C., Rombaut, D., Templé, M., Friedrich, C., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09156-8

Disordered but Different: Functional and Evolutionary Divergence of Transcription Factor Intrinsically Disordered RegionsPreprint

Song, S. E., & Akey, J. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.700206

Genetic variation shapes human mRNA translation and disease riskPreprint

Wang, S., Chen, C., Xiao, X. G., & Wang, Z. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.10.705206

A Universal, AI-based Design Framework for Efficient Manufacturing of mRNA TherapeuticsPreprint

Liao, K., Maccari, G., Ciano, G., Huber, R. G., von der Haar, T., Tham, C. Y., Ong, N. T. X., de Sessions, P. F., Saw, T. Y., Lim, T. W., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.09.710039

Integrin Beta 4 Protein Expression Bimodally Predicts Sensitivity to CDK4/6 Inhibition and Resistance to Immunotherapy in Breast Cancer

Zhu, Z., Hu, L. X., Ma, Y.-W., & Zhu, Q.-N. (2026) · The Breast Journal · doi:10.1155/tbj/7668096

Artificial intelligence for coordinating vaccine design, antiviral discovery, and real-world monitoring in the era of emerging and endemic viral threats

Akingbola, A., Adegbesan, A., Adewole, O. A., Adebiyi, K. O., Benson, A. E., Ojo, O., Jessica, O. U., Alabi, O. S., Ojeriakhi, O. J., & Shekoni, M. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1773609

Allele-resolved monosome and polysome sequencing identifies functional cis-acting variants affecting mRNA translation efficiencyPreprint

Alunno, L., Massignani, I., Hamadou, M. H., Mazza, F., Peroni, D., Belli, R., Dassi, E., Romanel, A., & Inga, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.07.723424

Loss of MAGEL2 Disrupts Pituitary Translation in a Mouse Model of PWS and Schaaf–Yang SyndromePreprint

Bayat, T., Sanchez, M. C. H., Almonacid, C. C. R., Štepihar, D., Tikhonova, E. B., Popy, F. Y., Gutierrez, J. S. S., Myers, S., Vittori, M., Karamyshev, A. L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.12.724462

Nascent protein retention at polysomes reduces kinetic barriers to self-assemblyPreprint

Venkatesan, S., Schulze, A. T. V., Lange, J. J., Jensen, J., Berkowicz, L. E., Tsuchiya, D., Zhang, N., Gardner, J., McCroskey, S., Zhang, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.17.725791

Inferring translational efficiency from transcriptomes improves noncanonical neoantigen prioritization and cancer patient stratification

Ma, Y., Gao, C., Xu, K., Wang, K., Ma, J., Cai, Y., Lv, D., Li, S., Jiang, Q., Wang, K., et al. (2026) · npj Precision Oncology · doi:10.1038/s41698-026-01567-y

Remodeling of mRNA by eIF4F in human translation initiationPreprint

Alvarado, C., Lapointe, C. P., Wang, J., Sokabe, M., Grosely, R., Dhepe, A., Stackhouse, C. I., Palo, M. Z., Mamot, A., Jemielity, J., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.19.733470

seq2ribo : structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences

Kaynar, G., & Kingsford, C. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag296

5UTRnet: A deep learning model for designing high-efficiency 5′ UTRs in mRNA therapeutics

Xin, J., Shi, Y., Qin, Z., Huang, L., Sun, J., Teng, Y., Zhao, S., Chen, Y., Tian, C., Li, G., et al. (2026) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2026.07.012

Global translational reprogramming in Trichophyton mentagrophytes -infected keratinocytes

Wan, J., Zhang, Y., Deng, Y., Zhang, R., Yang, K., Zhu, X., Zheng, J., Li, B., You, J., Fu, L., et al. (2026) · Virulence · doi:10.1080/21505594.2026.2710548

Smart Design: Integrating Artificial Intelligence and Gene Editing for Advanced mRNA Therapeutics

Shi, H., Liu, S., Dai, D., Jiang, S., Tian, T., Niu, Z., Xiang, Z., Zou, C., Liu, F., Tang, X., et al. (2026) · MedComm – Biomaterials and Applications · doi:10.1002/mba2.70062

Deep3MVPF: Multiview Deep Framework for the Prediction of Stability and m6A in mRNA 3′UTR

Liu, J., Zhang, Q., Song, J., & Yu, D. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01345

Programmable mRNA Nanotherapeutics through Logic Switch Design

Chen, P., Alhussan, A., Cullis, P. R., & Cabral, H. (2026) · ACS Nano Medicine · doi:10.1021/acsnanomed.6c00159

A trainable language model with potential to modulate translation rates in non-model organisms by generating upstream untranslated region sequence libraries

Duggan, A. D., Newman, M. P., & McMillen, D. R. (2026) · PLoS ONE · doi:10.1371/journal.pone.0348455

Artificial Intelligence in RNA Research: From Molecular Design to Translational Analytics and Quality Control

Enkmann, V., & Rajicic, N. (2026) · AI Chemistry · doi:10.3390/aichem1030015

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

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

Synonymous sequence design controls the folding, processing, and activity of the therapeutic protein ADAMTS13

Jankowska, K. I., Katneni, U., Lin, B., Brenner, H. M., Amarasinghe, R., Padhiar, N. H., Dopler, P., Hamasaki‐Katagiri, N., Wu, W. W., Zhu, H., et al. (2026) · Trends in biotechnology · doi:10.1016/j.tibtech.2026.09.003 · Cited by 1 · see citing works

Allele-resolved monosome and polysome sequencing identifies cis-variants affecting mRNA translation

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Predicting and optimizing the translation efficiency of messenger RNA in mammalian cells

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DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control

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RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes

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