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A "Silent" Polymorphism in the MDR 1 Gene Changes Substrate Specificity

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Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

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Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

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Evolution and tinkering.

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ROSE: A Deep Learning Based Framework for Predicting Ribosome StallingPreprint

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Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost

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Predicting gene sequences with AI to study codon usage patterns

Sidi, T., Elitzur, S. B., Tuller, T., & Kolodny, R. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2410003121 · Cited by 13

Selection for reduced translation costs at the intronic 5′ end in fungi

Zafrir, Z., Zur, H., & Tuller, T. (2016) · DNA Research · doi:10.1093/dnares/dsw019 · Cited by 12

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Zarai, Y., & Tuller, T. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006055 · Cited by 12

Controllability Analysis and Control Synthesis for the Ribosome Flow Model

Zarai, Y., Michael Margaliot, A., Sontag, E. D., & Tuller, T. (2017) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2017.2707420 · Cited by 14

Fine Tuning of Translation: A Complex Web of Mechanisms and Its Relevance to Plant Functional Genomics and Biotechnology

Кабардаева, К. В., Tyurin, A. A., Pavlenko, O. S., Алексеевна, Г. О., Deyneko, I. V., Kouchoro, F., Mustafaev, O. N., & Goldenkova-Pavlova, I. V. (2019) · Russian Journal of Plant Physiology · doi:10.1134/s1021443719060074 · Cited by 12

A report on DNA sequence determinants in gene expression

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Identification of differential key biomarkers in the synovial tissue between rheumatoid arthritis and osteoarthritis using bioinformatics analysis

Zhang, R., Zhou, X., Jin, Y., Chang, C., Wang, R., Liu, J., Fan, J., & He, D. (2021) · Clinical Rheumatology · doi:10.1007/s10067-021-05825-1 · Cited by 12

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

Kim, D. J., Kim, J., Lee, D. H., Lee, J., & Woo, H. M. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00202 · Cited by 12

Phage Predation Shapes the Population Structure of Shiga-Toxigenic Escherichia coli O157:H7 in the UK: An Evolutionary Perspective

Cowley, L. A., Dallman, T. J., Jenkins, C., & Sheppard, S. K. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00763 · Cited by 12

Nucleotide composition affects codon usage toward the 3'-end

Zahdeh, F., & Carmel, L. (2019) · PLoS ONE · doi:10.1371/journal.pone.0225633 · Cited by 11

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Panda, A., & Tuller, T. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00372-w · Cited by 11

Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model

Levin, D., & Tuller, T. (2018) · Scientific Reports · doi:10.1038/s41598-018-34496-3 · Cited by 12

Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts

Shahar, N., Weiner, I. N., Stotsky‐Oterin, L., Tuller, T., & Yacoby, I. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz151 · Cited by 11

Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design

Villada, J. C., Brustolini, O. J. B., & da Silveira, W. B. (2017) · DNA Research · doi:10.1093/dnares/dsx014 · Cited by 11

Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions

Goz, E., & Tuller, T. (2016) · Journal of Computational Biology · doi:10.1089/cmb.2016.0052 · Cited by 11

Whole genome sequence analysis of CPV-2 isolates from 1998 to 2020

Sarabandi, S., & Pourtaghi, H. (2023) · Virology Journal · doi:10.1186/s12985-023-02102-2 · Cited by 10

Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5’-Terminal End

Dewi, K. S., & Fuad, A. M. (2020) · Advanced Pharmaceutical Bulletin · doi:10.34172/apb.2020.073 · Cited by 12

Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5ʹ End of ORFeomes

Villada, J. C., Duran, M. F., & Lee, P. K. H. (2020) · mSystems · doi:10.1128/msystems.00613-20 · Cited by 9

PELSA-Decipher: A Software Tool for the Processing and Interpretation of Ligand–Protein Interaction Data Sets Acquired by PELSA

Zhu, H., Wang, K., Li, K., Fang, Z., Zhou, J., Xue, L., & Ye, M. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00365 · Cited by 8

Evaluation of the impact of polypeptide-p on diabetic rats upon its cloning, expression, and secretion in Saccharomyces boulardii

Yamchi, A., Rahimi, M., Javan, B., Abdollahi, D., Salmanian, M., & Shahbazi, M. (2023) · Archives of Microbiology · doi:10.1007/s00203-023-03773-9 · Cited by 10

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

Lauria, F., Tebaldi, T., Lunelli, L., Struffi, P., Gatto, P., Pugliese, A., Brigotti, M., Montanaro, L., Ciribilli, Y., Inga, A., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv781 · Cited by 8

Bioinformatic Analysis of Microbiome Data

Xia, Y., Sun, J., & Chen, D. (2018) · ICSA book series in statistics · doi:10.1007/978-981-13-1534-3_1 · Cited by 6

Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts

Abrahams, L., & Hurst, L. D. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx223 · Cited by 8

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

The discovery of multidrug resistant Staphylococcus aureus harboring novel SaRI isolated from retail foods

Zhang, F., Wu, S., Huang, J., Dai, J., Zhang, J., Yang, R., Xue, L., Zhao, M., Wang, J., Ding, Y., et al. (2021) · Food Control · doi:10.1016/j.foodcont.2021.108739 · Cited by 7

Design of typical genes for heterologous gene expression

Simm, D., Popova, B., Braus, G. H., Waack, S., & Kollmar, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-13089-1 · Cited by 7

Evolutionary selection against short nucleotide sequences in viruses and their related hosts

Zarai, Y., Zafrir, Z., Siridechadilok, B., Suphatrakul, A., Roopin, M., Julander, J. G., & Tuller, T. (2020) · DNA Research · doi:10.1093/dnares/dsaa008 · Cited by 8

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

Gao, N., He, Z., Zhu, Q., Jiang, P., Hu, S., & Chen, W. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.03.002 · Cited by 7

Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts

Elitzur, S. B., Cohen-Kupiec, R., Yacobi, D., Fine, L., Apt, B., Diament, A., & Tuller, T. (2021) · RNA Biology · doi:10.1080/15476286.2021.1978767 · Cited by 8

Protein yield is tunable by synonymous codon changes of translation initiation sitesPreprint

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C. J., & Gardner, P. P. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/726752 · Cited by 7

Directed evolution of Mesorhizobium loti carbonic anhydrase for carbon dioxide sequestration by MutaT7 and rational codon design

Ting, W., Effendi, S. S. W., Hu, R.-E., & Ng, I. (2023) · Journal of the Taiwan Institute of Chemical Engineers · doi:10.1016/j.jtice.2023.105065 · Cited by 6

A tool for CRISPR-Cas9 sgRNA evaluation based on computational models of gene expression

Cohen, S., Bergman, S., Lynn, N., & Tuller, T. (2024) · Genome Medicine · doi:10.1186/s13073-024-01420-6 · Cited by 8

Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins

Panda, A., & Tuller, T. (2020) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.005 · Cited by 6

Association of PCSK1 gene polymorphisms with abdominal fat content in broilers

Zhou, J., Yang, L., Yu, J., Zhang, K., Xu, Z., Cao, Z., Luan, P., Li, H., & Zhang, H. (2020) · Animal Science Journal · doi:10.1111/asj.13371 · Cited by 6

Modeling and Analyzing the Flow of Molecular Machines in Gene Expression

Zarai, Y., Michael Margaliot, A., & Tuller, T. (2018) · RNA technologies · doi:10.1007/978-3-319-92967-5_14 · Cited by 6

Standard Intein Gene Expression Ramps (SIGER) for Protein-Independent Expression Control

Fages‐Lartaud, M., Mueller, Y., Elie, F., Courtade, G., & Hohmann‐Marriott, M. F. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00530 · Cited by 5

Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling

Bordignon, P. D. C., & Pechmann, S. (2021) · FEBS Journal · doi:10.1111/febs.15748 · Cited by 6

A Dynamical Stochastic Model of Yeast Translation Across the Cell Cycle

Seeger, M., Flöttmann, M., & Klipp, E. (2020) · Heliyon · doi:10.1016/j.heliyon.2023.e13101 · Cited by 5

5′UTR Variant in KIT Associated With White Spotting in Horses

McFadden, A., Martin, K., Foster, G., Vierra, M., Lundquist, E. W., Everts, R. E., Martin, E., Volz, E., McLoone, K., Brooks, S. A., et al. (2023) · Journal of Equine Veterinary Science · doi:10.1016/j.jevs.2023.104563 · Cited by 5

Preferential use of minor codons in the translation initiation region of human genes

Park, J., Kwon, M., Yamaguchi, Y., Firestein, B. L., Park, J.-Y., Yun, J., Yang, J.-O., & Inouye, M. (2016) · Human Genetics · doi:10.1007/s00439-016-1735-x · Cited by 5

A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates

Harmon, L. M., Miller, J. B., Whiting, M. F., Kauwe, J. S. K., & Ridge, P. G. (2021) · Scientific Reports · doi:10.1038/s41598-020-78803-3 · Cited by 5

Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data

Neumann, T., & Tuller, T. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac021 · Cited by 7

The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface

Miller, J. B., Meurs, T. E., Hodgman, M. W., Song, B., Miller, K. N., Ebbert, M., Kauwe, J. S. K., & Ridge, P. G. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac039 · Cited by 5

Evaluation of GFP reporter utility for analysis of transcriptional slippage during gene expression

Wons, E., Koscielniak, D., Szadkowska, M., & Sęktas, M. (2018) · Microbial Cell Factories · doi:10.1186/s12934-018-0999-3 · Cited by 5

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · BMC Genomics · doi:10.1186/s12864-023-09482-3 · Cited by 4

Modeling coding sequence design for virus-based expression in tobacco

Burghardt, M., & Tuller, T. (2024) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2024.12.002 · Cited by 4

Hidden Silent Codes in Viral Genomes

Goz, E., Zur, H., & Tuller, T. (2017) · Springer eBooks · doi:10.1007/978-3-319-61569-1_5 · Cited by 4

How the Sequence of a Gene Specifies Structural Symmetry in Proteins

Shen, X., Huang, T., Wang, G., & Li, G. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144473 · Cited by 4

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

Ramp Sequence May Explain Synonymous Variant Association with Alzheimer’s Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA)

Miller, J. B., Brandon, J. A., Harmon, L. M., Sabra, H. W., Lucido, C. C., Murcia, J. D. G., Nations, K. A., Payne, S. H., Ebbert, M., Kauwe, J. S. K., et al. (2025) · Biomedicines · doi:10.3390/biomedicines13030739 · Cited by 3

Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression

Noßmann, M., Pieper, J., Hillmann, F., Brakhage, A. A., & Münder, T. (2017) · Current Genetics · doi:10.1007/s00294-017-0774-8 · Cited by 3

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast.

Cheng, J., Maier, K., Avsec, Z., Rus, P., & Gagneur, J. (2017) · MPG.PuRe (Max Planck Society) · Cited by 3

Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking

Zafrir, Z., & Tuller, T. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1497-z · Cited by 3

Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices

García, V., Zoller, S., & Anisimova, M. O. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200185 · Cited by 3

Conserved codon adaptation in highly expressed genes is associated with higher regularity in mRNA secondary structuresPreprint

Sterken, M. G., Wilbers, R. H. P., Prins, P., Snoek, B. L., Giambaşu, G. M., Slootweg, E. J., Holterman, M., Helder, J., Kammenga, J. E., Schots, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.23.393322 · Cited by 3

Yeast-derived low-purity FGF2 supports bovine ESC and MSC aggregates in suspension

Savyon, G., Tawil, S., Tadmor, Y., Atar, S., Porat, Y., Agmon, N., Schlesinger, S., Tuller, T., & Nachman, I. (2025) · Frontiers in Nutrition · doi:10.3389/fnut.2025.1679490 · Cited by 2

Bacterial gene 5′ ends have unusual mutation rates that can mislead tests of selection

Radrizzani, S., Rivas-Santisteban, J., Han, N., & Hurst, L. D. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003569 · Cited by 2

Mechanistic Modeling of In Vivo Translation in Escherichia coli Reliably Identifies Well-Adapted and Optimized RNA Sequences

Spindler, J., Giakissiklis, C., Stierle, C., Buschlüter, M., Liebeton, K., Siemann‐Herzberg, M., & Takors, R. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00578 · Cited by 2

Controlling the ribosomal density profile in mRNA translation

Zarai, Y., Michael Margaliot, A., Sontag, E. D., & Tuller, T. (2016) · IEEE Conference on Decision and Control (CDC) · doi:10.1109/cdc.2016.7798904 · Cited by 2

The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli

Zabolotskii, A. I., Kozlovskiy, S. V., & Katrukha, A. G. (2023) · Biochemistry (Moscow) · doi:10.1134/s0006297923140109 · Cited by 2

Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex

Himmelstrand, K., Durling, M. B., Karlsson, M., Stenlid, J., & Olson, Å. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1159811 · Cited by 2

Massive Factorial Design Untangles Coding Sequences Determinants of Translation EfficacyPreprint

Cambray, G., Guimaraes, J. C., & Arkin, A. P. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/208801 · Cited by 2

XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into DataPreprint

Berg, J. A., Belyeu, J. R., Morgan, J. T., Ouyang, Y., Bott, A. J., Quinlan, A. R., Gertz, J., & Rutter, J. P. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/704320 · Cited by 2

A tool for CRISPR-Cas9 gRNA evaluation based on computational models of gene expressionPreprint

Cohen, S., Bergman, S., Lynn, N., & Tuller, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.08.598047 · Cited by 2

Influence of 5′-UTR nucleotide composition on translation efficiency in Escherichia coli

Li, J., Li, J., Li, P., Zhang, J., Liu, Q., & Qi, H. (2024) · Research in Microbiology · doi:10.1016/j.resmic.2024.104260 · Cited by 1

Silent mutations in coding regions of Hepatitis C virus affect patterns of HCV RNA structures and attenuate viral replication and pathogenesis

Dabour, R., Bergman, S., Zafrir, Z., Davidovitch, A., Werbner, M., Gal-Tanamy, M., & Tuller, T. (2025) · Genome biology · doi:10.1186/s13059-025-03816-y · Cited by 1

Evaluation of synthetic post-transcription regulatory sequences reveals design principle to enhance mRNA stability and translation efficiency

Zhang, J., Mei, Z., Ren, J., Zhang, X., Gong, J., Xu, G., Li, H., Zhang, X., & Xu, Z. (2025) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2025.11.011 · Cited by 1

A motif in the 5′untranslated region of messenger RNAs regulates protein synthesis in a S6 kinase-dependent manner

Shin, H.-C., Bochkov, Y. A., Kim, K., Gern, J. E., Jarjour, N. N., & Esnault, S. J. (2023) · Advances in Biological Regulation · doi:10.1016/j.jbior.2023.100975 · Cited by 1

Less is more: slow-codon windows enhance eGFP mRNA resilience against RNA interference

Müller, J., Schwake, G., Reiser, A., Woschée, D., Alirezaeizanjani, Z., Rädler, J. O., & Rudorf, S. (2025) · Journal of The Royal Society Interface · doi:10.1098/rsif.2024.0582

CSN: unsupervised approach for inferring biological networks based on the genome alone

Galili, M., & Tuller, T. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-3479-9 · Cited by 1

Computational discovery and modeling of novel gene expression rules encoded in the mRNA

Elitzur, S. B., & Tuller, T. (2020) · Biochemical Society Transactions · doi:10.1042/bst20191048 · Cited by 1

Silence of the mutations

Mahadevan, S. (2022) · Journal of Biosciences · doi:10.1007/s12038-022-00320-4 · Cited by 1

Quantitative Principles of cis -translational control by general mRNA sequence features in eukaryotes

Li, J. J., Chew, G.-L., & Biggin, M. D. (2019) · doi:10.1101/587584 · Cited by 1

A Model for Competition for Ribosomes in the CellPreprint

Raveh, A., Michael Margaliot, A., Sontag, E. D., & Tuller, T. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1508.02408 · Cited by 1

Not so giant steps on tuning protein production and diminished genomes

Finger‐Bou, M. (2023) · doi:10.18174/632756 · Cited by 1

Effective sequence-to-expression prediction for membrane proteins using machine learning and computational protein designPreprint

Shen, Y., Underhill, J., Mulholland, A. J., Oyarzún, D. A., & Curnow, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.25.678317 · Cited by 1

Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaeaPreprint

Umu, S. U., Poole, A. M., Dobson, R. C. J., & Gardner, P. P. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/033613 · Cited by 1

Tuning for light and more : engineering phototrophy and membrane proteins in Escherichia coli

Claassens, N. J. (2017) · doi:10.18174/405559 · Cited by 1

Accounting for programmed ribosomal frameshifting in the computation of codonPreprint

García, V., Zoller, S., & Anisimova, M. O. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/293340

Structure-Function Relationships of the Nucleocapsid in Vesicular Stomatitis Virus

Gumpper, R. H. (2022) · Digital Archive @ GSU · doi:10.57709/13404554

Ribosome Flow Model with Extended ObjectsPreprint

Zarai, Y., Michael Margaliot, A., & Tuller, T. (2017) · arXiv (Cornell University) · doi:10.48550/arxiv.1705.09347

Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomesPreprint

Villada, J. C., Duran, M. F., & Lee, P. K. H. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/811612

Improving recombinant protein production using TISIGNER.comPreprint

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.09.196469

Tissue-specific ramp sequences correspond with increased gene expression in humans and SARS-CoV-2Preprint

Miller, J. B., Meurs, T. E., Hodgman, M. W., Song, B. P., Ebbert, M., Kauwe, J. S. K., & Ridge, P. G. (2021) · Research Square · doi:10.21203/rs.3.rs-738082/v1

Determinants of efficient modulation of ribosomal traffic jams

Vinokour, S., & Tuller, T. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.10.030

Expression comparison between two genes encoding CSF3 recombinant proteins having different codon composition at N-terminal in Escherichia coli

Dewi, K. S., Wahyuni, F. D., Salsabila, S., Aminah, Yanthi, N. D., & Fuad, A. M. (2021) · IOP Conference Series Earth and Environmental Science · doi:10.1088/1755-1315/948/1/012081

New approaches and software for sequence function prediction and gene design integrating specific knowledge on protein structure and translation

Simm, D. (2022) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9118

Revealing determinants of translation efficiency via whole-gene codon randomisation and machine learningPreprint

Nieuwkoop, T., Terlouw, B. R., de Ridder, D., John van der, O. O. S. T., & Claassens, N. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.05.486962

Enhancing functional expression of L-glycerophosphate oxidase in Escherichia coli by controlling the expression rate

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Influence of 5’-UTR base types on translation efficiency in Escherichia coliPreprint

Li, J., Li, J., Li, P., Zhang, J., Liu, Q., & Qi, H. (2023) · Research Square · doi:10.21203/rs.3.rs-3063204/v1

Deciphering the non-ribosomal code: the language of antibiotics and other natural products

Terlouw, B. R. (2023) · doi:10.18174/635495

Additional file 2 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658191

Additional file 1 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658188

Additional file 6 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658209

Additional file 7 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658212

Additional file 4 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658200

Additional file 5 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658206

Additional file 3 of The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

Bykova, A., Saura, A., Glazko, G. V., Roche-Lima, A., Yurchenko, V., & Rogozin, I. B. (2023) · Figshare · doi:10.6084/m9.figshare.23658197

Analyses of the 5’ Ends of Escherichia coli ORFsPreprint

Ward, M., & Curran, J. F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.27.457967

Initiation codons within 5′-leaders of mRNAs as regulators of translation

Geballe, A. P., & Morris, D. (1994) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(94)90277-1 · Cited by 205

Enrichment of rare codons at 5' ends of genes is a spandrel caused by evolutionary sequence turnover and does not improve translation

Sejour, R., Leatherwood, J., Yurovsky, A., & Futcher, B. (2023) · eLife · doi:10.7554/elife.89656 · Cited by 12

The influences of 5' codon context on translation termination

Mottagui‐Tabar, S. (1997)

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

Moreira, M. H., Barros, G. C., Requião, R. D., Rossetto, S., Domitrovic, T., & Palhano, F. L. (2019) · RNA Biology · doi:10.1080/15476286.2019.1661213 · Cited by 12