Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

An Introduction to the Bootstrap

Efron, B., & Tibshirani, R. J. (1994) · doi:10.1201/9780429246593 · Cited by 40,500 · see citing works

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works

The Proceedings of the National Academy of Sciences

Richards, J. W. (1915) · Science · doi:10.1126/science.42.1074.161 · Cited by 13,941 · see citing works

UniProt: the Universal Protein knowledgebase

Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H.-Z., Lopez, R., Magrane, M., et al. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gkh131 · Cited by 8,795 · see citing works

Biopython: freely available python tools for computational molecular biology and bioinformatics

Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080 · see citing works

A "Silent" Polymorphism in the <i>MDR</i> 1 Gene Changes Substrate Specificity

Kimchi-Sarfaty, C., Oh, J. M., Kim, I.-W., Sauna, Z. E., Calcagno, A. M., Ambudkar, S. V., & Gottesman, M. M. (2007) · Science · doi:10.1126/science.1135308 · Cited by 2,416 · 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

Journal of the Royal Statistical Society: Series B (Methodological)

(2018) · Journal of the Royal Statistical Society Series B (Methodological) · doi:10.1111/(issn)2517-6161 · Cited by 1,612 · see citing works

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90003-6 · Cited by 1,423 · see citing works

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

Drummond, D. A., & Wilke, C. O. (2008) · Cell · doi:10.1016/j.cell.2008.05.042 · Cited by 1,041 · see citing works

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

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

Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

Sussman, J. L., Lin, D., Jiang, J., Manning, N. O., Prilusky, J., Ritter, O., & Abola, E. E. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998009378 · Cited by 743 · see citing works

Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy

Akashi, H. (1994) · Genetics · doi:10.1093/genetics/136.3.927 · Cited by 742 · see citing works

The European nucleotide archive

Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq967 · Cited by 690 · see citing works

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

Hollingsworth, S. A., & Karplus, P. A. (2010) · BioMolecular Concepts · doi:10.1515/bmc.2010.022 · Cited by 429 · see citing works

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

Buhr, F., Jha, S., Thommen, M., Mittelstaet, J., Kutz, F., Schwalbe, H., Rodnina, M. V., & Komar, A. A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.008 · Cited by 395 · see citing works

Coevolution of codon usage and transfer RNA abundance

Bulmer, M. G. (1987) · Nature · doi:10.1038/325728a0 · Cited by 305 · see citing works

Heterologous Protein Expression Is Enhanced by Harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host

Angov, E., Hillier, C. J., Kincaid, R. L., & Lyon, J. A. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002189 · Cited by 284 · see citing works

A code within the genetic code: codon usage regulates co-translational protein folding

Liu, Y. (2020) · Cell Communication and Signaling · doi:10.1186/s12964-020-00642-6 · Cited by 252 · see citing works

Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution

Pagani, F., Raponi, M., & Baralle, F. E. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502288102 · Cited by 243 · see citing works

A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

Mohammad, F., Green, R., & Buskirk, A. R. (2019) · eLife · doi:10.7554/elife.42591 · Cited by 242 · see citing works

Exact and asymptotically robust permutation tests

Chung, E., & Romano, J. P. (2013) · The Annals of Statistics · doi:10.1214/13-aos1090 · Cited by 239 · see citing works

Codon optimization with deep learning to enhance protein expression

Fu, H., Liang, Y., Zhong, X., Pan, Z., Huang, L., Zhang, H., Xu, Y., Zhou, W., & Liu, Z. (2020) · Scientific Reports · doi:10.1038/s41598-020-74091-z · Cited by 232 · see citing works

A pan-cancer analysis of synonymous mutations

Sharma, Y., Miladi, M., Dukare, S., Boulay, K., Caudron‐Herger, M., Groß, M., Backofen, R., & Diederichs, S. (2019) · Nature Communications · doi:10.1038/s41467-019-10489-2 · Cited by 226 · see citing works

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

Walsh, I. M., Bowman, M. A., Santarriaga, I. F. S., Rodríguez, A., & Clark, P. L. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907126117 · Cited by 223 · 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

A Synonymous Single Nucleotide Polymorphism in ΔF508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein

Bartoszewski, R., Jablonsky, M. J., Bartoszewska, S., Stevenson, L. M., Dai, Q., Kappes, J. C., Collawn, J. F., & Bebők, Z. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.154575 · Cited by 202 · see citing works

Non-Synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association

Chen, R., Davydov, E. V., Sirota, M., & Butte, A. J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013574 · Cited by 195 · see citing works

Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

Alexaki, A., Kames, J. M., Holcomb, D. D., Athey, J. C., Santana-Quintero, L. V., Lam, P. V., Hamasaki‐Katagiri, N., Osipova, E., Simonyan, V. V., Bar, H., et al. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.04.021 · Cited by 180 · see citing works

The efficiency of folding of some proteins is increased by controlled rates of translation in vivo

Purvis, I. J., Bettany, A. J. E., Santiago, T. C., Coggins, J. R., Duncan, K., Eason, R. W., & Brown, A. J. P. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90230-0 · Cited by 178 · see citing works

The Yin and Yang of codon usage

Komar, A. A. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw207 · Cited by 175 · see citing works

Synonymous codon usage influences the local protein structure observed

Saunders, R., & Deane, C. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq495 · Cited by 165 · see citing works

The Effects of Codon Context on In Vivo Translation Speed

Chevance, F. F. V., Guyon, S. L., & Hughes, K. T. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004392 · Cited by 145 · see citing works

Transfer RNA Modification: Presence, Synthesis, and Function

Björk, G. R., & Hagervall, T. G. (2014) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0007-2013 · Cited by 124 · see citing works

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

Zhao, F., Yu, C.-H., & Liu, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx501 · Cited by 120 · see citing works

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens

Gu, W., Zhou, T., Ma, J., Sun, X. S., & Lu, Z. (2004) · Biosystems · doi:10.1016/j.biosystems.2003.10.001 · Cited by 112 · see citing works

Sense codons are found in specific contexts

Yarus, M., & Folley, L. S. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90239-6 · Cited by 110 · see citing works

Studies on the Relationships between the Synonymous Codon Usage and Protein Secondary Structural Units

GUPTA, S. K., Majumdar, S., Bhattacharya, T. K., & Ghosh, T. C. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.2351 · Cited by 110 · see citing works

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Keedy, D. A., Fraser, J. S., & van den Bedem, H. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004507 · Cited by 96 · see citing works

Optimal sequence alignment allowing for long gaps

Gotoh, O. (1990) · Bulletin of Mathematical Biology · doi:10.1007/bf02458577 · Cited by 91 · see citing works

Non‐random usage of ‘degenerate’ codons is related to protein three‐dimensional structure

Adzhubei, A. A., Adzhubeib, I. A., Krasheninnikov, I. A., & Neidle, S. (1996) · FEBS Letters · doi:10.1016/s0014-5793(96)01287-2 · Cited by 88 · see citing works

Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B

Simhadri, V. L., Hamasaki‐Katagiri, N., Lin, B. C., Hunt, R., Jha, S. S., Tseng, S. C., Wu, A., Bentley, A. A., Zichel, R., Lü, Q., et al. (2016) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2016-104072 · Cited by 85 · see citing works

Optimal sequence alignment allowing for long gaps

Gotoh, O. (1990) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(05)80216-2 · Cited by 79 · see citing works

Flexibility of α-Helices: Results of a Statistical Analysis of Database Protein Structures

Emberly, E. G., Mukhopadhyay, R., Wingreen, N. S., & Tang, C. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00097-4 · Cited by 71 · see citing works

Flexibility of β‐sheets: Principal component analysis of database protein structures

Emberly, E. G., Mukhopadhyay, R., Tang, C., & Wingreen, N. S. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10618 · Cited by 55 · see citing works

The Silent Sway of Splicing by Synonymous Substitutions

Mueller, W. F., Larsen, L. S. Z., Garibaldi, A., Hatfield, G. W., & Hertel, K. J. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.684035 · Cited by 55 · see citing works

A single synonymous mutation determines the phosphorylation and stability of the nascent protein

Karakostis, K., Gnanasundram, S. V., López, I., Thermou, A., Wang, L., Nylander, K., Olivares‐Illana, V., & Fåhræus, R. (2018) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjy049 · Cited by 52 · see citing works

An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria

Wei, Y., Silke, J. R., & Xia, X. (2019) · Scientific Reports · doi:10.1038/s41598-019-39369-x · Cited by 51 · see citing works

Assessing optimal: inequalities in codon optimization algorithms

Ranaghan, M. J., Li, J. J., Laprise, D., & Garvie, C. W. (2021) · BMC Biology · doi:10.1186/s12915-021-00968-8 · Cited by 45 · see citing works

Differential bicodon usage in lowly and highly abundant proteins

Diambra, L. A. (2017) · PeerJ · doi:10.7717/peerj.3081 · Cited by 38 · see citing works

Case for the genetic code as a triplet of triplets

Chevance, F. F. V., & Hughes, K. T. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614896114 · Cited by 37 · see citing works

Multidimensional Scaling

Boyarski, A., & Bronstein, A. M. (2020) · Springer eBooks · doi:10.1007/978-3-030-03243-2_827-1 · Cited by 21 · see citing works

ISSD Version 2.0: taxonomic range extended

Adzhubei, I. A., & Adzhubei, A. A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.268 · Cited by 18 · see citing works

Unraveling the Role of Silent Mutation in the ω-Subunit of Escherichia coli RNA Polymerase: Structure Transition Inhibits Transcription

Patel, U. R., Gautam, S., & Chatterji, D. (2019) · ACS Omega · doi:10.1021/acsomega.9b02103 · Cited by 15 · see citing works

A Comprehensive Analysis and Splicing Characterization of Naturally Occurring Synonymous Variants in the ATP7B Gene

Zhou, X., Zhou, W., Wang, C., Wang, L., Jin, Y., Jia, Z., Liu, Z., & Zheng, B. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.592611 · Cited by 14 · see citing works

Synonymous Codon Usage Bias Dependent on Local Nucleotide Context in the Class Deinococci

Cutler, R. W., & Chantawannakul, P. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9152-y · Cited by 4 · see citing works

Cod-confDB: a codon - conformation database

Singh, V. K., Suri, A., & Thomas-Cherian, S. (2005) · doi:10.1109/icisip.2005.1529475 · Cited by 1 · see citing works

Mechanisms and pathology of protein misfolding and aggregation

Louros, N. N., Schymkowitz, J. W. H., & Rousseau, F. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00647-2 · Cited by 259 · see citing works

Machine Learning-Guided Protein Engineering

Kouba, P., Kohout, P., Haddadi, F., Bushuiev, A., Samusevich, R., Sedlář, J., Damborský, J., Pluskal, T., Šivic, J., & Mazurenko, S. (2023) · ACS Catalysis · doi:10.1021/acscatal.3c02743 · Cited by 214 · see citing works

Computational and artificial intelligence-based methods for antibody development

Kim, J., McFee, M., Fang, Q., Abdin, O., & Kim, P. M. (2023) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.12.005 · Cited by 178 · see citing works

Codon language embeddings provide strong signals for use in protein engineering

Outeiral, C., & Deane, C. M. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00791-0 · Cited by 87 · see citing works

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

Wei, J., Stoesser, N. E., Matthews, P. C., Khera, T. K., Gethings, O., Diamond, I. D., Studley, R., Taylor, N. P., Peto, T., Walker, A. S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-44973-1 · Cited by 65 · see citing works

Variability in SOD1-associated amyotrophic lateral sclerosis: geographic patterns, clinical heterogeneity, molecular alterations, and therapeutic implications

Huang, M., Liu, Y., Yao, X., Qin, D., & Su, H. (2024) · Translational Neurodegeneration · doi:10.1186/s40035-024-00416-x · Cited by 68 · see citing works

Translation Rates and Protein Folding

Komar, A. A., Samatova, E., & Rodnina, M. V. (2023) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168384 · Cited by 55 · see citing works

Implementing computational methods in tandem with synonymous gene recoding for therapeutic development

Lin, B. C., Kaissarian, N. M., & Kimchi‐Sarfaty, C. (2022) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.09.008 · Cited by 21 · see citing works

Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life

Hallee, L., & Khomtchouk, B. B. (2023) · Scientific Reports · doi:10.1038/s41598-023-28965-7 · Cited by 19 · see citing works

The structural plasticity of polyglutamine repeats

Pereira, P. J. B., Manso, J. A., & Macedo‐Ribeiro, S. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102607 · Cited by 18 · see citing works

RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment

Sänger, L., Williams, H. M., Yu, D., Vogel, D., Kosinski, J., Rosenthal, M., & Uetrecht, C. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c07325 · Cited by 17 · see citing works

cdsBERT - Extending Protein Language Models with Codon AwarenessPreprint

Hallee, L., Rafailidis, N., & Gleghorn, J. P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.15.558027 · Cited by 17 · see citing works

An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units

Rosenberg, A. A., Yehishalom, N., Marx, A., & Bronstein, A. M. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2301064120 · Cited by 16 · see citing works

mRNA Cancer Vaccines: From Pandemic Paradigm to Personalized Oncology Therapeutics

Yang, B., Liu, J., Yang, L., & Liu, X. (2025) · Cancer Innovation · doi:10.1002/cai2.70041 · Cited by 16 · see citing works

Clinical and Therapeutic Evaluation of the Ten Most Prevalent CRB1 Mutations

da Costa, B. L., Kolesnikova, M., Levi, S. R., Cabral, T., Tsang, S. H., Maumenee, I. H., & Quinn, P. M. J. (2023) · Biomedicines · doi:10.3390/biomedicines11020385 · Cited by 14 · see citing works

Two birds with one stone: human SIRPα nanobodies for functional modulation and in vivo imaging of myeloid cells

Wagner, T. R., Blaess, S., Leske, I. B., Frecot, D. I., Gramlich, M., Traenkle, B., Kaiser, P. D., Seyfried, D., Maier, S. M., Rezza, A., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1264179 · Cited by 14 · see citing works

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study

Wang, Y., Selvaraj, M. S., Li, X., Li, Z., Holdcraft, J. A., Arnett, D. K., Bis, J. C., Blangero, J., Boerwinkle, E., Bowden, D. W., et al. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.09.003 · Cited by 12 · see citing works

Codon language embeddings provide strong signals for protein engineeringPreprint

Outeiral, C., & Deane, C. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.15.519894 · Cited by 12 · see citing works

Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones

Xu, H. (2022) · Biomolecules · doi:10.3390/biom12060832 · Cited by 10 · see citing works

Augmenting tomato functional genomics with a genome-wide induced genetic variation resource

Gupta, P., Dholaniya, P. S., Princy, K., Madhavan, A. S., Sreelakshmi, Y., & Sharma, R. P. (2024) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1290937 · Cited by 8 · see citing works

A dataset of alternately located segments in protein crystal structures

Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2024) · Scientific Data · doi:10.1038/s41597-024-03595-4 · Cited by 9 · see citing works

Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins

Balasco, N., Esposito, L., Simone, A. D., & Vitagliano, L. (2022) · Biomolecules · doi:10.3390/biom12091184 · Cited by 7 · see citing works

Quantifying negative selection on synonymous variants

Gudkov, M., Thibaut, L. M., & Giannoulatou, E. (2024) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2024.100262 · Cited by 7 · see citing works

Identification of clade-defining single nucleotide polymorphisms for improved rabies virus surveillance

Kumar, A., Tushir, S., Devasurmutt, Y., Nath, S. S., & Tatu, U. S. (2024) · New Microbes and New Infections · doi:10.1016/j.nmni.2024.101511 · Cited by 8 · see citing works

Influence of Stereochemistry in a Local Approach for Calculating Protein Conformations

da Rocha, W., Liberti, L., Mucherino, A., & Malliavin, T. E. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01232 · Cited by 3 · see citing works

Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli

Akeju, O. J., & Cope, A. L. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae080 · Cited by 3 · see citing works

Whole proteome-integrated and vaccinomics-based next generation mRNA vaccine design against Pseudomonas aeruginosa-A hierarchical subtractive proteomics approach.

Aiman, S., Ahmad, A., Malik, A., Chen, R., Hanif, M. F., Khan, A. A., Ansari, M. A., Farrukh, S., Xu, G.-X., Shahab, M., et al. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.142627 · Cited by 3 · see citing works

Machine learning approaches demonstrate that protein structures carry information about their genetic coding

Ackerman-Schraier, L., Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2022) · Scientific Reports · doi:10.1038/s41598-022-25874-z · Cited by 3 · see citing works

Combination of hydrophobicity and codon usage bias determines sorting of model K + channel protein to either mitochondria or endoplasmic reticulum

Engel, A. J., Paech, S., Langhans, M., Etten, J. L. V., Moroni, A., Thiel, G., & Rauh, O. (2023) · Traffic · doi:10.1111/tra.12915 · Cited by 3 · see citing works

Data-driven risk assessment of antibiotic mixtures against gram-negative and gram-positive bacteria: QSAR, joint toxic action, and component contribution

Sun, H., Xu, F., Luo, R., Liu, Y., Wang, J., Lei, B., Tang, L., Pu, X., & Wu, M. (2025) · Environment International · doi:10.1016/j.envint.2025.109639 · Cited by 2 · see citing works

Detecting Interspecific Positive Selection Using Convolutional Neural Networks

West, C., Walker, C. R., Arasti, S., Vasilev, V., Xu, X., De Maio, N., & Goldman, N. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf154 · Cited by 1 · see citing works

Form and Function in Biological Macromolecules: Kinetic Stability is Key, with Oblique Roles for Intramolecularity and Hydrophobicity in Enzyme Catalysis

Chandrasekhar, S. (2022) · International Journal of Biochemistry Research & Review · doi:10.9734/ijbcrr/2022/v31i9778 · Cited by 1 · see citing works

In-silico studies of some potent hybrid compounds against Alzheimer's disease through virtual screening, simulation techniques, and pharmacokinetic endowment

Ajala, A., Uzairu, A., Shallangwa, G. A., & Abechi, S. E. (2023) · Biocatalysis and Agricultural Biotechnology · doi:10.1016/j.bcab.2023.102941 · Cited by 1 · see citing works

High-throughput Experimental Validation of Synonymous Mutation Neutrality in the Human GenomePreprint

Rao, Y., Sokirniy, I., O'Brien, E. P., & Pritchard, J. R. (2025) · bioRxiv · doi:10.1101/2025.08.30.673250

Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease

Rosenberg, A. A., Bronstein, A. M., & Marx, A. (2022) · Springer eBooks · doi:10.1007/978-3-031-05616-1_3

Machine learning approaches demonstrate that protein structures carry information about their genetic codingPreprint

Ackerman-Schraier, L., Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2022) · Research Square · doi:10.21203/rs.3.rs-2041719/v1

Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residuesPreprint

Rosenberg, A. A., Yehishalom, N., Marx, A., & Bronstein, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.23.513383

Re-examining supposed correlations between synonymous codon usage and protein bond angles in E. coliPreprint

Akeju, O. J., & Cope, A. L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.26.513858

Transcriptome-wide meta-analysis of codon usage in Escherichia coliPreprint

Sutradhar, A., Pointon, J., Lennon, C., & Stracquadanio, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.31.555696

Novel Bio-Engineering Techniques for Construction of Next-Generation Monoclonal Antibodies in the Framework of Personalized Medicine

Barazesh, M., Mohammadi, S., & Jalili, S. (2024) · IntechOpen eBooks · doi:10.5772/intechopen.1006051

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant

González-Delgado, J., Mier, P., Bernadó, P., Neuvial, P., & Cortés, J. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2503264122

The NOX3-N64Y mutation as a driver of electron transport defects and enhanced ROS productionPreprint

Nakamura, T. K. E., & Porcionatto, M. A. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5447930

Nucleation of high-resolution protein crystals on tailored hydrogel membranes: Secondary conformation transition

Chen, W., Xu, J., Tao, T., Yao, T., Wang, J., Yang, H., Gao, Z., Heng, J. Y. Y., & Gong, J. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.169767

Evaluation of antileukemic potentials of maslinic acid through targeting responsive proteins of human leukemia: a mechanistic perception on molecular modelling and dynamic stimulations

Banerjee, J., Samanta, S., Afiadenyo, M., Ahmed, R., Das, S., Hasan, S. N., & Dash, S. K. (2025) · In Silico Pharmacology · doi:10.1007/s40203-025-00478-3

Statistical methods for the structural analysis of highly flexible proteins

González-Delgado, J. (2023) · theses.fr (ABES) · doi:10.70675/f85d87dazad73z4e9azb404z56bec6b9988b

APPLICATION OF RING-POLYHEDRAL MODELS OF AMINO ACIDS FOR PROTEIN STRUCTURE MODELING

Kozhevnikov, D., & Kushelev, A. (2026) · Molekulyarnaya Meditsina (Molecular medicine) · doi:10.29296/24999490-2026-02-06

Synonymous mutations in essential genes infrequently produce fitness effects in human cell lines

Rao, Y., Sokirniy, I., O’Brien, E. P., & Pritchard, J. R. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag733 · Cited by 1 · see citing works

Synonymous Gene Recoding Affects the Accuracy of Protein Quantification Measurements

Kaissarian, N. M., Padhiar, N. H., Clement, N., Wu, W. W., Katneni, U., Komar, A. A., & Kimchi‐Sarfaty, C. (2026) · The AAPS Journal · doi:10.1208/s12248-026-01310-2

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant

González-Delgado, J., Mier, P., Bernadó, P., Neuvial, P., & Cortés, J. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2503264122

Statistical signals indicate a dependence between amino acid backbone conformation and the translated synonymous codonPreprint

Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.02.712692

A code within the genetic code: codon usage regulates co-translational protein folding

Liu, Y. (2020) · Cell Communication and Signaling · doi:10.1186/s12964-020-00642-6 · Cited by 252 · see citing works

Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli

Akeju, O. J., & Cope, A. L. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae080 · Cited by 3 · see citing works

Synonymous codon usage influences the local protein structure observed

Saunders, R., & Deane, C. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq495 · Cited by 165 · see citing works