Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860 · see citing works

Mfold web server for nucleic acid folding and hybridization prediction

Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404 · 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

The ‘effective number of codons’ used in a gene

Wright, F. (1990) · Gene · doi:10.1016/0378-1119(90)90491-9 · Cited by 2,318 · 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

Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds

Pauwels, R., Balzarini, J. M., Baba, M., Snoeck, R., Schols, D., Herdewijn, P. A., Desmyter, J., & Clercq, E. D. (1988) · Journal of Virological Methods · doi:10.1016/0166-0934(88)90134-6 · Cited by 1,646 · see citing works

Virus attenuation by genome-scale changes in codon pair bias

Coleman, J. R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E., & Mueller, S. (2008) · Science · doi:10.1126/science.1155761 · Cited by 715 · see citing works

Codon usage limitation in the expression of HIV-1 envelope glycoprotein

Haas, J., Park, E.-C., & Seed, B. (1996) · Current Biology · doi:10.1016/s0960-9822(02)00482-7 · Cited by 531 · see citing works

Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression

Karn, J., & Stoltzfus, C. M. (2012) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a006916 · Cited by 437 · see citing works

Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity

Mueller, S., Papamichail, D., Coleman, J. R., Skiena, S., & Wimmer, E. (2006) · Journal of Virology · doi:10.1128/jvi.00738-06 · Cited by 383 · see citing works

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11

Li, M., Kao, E., Gao, X., Sandig, H., Limmer, K., Pavon-Eternod, M., Jones, T. E., Landry, S., Pan, T., Weitzman, M. D., et al. (2012) · Nature · doi:10.1038/nature11433 · Cited by 375 · see citing works

The role of mutational robustness in RNA virus evolution

Lauring, A. S., Frydman, J., & Andino, R. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3003 · Cited by 354 · see citing works

Live attenuated influenza virus vaccines by computer-aided rational design

Mueller, S., Coleman, J. R., Papamichail, D., Ward, C. B., Nimnual, A., Futcher, B., Skiena, S., & Wimmer, E. (2010) · Nature Biotechnology · doi:10.1038/nbt.1636 · Cited by 275 · see citing works

Nonrandom utilization of codon pairs in Escherichia coli.

Gutman, G. A., & Hatfield, G. W. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.10.3699 · Cited by 261 · cited 1× · see citing works

Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region

Burns, C. C., Shaw, J., Campagnoli, R. P., Jorba, J. C., Vincent, A., Quay, J., & Kew, O. M. (2006) · Journal of Virology · doi:10.1128/jvi.80.7.3259-3272.2006 · Cited by 257 · see citing works

HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: A view from the clinic and ex vivo

Martínez‐Picado, J., & Martı́nez, M. Á. (2008) · Virus Research · doi:10.1016/j.virusres.2007.12.021 · Cited by 146 · see citing works

Codon Usage Determines the Mutational Robustness, Evolutionary Capacity, and Virulence of an RNA Virus

Lauring, A. S., Acevedo, A., Cooper, S., & Andino, R. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.10.008 · Cited by 135 · see citing works

HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1

Miura, T., Brockman, M. A., Brumme, Z. L., Brumme, C. J., Pereyra, F., Piechocka‐Trocha, A., Block, B. L., Schneidewind, A., Allen, T. M., Heckerman, D. E., et al. (2008) · Journal of Virology · doi:10.1128/jvi.01471-08 · Cited by 127 · see citing works

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

Cuevas, J. M., Domingo‐Calap, P., & Sanjuán, R. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr179 · Cited by 117 · see citing works

tRNA properties help shape codon pair preferences in open reading frames

Buchan, J. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj488 · Cited by 108 · see citing works

The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins

Berkhout, B., & van Hemert, F. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.9.1705 · Cited by 95 · see citing works

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

van der Kuyl, A. C., & Berkhout, B. (2012) · Retrovirology · doi:10.1186/1742-4690-9-92 · Cited by 94 · see citing works

Analysis of resistance to human immunodeficiency virus type 1 protease inhibitors by using matched bacterial expression and proviral infection vectors

Maschera, B., Furfine, E. S., & Blair, E. D. (1995) · Journal of Virology · doi:10.1128/jvi.69.9.5431-5436.1995 · Cited by 75 · see citing works

Nucleotide composition bias and CpG dinucleotide content in the genomes of HIV and HTLV

Kypr, J., Mrázek, J., & Reich, J. (1989) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/0167-4781(89)90114-0 · Cited by 53 · see citing works

Fitness Landscape of Human Immunodeficiency Virus Type 1 Protease Quasispecies

Fernández, G., Clotet, B., & Martı́nez, M. Á. (2006) · Journal of Virology · doi:10.1128/jvi.01594-06 · Cited by 51 · see citing works

Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design

Song, Y., Liu, Y., Ward, C. B., Mueller, S., Futcher, B., Skiena, S., Paul, A. V., & Wimmer, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211484109 · Cited by 48 · see citing works

A detailed comparative analysis on the overall codon usage patterns in Hepatitis A virus

Andrea, L. D., Pintó, R. M., Bosch, A., Musto, H., & Cristina, J. (2011) · Virus Research · doi:10.1016/j.virusres.2011.01.012 · Cited by 37 · see citing works

Interplay between RNA Structure and Protein Evolution in HIV-1

Sanjuán, R., & Bordería, A. V. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq329 · Cited by 36 · see citing works

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

Keating, C. P., Hill, M. K., Hawkes, D. J., Smyth, R. P., Isel, C., Le, S.-Y., Palmenberg, A. C., Marshall, J. A., Marquet, R., Nabel, G. J., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn1015 · Cited by 35 · see citing works

Mechanisms Involved in the Selection of HIV-1 Reverse Transcriptase Thumb Subdomain Polymorphisms Associated with Nucleoside Analogue Therapy Failure

Betancor, G., Puertas, M. C., Nevot, M., Garriga, C., Martı́nez, M. Á., Martínez‐Picado, J., & Menéndez‐Arias, L. (2010) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00716-10 · Cited by 30 · see citing works

The different pathways of HIV genomic RNA translation

Chamond, N., Locker, N., & Sargueil, B. (2010) · Biochemical Society Transactions · doi:10.1042/bst0381548 · Cited by 28 · see citing works

Computationally designed adeno-associated virus (AAV) Rep 78 is efficiently maintained within an adenovirus vector

Sitaraman, V., Hearing, P., Ward, C., Gnatenko, D., Wimmer, E., Mueller, S., Skiena, S., & Bahou, W. (2011) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1102883108 · Cited by 20 · see citing works

Phenotypic Hypersusceptibility to Multiple Protease Inhibitors and Low Replicative Capacity in Patients Who Are Chronically Infected with Human Immunodeficiency Virus Type 1

Martínez‐Picado, J., Wrin, T., Frost, S. D. W., Clotet, B., Ruiz, L., Brown, A., Petropoulos, C. J., & Parkin, N. T. (2005) · Journal of Virology · doi:10.1128/jvi.79.10.5907-5913.2005 · Cited by 17 · see citing works

Thymidine Analogue Excision and Discrimination Modulated by Mutational Complexes Including Single Amino Acid Deletions of Asp-67 or Thr-69 in HIV-1 Reverse Transcriptase

Kisic, M., Matamoros, T., Nevot, M., Mendieta, J., Martínez‐Picado, J., Martı́nez, M. Á., & Menéndez‐Arias, L. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.226100 · Cited by 15 · see citing works

RNA Interference as a Tool for Exploring HIV-1 Robustness

Nevot, M., Martrus, G., Clotet, B., & Martı́nez, M. Á. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.08.035 · Cited by 15 · see citing works

Genetic Screen for Monitoring Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

Parera, M., Clotet, B., & Martı́nez, M. Á. (2004) · Journal of Virology · doi:10.1128/jvi.78.24.14057-14061.2004 · Cited by 15 · see citing works

Evolution of the human immunodeficiency virus type 1 protease: effects on viral replication capacity and protease robustness

Capel, E., Martrus, G., Parera, M., Clotet, B., & Martı́nez, M. Á. (2012) · Journal of General Virology · doi:10.1099/vir.0.045492-0 · Cited by 7 · see citing works

Corrections and Clarifications

(2007) · Science · doi:10.1126/science.318.5855.1382 · Cited by 6 · see citing works

Translational Control in Virus-Infected CellsPreprint

Stern‐Ginossar, N., Thompson, S. R., Mathews, M. B., & Mohr, I. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a033001 · Cited by 201 · see citing works

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

Tulloch, F., Atkinson, N. J., Evans, D. J., Ryan, M. D., & Simmonds, P. (2014) · eLife · doi:10.7554/elife.04531 · Cited by 178 · see citing works

Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization

Nouën, C. L., Brock, L. G., Luongo, C., McCarty, T. C., Yang, L., Mehedi, M., Wimmer, E., Mueller, S., Collins, P. L., Buchholz, U. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1411290111 · Cited by 123 · see citing works

Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection

Gaunt, E., Wise, H. M., Zhang, H., Lee, L. N., Atkinson, N. J., Nicol, M. Q., Highton, A. J., Klenerman, P., Beard, P. M., Dutia, B. M., et al. (2016) · eLife · doi:10.7554/elife.12735 · Cited by 107 · see citing works

Mechanism of Virus Attenuation by Codon Pair Deoptimization

Groenke, N., Trimpert, J., Merz, S., Conradie, A. M., Wyler, E., Zhang, H., Hazapis, O.-G., Rausch, S., Landthaler, M., Osterrieder, N., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107586 · Cited by 85 · see citing works

Evolutionary reversion of live viral vaccines: Can genetic engineering subdue it?

Bull, J. J. (2015) · Virus Evolution · doi:10.1093/ve/vev005 · Cited by 82 · see citing works

Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness

Martı́nez, M. Á., Jordan-Paiz, A., Franco, S., & Nevot, M. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.11.002 · Cited by 81 · see citing works

Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication

Jin, D., & Musier-Forsyth, K. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev118.002957 · Cited by 67 · see citing works

CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry

Fros, J. J., Dietrich, I., Alshaikhahmed, K., Passchier, T. C., Evans, D. J., & Peter Simmonds, K. (2017) · eLife · doi:10.7554/elife.29112 · Cited by 58 · see citing works

Attenuation of a very virulent Marek's disease herpesvirus (MDV) by codon pair bias deoptimization

Eschke, K., Trimpert, J., Osterrieder, N., & Kunec, D. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006857 · Cited by 53 · see citing works

Synthetic Genomics: From DNA Synthesis to Genome Design

Wang, L., Jiang, S., Chen, C., He, W., Wu, X., Wang, F., Tong, T., Zou, X., Li, Z., Luo, J., et al. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201708741 · Cited by 51 · see citing works

Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation In Vivo while Inducing a Strong Neutralizing Antibody Response

Segundo, F. D.-S., Medina, G. N., Ramírez-Medina, E., Velázquez-Salinas, L., Koster, M. J., Grubman, M. J., & Santos, T. D. L. (2015) · Journal of Virology · doi:10.1128/jvi.02167-15 · Cited by 48 · see citing works

Sequence-Specific Sensing of Nucleic Acids

Vabret, N., Bhardwaj, N., & Greenbaum, B. D. (2017) · Trends in Immunology · doi:10.1016/j.it.2016.10.006 · Cited by 45 · see citing works

Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication

Takata, M. A., Soll, S. J., Emery, A., Blanco-Melo, D., Swanstrom, R. I., & Bieniasz, P. D. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006824 · Cited by 45 · see citing works

Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding

de Fabritus, L., Nougaırède, A., Aubry, F., Gould, E. A., & de Lamballerie, X. N. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004738 · Cited by 41 · see citing works

Compensating the Fitness Costs of Synonymous Mutations

Knöppel, A., Näsvall, J., & Andersson, D. I. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw028 · Cited by 40 · see citing works

Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication

Antzin-Anduetza, I., Mahiet, C., Granger, L. A., Odendall, C., & Swanson, C. M. (2017) · Retrovirology · doi:10.1186/s12977-017-0374-1 · Cited by 39 · see citing works

Compositional biases in RNA viruses: Causes, consequences and applications

Gaunt, E. R., & Digard, P. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1679 · Cited by 34 · see citing works

Mechanisms of Attenuation by Genetic Recoding of Viruses

Gonçalves-Carneiro, D., & Bieniasz, P. D. (2021) · mBio · doi:10.1128/mbio.02238-20 · Cited by 29 · see citing works

Feasibility of vaccination against Macrobrachium rosenbergii nodavirus infection in giant freshwater prawn

Chen-Fei, L., Chong, C. M., & Jiun-Yan, L. (2020) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2020.06.039 · Cited by 26 · see citing works

Molecular biology of Macrobrachium rosenbergii nodavirus infection in giant freshwater prawn

Low, C., Yusoff, M. R. M., Kuppusamy, G., & Nadzri, N. F. A. (2018) · Journal of Fish Diseases · doi:10.1111/jfd.12895 · Cited by 25 · see citing works

Field porcine reproductive and respiratory syndrome viruses (PRRSV) attenuated by codon pair deoptimization (CPD) in NSP1 protected pigs from heterologous challenge

Park, C., Baek, J. H., Cho, S. H., Jeong, J., Chae, C., You, S.-H., & Cha, S. (2019) · Virology · doi:10.1016/j.virol.2019.10.019 · Cited by 23 · see citing works

Association of Zinc Finger Antiviral Protein Binding to Viral Genomic RNA with Attenuation of Replication of Echovirus 7

Goonawardane, N., Nguyen, D. V., & Peter Simmonds, K. (2021) · mSphere · doi:10.1128/msphere.01138-20 · Cited by 21 · see citing works

Dengue virus preferentially uses human and mosquito non-optimal codons

Castellano, L. A., McNamara, R. J., Pallarés, H. M., Gamarnik, A. V., Alvarez, D. E., & Bazzini, A. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00052-7 · Cited by 20 · see citing works

Large-Scale Nucleotide Optimization of Simian Immunodeficiency Virus Reduces Its Capacity To Stimulate Type I Interferon In Vitro

Vabret, N., Bailly‐Bechet, M., Lepelley, A., Najburg, V., Schwartz, O., Verrier, B., & Tangy, F. (2014) · Journal of Virology · doi:10.1128/jvi.03223-13 · Cited by 20 · see citing works

Regulation of human immunodeficiency virus type 1 (HIV-1) mRNA translation

Hidalgo, L., & Swanson, C. M. (2017) · Biochemical Society Transactions · doi:10.1042/bst20160357 · Cited by 20 · see citing works

Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases

He, Z., Qin, L., Xu, X., & Ding, S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.021 · Cited by 20 · see citing works

Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies

Martı́nez, M. Á., Jordan-Paiz, A., Franco, S., & Nevot, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz831 · Cited by 18 · see citing works

Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days

de Fabritus, L., Nougaırède, A., Aubry, F., Gould, E. A., & de Lamballerie, X. N. (2016) · PLoS ONE · doi:10.1371/journal.pone.0159564 · Cited by 17 · see citing works

Extensive genomic recoding by codon-pair deoptimization selective for mammals is a flexible tool to generate attenuated vaccine candidates for dengue virus 2

Stauft, C. B., Song, Y., Gorbatsevych, O., Pantoja, P., Rodríguez, I. V., Futcher, B., Sariol, C. A., & Wimmer, E. (2019) · Virology · doi:10.1016/j.virol.2019.09.003 · Cited by 16 · see citing works

Intradermal co-inoculation of codon pair deoptimization (CPD)-attenuated chimeric porcine reproductive and respiratory syndrome virus (PRRSV) with Toll like receptor (TLR) agonists enhanced the protective effects in pigs against heterologous challenge

Park, C., Lee, M., Baek, J. H., Cho, S. H., Hyun, B., You, S.-H., & Cha, S. (2021) · Veterinary Microbiology · doi:10.1016/j.vetmic.2021.109048 · Cited by 16 · see citing works

Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines

Pereira-Gómez, M., Carrau, L., Fajardo, Á., Moreno, P., & Moratorio, G. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.676582 · Cited by 16 · see citing works

Intranasal respiratory syncytial virus vaccine attenuated by codon-pair deoptimization of seven open reading frames is genetically stable and elicits mucosal and systemic immunity and protection against challenge virus replication in hamsters

Levy, M. E., Chen, J. W., Kaiser, J. A., Park, H.-S., Liu, X., Yang, L., Santos, C. P., Buchholz, U. J., & Nouën, C. L. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012198 · Cited by 15 · see citing works

ΦX174 Attenuation by Whole-Genome Codon Deoptimization

Leuven, J. T. V., Ederer, M. M., Burleigh, K., Scott, L., Hughes, R. A., Codrea, V., Ellington, A. D., Wichman, H. A., & Miller, C. R. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa214 · Cited by 15 · see citing works

Exploratory re-encoding of yellow fever virus genome: new insights for the design of live-attenuated viruses

Klitting, R., Riziki, T., Moureau, G., Piorkowski, G., Gould, E. A., & de Lamballerie, X. N. (2018) · Virus Evolution · doi:10.1093/ve/vey021 · Cited by 15 · see citing works

Optimization of the Codon Pair Usage of Human Respiratory Syncytial Virus Paradoxically Resulted in Reduced Viral Replication In Vivo and Reduced Immunogenicity

Nouën, C. L., Luongo, C., Yang, L., Mueller, S., Wimmer, E., DiNapoli, J. M., Collins, P. L., & Buchholz, U. J. (2019) · Journal of Virology · doi:10.1128/jvi.01296-19 · Cited by 14 · see citing works

Single Synonymous Mutations in KRAS Cause Transformed Phenotypes in NIH3T3 Cells

Waters, A. M., Bagni, R., Portugal, F. H., & Hartley, J. L. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163272 · Cited by 14 · see citing works

Synonymous Codon Pair Recoding of the HIV-1 env Gene Affects Virus Replication Capacity

Jordan-Paiz, A., Franco, S., & Martı́nez, M. Á. (2021) · Cells · doi:10.3390/cells10071636 · Cited by 13 · see citing works

Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013

van der Kuyl, A. C., Bakker, M. E., Jurriaans, S., Back, N. K. T., Pasternak, A. O., Cornelissen, M. T. E., & Berkhout, B. (2013) · Retrovirology · doi:10.1186/1742-4690-10-93 · Cited by 13 · see citing works

Schlafen14 Impairs HIV-1 Expression in a Codon Usage-Dependent Manner

Valenzuela, C. A., Saucedo, S., & Llano, M. (2024) · Viruses · doi:10.3390/v16040502 · Cited by 12 · see citing works

Impact of Synonymous Genome Recoding on the HIV Life Cycle

Jordan-Paiz, A., Franco, S., & Martı́nez, M. Á. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.606087 · Cited by 12 · see citing works

Codon pair bias deoptimization of the major oncogene meq of a very virulent Marek’s disease virus

Khedkar, P. H., Osterrieder, N., & Kunec, D. (2018) · Journal of General Virology · doi:10.1099/jgv.0.001136 · Cited by 11 · see citing works

Recoding anaerobic regulator fnr of Salmonella Typhimurium attenuates it's pathogenicity

Nikhil, K. C., Noatia, L., Priyadarsini, S., Pashupathi, M., Gali, J. M., Ali, M. A., Behera, S. K., Sharma, B., Roychoudhury, P., Kumar, A., et al. (2022) · Microbial Pathogenesis · doi:10.1016/j.micpath.2022.105591 · Cited by 11 · see citing works

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Khandia, R., Khan, A. A., Karuvantevida, N. S., Gurjar, P., Rzhepakovsky, I. V., & Legáz, I. (2023) · Pathogens · doi:10.3390/pathogens12020325 · Cited by 11 · see citing works

Use of Synonymous Deoptimization to Derive Modified Live Attenuated Strains of Foot and Mouth Disease Virus

Segundo, F. D.-S., Medina, G. N., Spinard, E. J., Kloc, A., Ramírez-Medina, E., Azzinaro, P. A., Mueller, S., Rieder, E. A., & Santos, T. D. L. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.610286 · Cited by 11 · see citing works

Synthetically recoded virus sCPD9 – A tool to accelerate SARS-CoV-2 research under biosafety level 2 conditions

Kunec, D., Osterrieder, N., & Trimpert, J. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.08.027 · Cited by 11 · see citing works

Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased

Osterrieder, N., & Kunec, D. (2018) · Current Clinical Microbiology Reports · doi:10.1007/s40588-018-0080-3 · Cited by 10 · see citing works

Genome recoding strategies to improve cellular properties: mechanisms and advances

Singh, T., Yadav, S. K., Vainstein, A., & Kumar, V. S. (2020) · aBIOTECH · doi:10.1007/s42994-020-00030-1 · Cited by 9 · see citing works

Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation

Khandia, R., Pandey, M. K., Khan, A. A., Rzhepakovsky, I. V., Gurjar, P., & Karobari, M. I. (2022) · Vaccines · doi:10.3390/vaccines10111874 · Cited by 9 · see citing works

Changing the Codon Usage of hfq Gene has Profound Effect on Phenotype and Pathogenicity of Salmonella Typhimurium

Behera, P., Kutty, V. H. M., Kumar, A., & Sharma, B. (2015) · Current Microbiology · doi:10.1007/s00284-015-0951-2 · Cited by 9 · see citing works

Evolution shapes and conserves genomic signatures in viruses

Holmudden, M., Gustafsson, J., Bertrand, Y., Schliep, A., & Norberg, P. (2024) · Communications Biology · doi:10.1038/s42003-024-07098-1 · Cited by 8 · see citing works

HIV-1 Protease Evolvability Is Affected by Synonymous Nucleotide Recoding

Nevot, M., Jordan-Paiz, A., Martrus, G., Andrés, C., García‐Cehic, D., Gregori, J., Franco, S., Quer, J., & Martı́nez, M. Á. (2018) · Journal of Virology · doi:10.1128/jvi.00777-18 · Cited by 8 · see citing works

Interaction of virus populations with their hosts

Domingo, E. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816331-3.00004-0 · Cited by 8 · see citing works

Codon Pair Deoptimization (CPD)-Attenuated PRRSV-1 Vaccination Exhibit Immunity to Virulent PRRSV Challenge in Pigs

Lee, M., You, S.-H., Jayaramaiah, U., Shin, E.-G., Song, S.-M., Ju, L., Kang, S. J., Cho, S. H., Hyun, B., & Lee, H.-S. (2023) · Vaccines · doi:10.3390/vaccines11040777 · Cited by 8 · see citing works

HIV-1 Lethality and Loss of Env Protein Expression Induced by Single Synonymous Substitutions in the Virus Genome Intronic-Splicing Silencer

Jordan-Paiz, A., Nevot, M., Lamkiewicz, K., Lataretu, M., Franco, S., Marz, M., & Martı́nez, M. Á. (2020) · Journal of Virology · doi:10.1128/jvi.01108-20 · Cited by 8 · see citing works

HIV-1 tolerates changes in A-count in a small segment of the pol gene

Klaver, B., van der Velden, Y. U., van Hemert, F. J., van der Kuyl, A. C., & Berkhout, B. (2017) · Retrovirology · doi:10.1186/s12977-017-0367-0 · Cited by 7 · see citing works

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 7 · see citing works

Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region

Gomes, S. T. M., Amoras, E. D. S. G., Gomes, É. R., Queiroz, M. A. F., Sousa, E. C., Massafra, J. M. D. V., Lemos, P. D. S., Júnior, J. L. D. S. G. V., Ishak, R., & Vallinoto, A. C. R. (2020) · BMC Infectious Diseases · doi:10.1186/s12879-020-05268-0 · Cited by 6 · see citing works

Tailoring the Immune Response via Customization of Pathogen Gene Expression

Runco, L. M., Stauft, C. B., & Coleman, J. R. (2014) · Journal of Pathogens · doi:10.1155/2014/651568 · Cited by 5 · see citing works

The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host

Kula, A., Saelens, J. W., Cox, J., Schubert, A. M., Travisano, M., & Putonti, C. (2018) · Scientific Reports · doi:10.1038/s41598-018-25914-7 · Cited by 5 · see citing works

Interaction of Virus Populations with Their Hosts

Domingo, E. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800837-9.00004-6 · Cited by 4 · see citing works

Evaluation and Determination of a Suitable Passage Number of Codon Pair Deoptimized PRRSV-1 Vaccine Candidate in Pigs

Lee, M., You, S.-H., Jayaramaiah, U., Shin, E.-G., Song, S.-M., Ju, L., Kang, S. J., Cho, S.-H., Hyun, B., & Lee, H.-S. (2023) · Viruses · doi:10.3390/v15051071 · Cited by 4 · see citing works

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 · see citing works

Reducing HIV-1 env gene CpG frequency increases the replication capacity of the HXB2 virus strain

Jordan-Paiz, A., Franco, S., & Martı́nez, M. Á. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198685 · Cited by 3 · see citing works

Generation and comparative genomics of synthetic dengue viruses

Goz, E., Tsalenchuck, Y., Benaroya, R. O., Zafrir, Z., Atar, S., Altman, T., Julander, J. G., & Tuller, T. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2132-3 · Cited by 3 · see citing works

Genome recoding: a review of basic concepts, current research and future prospects of virus attenuation for controlling plant viral diseases

Kumar, V. S., & Singh, T. (2020) · Journal of Plant Biochemistry and Biotechnology · doi:10.1007/s13562-020-00583-8 · Cited by 3 · see citing works

Synthetic Biology Approaches for Vaccine Development

Shen, S. H., Futcher, B., Yang, C., & Wimmer, E. (2014) · Wiley-VCH eBooks · doi:10.1002/3527600906.mcb.20120059 · Cited by 3 · see citing works

Involvement of a Rarely Used Splicing SD2b Site in the Regulation of HIV-1 vif mRNA Production as Revealed by a Growth-Adaptive Mutation

Koma, T., Doi, N., Le, B. Q., Kondo, T., Ishizue, M., Tokaji, C., Tsukada, C., Adachi, A., & Nomaguchi, M. (2023) · Viruses · doi:10.3390/v15122424 · Cited by 2 · see citing works

cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences

Puustusmaa, M., & Abroi, A. (2019) · PeerJ · doi:10.7717/peerj.6176 · Cited by 2 · see citing works

Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery

Ekpenyong, M. E., Adegoke, A. A., Edoho, M. E., Inyang, U. G., Udo, I. J., Ekaidem, I. S., Osang, F. B., Uto, N. P., & Geoffery, J. I. (2022) · Current HIV Research · doi:10.2174/1570162x20666220210142209 · Cited by 1 · see citing works

Synthetische Genomik: von der DNA‐Synthese zu Designer‐Genomen

Wang, L., Jiang, S., Chen, C., He, W., Wu, X., Wang, F., Tong, T., Zou, X., Li, Z., Luo, J., et al. (2017) · Angewandte Chemie · doi:10.1002/ange.201708741 · Cited by 1 · see citing works

Generation and Comparative Genomics of Synthetic Dengue Viruses

Goz, E., Tsalenchuck, Y., Benaroya, R. O., Atar, S., Altman, T., Julander, J. G., & Tuller, T. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-67979-2_3 · Cited by 1 · see citing works

Optimal codon pair bias design (extended abstract)

Donoghue, N. P., Gardin, J., Futcher, B., & Skiena, S. (2017) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2017.8217703 · Cited by 1 · see citing works

Synthetic Viruses

Stauft, C. B., & Wimmer, E. (2018) · Wiley eBooks · doi:10.1002/9780470015902.a0027771 · Cited by 1 · see citing works

Development of a foot-and-mouth disease virus replicon system for the study of RNA replication

Tulloch, F. (2015) · St Andrews Research Repository (St Andrews Research Repository)

virus (SIV) reduces its capacity to stimulate type-I IFN in vitro

Bailly‐Bechet, M., Lepelley, A., Najburg, V., Verrier, B., Tangy, F., & Lyon, B. (2014)

Changes in Codon-Pair Bias of Human Immunodeficiency Virus Type 1 Affect Virus Replication

Martı́nez, M. Á. (2015) · Trends in mathematics · doi:10.1007/978-3-319-22129-8_23

Exploratory re-encoding of Yellow Fever Virus genome: new insights for the design of live-attenuated virusesPreprint

Klitting, R., Riziki, T., Moureau, G., Piorkowski, G., Gould, E. A., & de Lamballerie, X. N. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/256610

Atténuation virale par ré-encodage des codons : applications aux virus Chikungunya et de l'encéphalite à tiques

de Fabritus, L. (2015) · theses.fr (ABES) · doi:10.70675/076d7622z5fd0z4238za7aczf4435a7232a4

Attenuation of viscerotropic flaviviruses

Klitting, R. (2017) · theses.fr (ABES) · doi:10.70675/d3cc34d0z2cb7z4b75z831bz1574ac11f93c

Caractérisation de méthodes de génétique inverse innovantes et application au développement de vaccins vivants atténués de nouvelle génération du virus de l’encéphalite à tiques

Driouich, J. (2019) · theses.fr (ABES) · doi:10.70675/cb43b652z534ez4e11zab37z937e2ba6193a

For the Love of Poliovirus

Wimmer, E. (2026) · Annual Review of Virology · doi:10.1146/annurev-virology-100422-040205

Role of synthetic biology in biodrug production and human wellness

Arte, P. A., Mishra, P., & Tungare, K. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-34129-8.00002-x

Attenuation without protective immunogenicity: effects of codon-pair deoptimization on foot-and-mouth disease virus serotype O in swine

Lorenz, C., Wisnewski, K., Weber, S., Deutschmann, P., Beer, M., & Eschbaumer, M. (2026) · Scientific Reports · doi:10.1038/s41598-026-61879-8

Synonymous Codon Pair Recoding of the HIV-1 env Gene Affects Virus Replication Capacity

Jordan-Paiz, A., Franco, S., & Martı́nez, M. Á. (2021) · Cells · doi:10.3390/cells10071636 · Cited by 13 · see citing works

Codon Usage Bias Study Reveals the Function of the Genomes in Human Immuno-Deficiency Virus

Barik, S. K., Sewalikar, A., Ghuge, R., Harke, S. N., Khemnar, A. S., Panche, A. N., Mulay, M. V., Kulkarni, S. S., Deshmukh, A. S., Deshmukh, P. D., et al. (2024) · Sylwan · doi:10.59879/dbmpf

Open Access

Martı́nez, M. Á. (2014)

Introduction of human codon-optimised sequences into the HIV-1 genome generates replication defective virions

Keating, C., Hill, M. K., Shehu-Xhilaga, M., Crowe, S., Huang, Y., Nabel, G. J., & Mak, J. (2002)

Molecular mechanism of virus attenuation by codon pair deoptimization

Groenke, N. (2021) · Refubium (Universitätsbibliothek der Freien Universität Berlin) · doi:10.17169/refubium-27096 · Cited by 1 · see citing works