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Claudia Tregnago, Maddalena Benetton, Rhonda E. Ries, Jack H. Peplinski, Todd A. Alonzo, Derek Stirewalt, Megan Othus, Nicolas Duployez, Edwin Sonneveld, Jonas Abrahamsson, Linda Fogelstrand, Nils von Neuhoff, Henrik Hasle, Dirk Reinhardt, Soheil Meshinchi, Franco Locatelli, Martina Pigazzi

Tuhin Manna, Subhamoy Dey, Monalisha Karmakar, Amiya Kumar Panda, Chandradipa Ghosh

Nigam H Padhiar, Tigran Ghazanchyan, Sarah E Fumagalli, Michael DiCuccio, Guy Cohen, Alexander Ginzburg, Brian Rikshpun, Almog Klein, Luis Santana-Quintero, Sean Smith, Anton A Komar, Chava Kimchi-Sarfaty

Lucio Aliperti Car, Ignacio E. Sánchez

Rekha Khandia, Pankaj Gurjar, Victoria Romashchenko, Sami A. Al-Hussain, Athanasios Alexiou, George Zouganelis, Magdi E.A. Zaki

Sarah E. Fumagalli, Sean Smith, Tigran Ghazanchyan, Douglas Meyer, Rahul Paul, Collin Campbell, Luis Santana-Quintero, Anton Golikov, Juan Ibla, Haim Bar, Anton A. Komar, Ryan C. Hunt, Brian Lin, Michael DiCuccio, Chava Kimchi-Sarfaty

Nikita Vostrosablin, Shuhui Lim, Pooja Gopal, Kveta Brazdilova, Sushmita Parajuli, Xiaona Wei, Anna Gromek, David Prihoda, Martin Spale, Anja Muzdalo, Jamie Greig, Constance Yeo, Joanna Wardyn, Petr Mejzlik, Brian Henry, Anthony W Partridge, Danny A Bitton

Andres M Alonso, Luis Diambra

Luciana I. Escobar, Andres M. Alonso, Jorge R. Ronderos, Luis Diambra

Randall A. Meyer, Sara Trabulo, Julie A. Douthwaite, Jose Luis Santos

Guillermo Lamolle, Andrés Iriarte, Héctor Musto

Aviv A. Rosenberg, Ailie Marx, Alex M. Bronstein

Brian C. Lin, Katarzyna I. Jankowska, Douglas Meyer, Upendra K. Katneni

Linor Ackerman-Schraier, Aviv A. Rosenberg, Ailie Marx, Alex M. Bronstein

Ewan P. Plant, Zhiping Ye

Anna Masłowska-Górnicz, Melanie R.M. van den Bosch, Edoardo Saccenti, Maria Suarez-Diez

Yanqun Wang, Jie Li, Lu Zhang, Hai-Xi Sun, Zhaoyong Zhang, Jinjin Xu, Yonghao Xu, Yu Lin, Airu Zhu, Yuxue Luo, Haibo Zhou, Yan Wu, Shanwen Lin, Yuzhe Sun, Fei Xiao, Ruiying Chen, Liyan Wen, Wei Chen, Fang Li, Rijing Ou, Yanjun Zhang, Tingyou Kuo, Yuming Li, Lingguo Li, Jing Sun, Kun Sun, Zhen Zhuang, Haorong Lu, Zhao Chen, Guoqiang Mai, Jianfen Zhuo, Puyi Qian, Jiayu Chen, Huanming Yang, Jian Wang, Xun Xu, Nanshan Zhong, Jingxian Zhao, Junhua Li, Jincun Zhao, Xin Jin

Brian Dehlinger, Jared Jurss, Karson Lychuk, Catherine Putonti

Julie D. Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel

Stephany Francisco, Margarida Ferreira, Gabriela Moura, Ana Raquel Soares, Manuel A.S. Santos

Andres Mariano Alonso, Luis Diambra

Artem Kim, Jérôme Le Douce, Farah Diab, Monika Ferovova, Christèle Dubourg, Sylvie Odent, Valérie Dupé, Véronique David, Luis Diambra, Erwan Watrin, Marie de Tayrac

Gopal Dila, Christian J. Michel, Olivier Poch, Raymond Ripp, Julie D. Thompson

Aikaterini Alexaki, Gaya K. Hettiarachchi, John C. Athey, Upendra K. Katneni, Vijaya Simhadri, Nobuko Hamasaki-Katagiri, Puja Nanavaty, Brian Lin, Kazuyo Takeda, Darón Freedberg, Dougald Monroe, Joseph R. McGill, Robert Peters, Jacob M. Kames, David D. Holcomb, Ryan C. Hunt, Zuben E. Sauna, Amy Gelinas, Nebojsa Janjic, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty

Aikaterini Alexaki, Jacob Kames, David D. Holcomb, John Athey, Luis V. Santana-Quintero, Phuc Vihn Nguyen Lam, Nobuko Hamasaki-Katagiri, Ekaterina Osipova, Vahan Simonyan, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty

Proyasha Roy, Sumanta Dey, Ashesh Nandy, Subhash C. Basak, Sukhen Das

Christina McCarthy, Alejandra Carrea, Luis Diambra

Yuriko Harigaya, Roy Parker

2025	Influence of Nucleophosmin ( NPM1 ) Genotypes on Outcome of Patients With AML: An AIEOP-BFM and COG-SWOG Intergroup Collaboration Journal of Clinical Oncology Claudia Tregnago, Maddalena Benetton, Rhonda E. Ries, Jack H. Peplinski, Todd A. Alonzo, Derek Stirewalt, Megan Othus, Nicolas Duployez, Edwin Sonneveld, Jonas Abrahamsson, Linda Fogelstrand, Nils von Neuhoff, Henrik Hasle, Dirk Reinhardt, Soheil Meshinchi, Franco Locatelli, Martina Pigazzi
2025	Investigations on genomic, topological and structural properties of diguanylate cyclases involved in Vibrio cholerae biofilm signalling using in silico techniques: Promising drug targets in combating cholera Current Research in Structural Biology Tuhin Manna, Subhamoy Dey, Monalisha Karmakar, Amiya Kumar Panda, Chandradipa Ghosh
2025	SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period Virus Evolution Nigam H Padhiar, Tigran Ghazanchyan, Sarah E Fumagalli, Michael DiCuccio, Guy Cohen, Alexander Ginzburg, Brian Rikshpun, Almog Klein, Luis Santana-Quintero, Sean Smith, Anton A Komar, Chava Kimchi-Sarfaty
2025	Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage Journal of Molecular Evolution Lucio Aliperti Car, Ignacio E. Sánchez
2024	In-silico Codon Context and Synonymous Usage Analysis of Genes for Molecular Mechanisms Inducing Autophagy and Apoptosis with Reference to Neurodegenerative Disorders Journal of Alzheimer’s Disease Rekha Khandia, Pankaj Gurjar, Victoria Romashchenko, Sami A. Al-Hussain, Athanasios Alexiou, George Zouganelis, Magdi E.A. Zaki
2024	Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages BMC Bioinformatics Sarah E. Fumagalli, Sean Smith, Tigran Ghazanchyan, Douglas Meyer, Rahul Paul, Collin Campbell, Luis Santana-Quintero, Anton Golikov, Juan Ibla, Haim Bar, Anton A. Komar, Ryan C. Hunt, Brian Lin, Michael DiCuccio, Chava Kimchi-Sarfaty
2024	mRNAid, an open-source platform for therapeutic mRNA design and optimization strategies NAR Genomics and Bioinformatics Nikita Vostrosablin, Shuhui Lim, Pooja Gopal, Kveta Brazdilova, Sushmita Parajuli, Xiaona Wei, Anna Gromek, David Prihoda, Martin Spale, Anja Muzdalo, Jamie Greig, Constance Yeo, Joanna Wardyn, Petr Mejzlik, Brian Henry, Anthony W Partridge, Danny A Bitton
2023	Dicodon-based measures for modeling gene expression Bioinformatics Andres M Alonso, Luis Diambra
2023	Distal nucleotides affect the rate of stop codon read‐through Quantitative Biology Luciana I. Escobar, Andres M. Alonso, Jorge R. Ronderos, Luis Diambra
2022	RNA Technologies Randall A. Meyer, Sara Trabulo, Julie A. Douthwaite, Jose Luis Santos
2022	Codon usage in the flatworm Schistosoma mansoni is shaped by the mutational bias towards A+T and translational selection, which increases GC-ending codons in highly expressed genes Molecular and Biochemical Parasitology Guillermo Lamolle, Andrés Iriarte, Héctor Musto
2022	Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon Nature Communications Aviv A. Rosenberg, Ailie Marx, Alex M. Bronstein
2022	Single Nucleotide Polymorphisms Brian C. Lin, Katarzyna I. Jankowska, Douglas Meyer, Upendra K. Katneni
2022	Machine learning approaches demonstrate that protein structures carry information about their genetic coding Scientific Reports Linor Ackerman-Schraier, Aviv A. Rosenberg, Ailie Marx, Alex M. Bronstein
2022	Bias at the third nucleotide of codon pairs in virus and host genomes Scientific Reports Ewan P. Plant, Zhiping Ye
2022	A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content, protein functional domains and bacterial phenotypes Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Anna Masłowska-Górnicz, Melanie R.M. van den Bosch, Edoardo Saccenti, Maria Suarez-Diez
2022	Plasma cell-free RNA characteristics in COVID-19 patients Genome Research Yanqun Wang, Jie Li, Lu Zhang, Hai-Xi Sun, Zhaoyong Zhang, Jinjin Xu, Yonghao Xu, Yu Lin, Airu Zhu, Yuxue Luo, Haibo Zhou, Yan Wu, Shanwen Lin, Yuzhe Sun, Fei Xiao, Ruiying Chen, Liyan Wen, Wei Chen, Fang Li, Rijing Ou, Yanjun Zhang, Tingyou Kuo, Yuming Li, Lingguo Li, Jing Sun, Kun Sun, Zhen Zhuang, Haorong Lu, Zhao Chen, Guoqiang Mai, Jianfen Zhuo, Puyi Qian, Jiayu Chen, Huanming Yang, Jian Wang, Xun Xu, Nanshan Zhong, Jingxian Zhao, Junhua Li, Jincun Zhao, Xin Jin
2021	The Dynamic Codon Biaser: calculating prokaryotic codon usage biases Microbial Genomics Brian Dehlinger, Jared Jurss, Karson Lychuk, Catherine Putonti
2021	Potential role of the X circular code in the regulation of gene expression Biosystems Julie D. Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel
2020	Does proteostasis get lost in translation? Implications for protein aggregation across the lifespan Ageing Research Reviews Stephany Francisco, Margarida Ferreira, Gabriela Moura, Ana Raquel Soares, Manuel A.S. Santos
2020	SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage Frontiers in Cell and Developmental Biology Andres Mariano Alonso, Luis Diambra
2020	Synonymous variants in holoprosencephaly alter codon usage and impact the Sonic Hedgehog protein Brain Artem Kim, Jérôme Le Douce, Farah Diab, Monika Ferovova, Christèle Dubourg, Sylvie Odent, Valérie Dupé, Véronique David, Luis Diambra, Erwan Watrin, Marie de Tayrac
2019	Synonymous Codon Usage—a Guide for Co-Translational Protein Folding in the Cell Molecular Biology A. A. Komar
2019	Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes Biosystems Gopal Dila, Christian J. Michel, Olivier Poch, Raymond Ripp, Julie D. Thompson
2019	Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies Scientific Reports Aikaterini Alexaki, Gaya K. Hettiarachchi, John C. Athey, Upendra K. Katneni, Vijaya Simhadri, Nobuko Hamasaki-Katagiri, Puja Nanavaty, Brian Lin, Kazuyo Takeda, Darón Freedberg, Dougald Monroe, Joseph R. McGill, Robert Peters, Jacob M. Kames, David D. Holcomb, Ryan C. Hunt, Zuben E. Sauna, Amy Gelinas, Nebojsa Janjic, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
2019	Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design Journal of Molecular Biology Aikaterini Alexaki, Jacob Kames, David D. Holcomb, John Athey, Luis V. Santana-Quintero, Phuc Vihn Nguyen Lam, Nobuko Hamasaki-Katagiri, Ekaterina Osipova, Vahan Simonyan, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
2018	Base Distribution in Dengue Nucleotide Sequences Differs Significantly from Other Mosquito-Borne Human-Infecting Flavivirus Members Current Computer-Aided Drug Design Proyasha Roy, Sumanta Dey, Ashesh Nandy, Subhash C. Basak, Sukhen Das
2017	Bicodon bias can determine the role of synonymous SNPs in human diseases BMC Genomics Christina McCarthy, Alejandra Carrea, Luis Diambra
2017	The link between adjacent codon pairs and mRNA stability BMC Genomics Yuriko Harigaya, Roy Parker
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