Research group

Analysis packages (R, Python, etc.), Bioinformatics Software and Tools, Data Analysis, Data Visualization, Genomics, Model organisms, Molecular evolution, Omics, Sequence analysis, Systems Biology, Transcriptomics

Álvarez-Rodríguez, B., Velandia-Álvarez, S., Toft, C., & Geller, R. (2024). Mapping the mutational landscape of a full viral proteome reveals distinct profiles of mutation tolerability. https://doi.org/10.1101/2024.03.07.583990

Castiglioni, V. G., Villena-Giménez, A., González-Sánchez, A., Toft, C., Gómez, G. G., & Elena, S. F. (2024). Chronic infection ofCaenorhabditis elegansby Orsay virus induces age-dependent immunity and superinfection exclusion. https://doi.org/10.1101/2024.12.26.630373

Mattenberger, F., Fares, M., Toft, C., & Sabater-Muñoz, B. (2021). The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae. International Journal of Molecular Sciences, 22(22), 12293. https://doi.org/10.3390/ijms222212293

Sabater-Muñoz, B., Mattenberger, F., Fares, M. A., & Toft, C. (2020). Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae. MSystems, 5(4). https://doi.org/10.1128/msystems.00416-20

Macías, L. G., Barrio, E., & Toft, C. (2020). GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level. G3 Genes|Genomes|Genetics, 10(12), 4369–4372. https://doi.org/10.1534/g3.120.401874

Mattenberger, F., Sabater-Muñoz, B., Toft, C., & Fares, M. A. (2017). The Phenotypic Plasticity of Duplicated Genes inSaccharomyces cerevisiaeand the Origin of Adaptations. G3 Genes|Genomes|Genetics, 7(1), 63–75. https://doi.org/10.1534/g3.116.035329

Ibáñez, C., Pérez-Torrado, R., Morard, M., Toft, C., Barrio, E., & Querol, A. (2017). RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments. International Journal of Food Microbiology, 257, 262–270. https://doi.org/10.1016/j.ijfoodmicro.2017.07.001

Fares, M. A., Sabater-Muñoz, B., & Toft, C. (2017). Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations. Genome Biology and Evolution, 9(5), 1229–1240. https://doi.org/10.1093/gbe/evx085

Mattenberger, F., Sabater-Muñoz, B., Toft, C., Sablok, G., & Fares, M. A. (2017). Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Research, 24(6), 559–570. https://doi.org/10.1093/dnares/dsx025

Sabater-Muñoz, B., Toft, C., Alvarez-Ponce, D., & Fares, M. A. (2017). Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. The ISME Journal, 11(6), 1291–1304. https://doi.org/10.1038/ismej.2017.18

Alvarez-Ponce, D., Sabater-Muñoz, B., Toft, C., Ruiz-González, M. X., & Fares, M. A. (2016). Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments inEscherichia coli. Genome Biology and Evolution, 8(9), 2914–2927. https://doi.org/10.1093/gbe/evw205

Keane, O. M., Toft, C., Carretero-Paulet, L., Jones, G. W., & Fares, M. A. (2014). Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. Genome Research, 24(11), 1830–1841. https://doi.org/10.1101/gr.176792.114

Williams, T. A., Codoñer, F. M., Toft, C., & Fares, M. A. (2010). Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends in Genetics, 26(2), 47–51. https://doi.org/10.1016/j.tig.2009.11.009

Toft, C., & Fares, M. A. (2010). Structural Calibration of the Rates of Amino Acid Evolution in a Search for Darwin in Drifting Biological Systems. Molecular Biology and Evolution, 27(10), 2375–2385. https://doi.org/10.1093/molbev/msq123

Toft, C., & Andersson, S. G. E. (2010). Evolutionary microbial genomics: insights into bacterial host adaptation. Nature Reviews Genetics, 11(7), 465–475. https://doi.org/10.1038/nrg2798

Toft, C., & Fares, M. A. (2009). Selection for Translational Robustness in Buchnera aphidicola, Endosymbiotic Bacteria of Aphids. Molecular Biology and Evolution, 26(4), 743–751. https://doi.org/10.1093/molbev/msn301

Fares, M. A., & Toft, C. (2009). Molecular Coevolution and the Three-Dimensionality of Natural Selection. Evolutionary Biology, 237–251. https://doi.org/10.1007/978-3-642-00952-5_14

Commins, J., Toft, C., & Fares, M. A. (2009). Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects. Biological Procedures Online, 11(1). https://doi.org/10.1007/s12575-009-9004-1

Toft, C., & Fares, M. A. (2008). The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial Genomes. Molecular Biology and Evolution, 25(9), 2069–2076. https://doi.org/10.1093/molbev/msn153

Toft, C., & Fares, M. A. (2006). GRAST: a new way of genome reduction analysis using comparative genomics. Bioinformatics, 22(13), 1551–1561. https://doi.org/10.1093/bioinformatics/btl139