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An updated list of publications

2019

  1. Macías LG, Morard M, Toft C and Barrio E (2019) Comparative genomics between Saccharomyces kudriavzevii and S. cerevisiae applied to identify mechanisms involved in adaptation. Re-submitted to Frontiers in Genetics 10:187. doi: 10.3389/fgene.2019.00187.
  2. Morard M, Macías LG, Adam AC, Lairon-Peris M Pérez-Torrado R, Toft C and Barrio E (2019). Aneuploidy and ethanol tolerance in Saccharomyces cerevisiae. Frontiers in Genetics 10:82. doi: 10.3389/fgene.2019.00082.

 

2017

  1. Ibáñez, Pérez-Torrado R, Morard M, Toft C, Barrio E and Querol A. (2017) RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments. International Journal of Food Microbiology 18;257:262-270.
  2. Mattenberger F, Sabater-Muñoz B, Toft C, Sablok G, Fares MA (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.
  3. Sabater-Muñoz B*, Toft C*, Alvarez-Ponce D, and Fares MA. (2017) Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. The ISME Journal 11(6):1291-1304. * Shared first authors
  4. Fares MA, 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.
  5. Mattenberger F, Sabater-Muñoz B, Toft C, Fares MA. (2017) The phenotypic plasticity of duplicated genes in Saccharomyces cerevisiae and the origin of adaptations. G3 (Genes| Genomes| Genetics). 7(1):63-75.

 

2016

  1. Alvarez-Ponce D, Sabater-Muñoz B, Toft C, Ruiz-González MX, Fares MA. (2016) Essentiality is a strong determinant of protein rates of evolution during mutation accumulation experiments in Escherichia coli. Genome Biology and Evolution. 8(9):2914-2927.

 

2015

  1. Sabater-Muñoz B, Prats-Escriche M, Montagud-Martínez R, López-Cerdán A, Toft C, Aguilar-Rodríguez J, Wagner A, Fares MA. (2015) Fitness trade-offs determine the role of the molecular chaperonin GroEL in buffering mutations. Molecular Biology and Evolution. 32(10):2681-93.

 

2014

  1. Keane OM*, Toft C*, Carretero-Paulet L, Jones GW, Fares MA. (2014) Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. Genome Research. 24(11):1830-41. * Shared first authors
  2. Fares MA and Toft C (2014) Inferring functional divergence in protein sequences. İn Natural Selection: Methods and Applications, 83.

 

2013

  1. Guy L, Nystedt B, Toft C, Zaremba-Niedzwiedzka K, Berglund EC, Granberg F, Näslund K, Eriksson AS, Andersson SG. (2013) A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella. PLoS Genetics. 9(3):e1003393.
  2. Fares MA, Keane OM, Toft C, Carretero-Paulet L, Jones GW. (2013) The roles of whole- genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PLoS Genetics. 9(1):e1003176.

 

2012

  1. Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA. (2012) Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations. PLoS ONE. 7(4):e35659.

 

2010

  1. Toft C and Andersson SG. (2010) Evolutionary microbial genomics: insights into bacterial host adaptation. Nature Reviews Genetics. 11(7):465-475.
  2. Toft C and Fares MA. (2010) Structural calibration of the rates of amino acids evolution in a search for Darwin in drifting biological systems. Molecular Biology and Evolution. 27(10):2375-2385.
  3. Williams TA, Codoñer FM, Toft C and Fares MA. (2010) Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends in Genetics. 26(2):47-51.

 

2009

  1. Commins J*, Toft C*, Fares MA. (2009) Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. Biological Procedures Online. 11(1):52 – 78 * Shared first authors
  2. Toft C, Williams TA and Fares MA. (2009). Genome-wide functional divergence after the symbiosis of proteobacteria with insects unravelled through a new computational approach. PLoS Computational Biology 5(4):e1000344.
  3. Toft C and Fares MA. (2009). Selection for translational robustness in Buchnera aphidicola, endosymbiotic bacteria of aphids. Molecular Biology and Evolution. 26(4):743-751.
  4. Fares MA and Toft C (2009). Molecular co-evolution and the three-dimensionality of natural selection. In Evolutionary Biology: Concept, Modeling, and Application: 237- 251.


 

2008

  1. Toft C and Fares MA. (2008). The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Molecular Biology and Evolution. 25:2069-2076.

 

2006

  1. Toft C and Fares MA. (2006). GRAST: a new way of genome reduction analysis using comparative genomics. Bioinformatics 22(13): 1551-1561.