Most Significant Publications

1. Keane OM, Toft C, Carretero-Paulet L, Jones GW, and Fares MA. (2014) Preservation of genetic and regulatory robustness in ancient gene duplicates of Sacchaormyces cerevisiae.  Genome Research In press.

2. Henderson B, Fares MA, Lund PA. (2013) Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biol. Rev. Camb. Philos. Soc. 88(4):955-87.

3. 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 Genet. 9(1):e1003176.

4. Carretero-Paulet L, Fares MA. (2012) Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Mol. Biol. Evol. 29(11):3541-51.

5. Williams TA, Codoñer FM, Toft C, Fares MA. (2010) Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet. Feb;26(2):47-51.

6. Toft C, Fares MA. (2008) The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Mol. Biol. Evol. 25(9):2069-2076.

7. Fares, M.A. and S.A. Travers. (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics 173(1): 9-23.

8. Fares, M.A., M.X. Ruiz-Gonzalez, A. Moya, S.F. Elena, and E. Barrio. (2002) Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417(6887): 398.



Full List of Publications
  • Keane OM, Toft C, Carretero-Paulet L, Jones GW, and Fares MA. (2013) Preservation of genetic and regulatory robustness in ancient gene duplicates of Sacchaormyces cerevisiae.  Genome Research In press.
  • Hasiów-Jaroszewska B, Fares MA, Elena SF. (2014) Molecular evolution of viral multifunctional proteins: the case of potyvirus HC-Pro. J. Mol. Evol. 78(1):75-86.
  • Ruiz-González MX, Fares MA. (2013) Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L. BMC Evol. Biol. 22;13:156.
  • Carretero-Paulet L, Albert VA, Fares MA. (2013) Molecular evolutionary mechanisms driving functional diversification of the HSP90A family of heat shock proteins in eukaryotes. Mol. Biol. Evol. 30(9):2035-43.
  • Henderson B, Fares MA, Lund PA. (2013) Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biol Rev Camb Philos Soc. 88(4):955-87.
  • 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 Genet. 9(1):e1003176.
  • Sablok G, Mudunuri SB, Patnana S, Popova M, Fares MA, Porta NL. (2013) ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics. DNA Res. 20(2):127-33.
  • Sen L, Fares MA, Su YJ, Wang T. (2012) Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern. BMC Evol. Biol. 16;12:145.
  • Alvarez-Ponce D, Fares MA. (2012) Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biol. Evol. 4(12):1263-74.
  • Carretero-Paulet L, Fares MA. (2012) Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Mol. Biol. Evol. 29(11):3541-51.
  • 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.
  • Rodrigo G, Fares MA. (2012) Describing the structural robustness landscape of bacterial small RNAs. BMC Evol. Biol. 13;12:52.
  • Jiang X, Fares MA. (2011) Functional diversification of the twin-arginine translocation pathway mediates the emergence of novel ecological adaptations. Mol. Biol. Evol. 28(11): 3183-3193.
  • Sen L, Fares MA, Liang B, Gao L, Wang B, Wang T, Su YJ. (2011) Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biol. Direct. 3;6:29.
  • Fares MA, Ruiz-González MX, Labrador JP. (2011) Protein coadaptation and the design of novel approaches to identify protein-protein interactions. IUBMB Life 63(4): 264-271.
  • Codoñer FM, Alfonso-Loeches S, Fares MA. (2010) Mutational dynamics of murine angiogenin duplicates. BMC Evol. Biol. 15;10:310.
  • Williams TA, Fares MA. (2010) The effect of chaperonin buffering on protein evolution. Genome Biol. Evol. 2:609-619.
  • Toft C, Fares MA. (2010) Structural calibration of the rates of amino acid evolution in a search for Darwin in drifting biological systems. Mol. Biol. Evol. 27(10): 2375-2385.
  • Williams TA, Codoñer FM, Toft C, Fares MA. (2010) Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet. Feb;26(2):47-51.
  • Garceau V, Smith J, Paton IR, Davey M, Fares MA, Sester DP, Burt DW, Hume DA. (2010) Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products. J Leukoc Biol. 87(5): 753-764.
  • Jiang X, Fares MA. (2010) IDENTIFYING COEVOLUTIONARY PATTERNS IN HUMAN LEUKOCYTE ANTIGEN (HLA) MOLECULES. Evolution. 64(5): 1429-1445.
  • Reardon W, Fitzpatrick DA, Fares MA, Nugent JM.(2009) Evolution of flower shape in Plantago lanceolata. Plant Mol. Biol.  Oct;71(3):241-50.
  • Commins, J., Toft, C. and Fares, M.A. (2009) Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects Biological Procedures. Biol Proced Online 11:52-78.
  • Toft C, Williams TA, Fares MA. (2009) Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PLoS Comput Biol. 5(4):e1000344.
  • Tully DC, Fares MA. (2009) Shifts in the selection-drift balance drive the evolution and epidemiology of foot-and-mouth disease virus. J. Virol. 83(2):781-90.
  • Toft C, Fares MA. (2009) Selection for Translational Robustness in Buchnera aphidicola, Endosymbiotic Bacteria of Aphids. Mol. Biol. Evol. 26(4):743-51.
  • Williams TA, Wolfe KH, Fares MA. (2009) No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Mol. Biol. Evol. 26(2):445-50.
  • Codoñer FM, O'Dea S, Fares MA. (2008) Reducing the false positive rate in the non-parametric analysis of molecular coevolution. BMC Evol Biol. 10;8:106.
  • Toft C, Fares MA. (2008) The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Mol. Biol. Evol. 25(9):2069-76.
  • Llorens C, Fares MA, Moya A.(2008)  Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evol. Biol.  8;8:276.
  • Tully DC, Fares MA. (2008) The tale of a modern animal plague: tracing the evolutionary history and determining the time-scale for foot and mouth disease virus. Virology. 382(2):250-6.
  • Codoñer, F.M. and M.A. Fares. (2008) Why should we care about molecular Coevolution? Evolutionary Bioinformatics Online, 14;4:29-38.
  • Travers SA, Tully DC, McCormack GP, Fares MA. (2007) A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Mol. Biol. Evol. 24(12):2787-801.
  • Radhakrishnan Y, Fares MA., French FS.,  Hall SH. (2007) Comparative genomic analysis of a mammalian beta-defensin gene cluster. Physiol. Genomics. 30(3):213-22.
  • McNally D., Fares MA. (2007) In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae. BMC Evol. Biol. 7:81.
  • Ruano-Rubio V.,  Fares MA. (2007) Testing the neutral fixation of hetero-oligomerism in the archaeal chaperonin CCT. Mol. Biol. Evol. 24(6):1384-96.
  • Ruano-Rubio V.,  Fares MA. (2007) Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly. Syst. Biol. 56(1):68-82.
  • Travers SA., Fares MA. (2007) Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Mol. Biol. Evol, 24(4):1032-1044.
  • Codoñer F.M., Fares MA., Elena SF. (2006) Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus. J. Virol., 80(12): 5833-5840.
  • Fares, M.A. (2006) Computational and Statistical methods to Explore the Various Dimensions of Protein Evolution. Current Bioinformatics, 1:207-217.
  • Fares, M.A., Byrne KP., Wolfe KH. (2006)  Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol Evol. 23(2):245-53.
  • Fares MA. and McNally D. (2006) CAPS: coevolution analysis using protein sequences. Bioinformatics 22(22):2821-2822.
  • Fares MA. and Travers SA. (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics, 173(1):9-23.
  • Toft C. and Fares MA. (2006) GRAST: a new way of genome reduction analysis using comparative genomics. Bioinformatics 22(13): 1551-1561.
  • Tully DC. and Fares MA. (2006) Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV) Serotypes. Evolutionary Bioinformatics Online, 1:223-237.
  • Fares MA., Moya A., Barrio E. (2005) Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects. J. Evol. Biol. 18(3):651-660.
  • Fares MA. SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics 20(16):2867-2868.
  • Fares MA.,  Moya A., Barrio E. (2004) GroEL and the maintenance of bacterial endosymbiosis. Trends Genet. 20(9):413-416.
  • Lynn DJ., Higgs R., Gaines S., Tierney J., James T., Lloyd AT., Fares MA., Mulcahy G., O'Farrelly C. (2004) Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken. Immunogenetics 56(3):170-177.
  • Lynn DJ., Lloyd AT., Fares MA., O'Farrelly C. (2004) Evidence of positively selected sites in mammalian alpha-defensins. Mol. Biol. Evol. 21(5):819-827.
  • Fares MA., Bezemer D., Moya A., Marin I. (2003) Selection on coding regions determined Hox7 genes evolution. Mol. Biol. Evol. 20(12):2104-2112.
  • Fares MA., Wolfe KH. (2003) Positive selection and subfunctionalization of duplicated CCT chaperonin subunits. Mol. Biol. Evol. 20(10):1588-1597.
  • Wong S., Fares MA., Zimmermann W., Butler G., Wolfe KH. (2003) Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata. Genome Biol. 4(2): R10.
  • Fares MA., Barrio E., Sabater-Munoz B., Moya A. (2002) The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol. Biol. Evol. 19(7):1162-1170.
  • Fares MA., Elena SF., Ortiz J., Moya A., Barrio E. (2002) A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol Evol. 55(5):509-521.
  • Fares MA. Holmes EC. (2002) A revised evolutionary history of hepatitis B virus (HBV). J. Mol. Evol. 54(6): 807-814.
  • Fares MA., Ruiz-Gonzalez MX., Moya A., Elena SF., Barrio E. (2002) Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417(6887): 398.
  • Fares MA., Moya A., Escarmis C., Baranowski E., Domingo E., Barrio E. (2001) Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol. Biol. Evol. 18(1):10-21.
  • Marin I., Fares MA., Gonzalez-Candelas F., Barrio E., Moya A. (2001)  Detecting changes in the functional constraints of paralogous genes. J. Mol. Evol. 52(1):17-28.
  • Fares MA., Barrio E., Becerra N., Escarmis C., Domingo E., Moya A. (1998) The foot-and-mouth disease RNA virus as a model in experimental phylogenetics. Int. Microbiol. 1(4):311-318.