Mario A. Fares - Publications

Affiliations: 
Smurfit Institute of Genetics Trinity College, Dublin, Dublin, County Dublin, Ireland 

83 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mattenberger F, Fares MA, Toft C, Sabater-Muñoz B. The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast . International Journal of Molecular Sciences. 22. PMID 34830177 DOI: 10.3390/ijms222212293  0.812
2020 Sabater-Muñoz B, Mattenberger F, Fares MA, Toft C. Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae. Msystems. 5. PMID 32788405 DOI: 10.1128/mSystems.00416-20  0.809
2020 Hermida-Carrera C, Fares MA, Font-Carrascosa M, Kapralov MV, Koch MA, Mir A, Molins A, Ribas-Carbó M, Rocha J, Galmés J. Exploring molecular evolution of Rubisco in C and CAM Orchidaceae and Bromeliaceae. Bmc Evolutionary Biology. 20: 11. PMID 31969115 DOI: 10.1186/S12862-019-1551-8  0.341
2019 Alvarez-Ponce D, Aguilar-Rodríguez J, Fares MA. Molecular chaperones accelerate the evolution of their protein clients in yeast. Genome Biology and Evolution. PMID 31297528 DOI: 10.1093/Gbe/Evz147  0.814
2019 Aguilar-Rodríguez J, Fares MA, Wagner A. Chaperonin overproduction and metabolic erosion caused by mutation accumulation in Escherichia coli. Fems Microbiology Letters. 366. PMID 31150542 DOI: 10.1093/Femsle/Fnz121  0.808
2018 Alvarez-Ponce D, Ruiz-González MX, Vera-Sirera F, Feyertag F, Perez-Amador MA, Fares MA. Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions. International Journal of Molecular Sciences. 19. PMID 30081447 DOI: 10.3390/Ijms19082276  0.693
2018 Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, et al. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. Fems Microbiology Reviews. PMID 29893835 DOI: 10.1093/Femsre/Fuy026  0.317
2018 Rodrigo G, Fares MA. Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach. Elife. 7. PMID 29303479 DOI: 10.7554/Elife.29739  0.498
2017 Hermida-Carrera C, Fares MA, Fernández Á, Gil-Pelegrín E, Kapralov MV, Mir A, Molins A, Peguero-Pina JJ, Rocha J, Sancho-Knapik D, Galmés J. Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. Plos One. 12: e0183970. PMID 28859145 DOI: 10.1371/Journal.Pone.0183970  0.367
2017 Mattenberger F, Sabater-Muñoz B, Toft C, Sablok G, Fares MA. Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 28633360 DOI: 10.1093/Dnares/Dsx025  0.799
2017 Fares MA, Sabater-Muñoz B, Toft C. Genome mutational and transcriptional hotspots are traps for duplicated genes and sources of adaptations. Genome Biology and Evolution. PMID 28459980 DOI: 10.1093/Gbe/Evx085  0.828
2017 Sabater-Muñoz B, Toft C, Alvarez-Ponce D, Fares MA. Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. The Isme Journal. PMID 28323281 DOI: 10.1038/Ismej.2017.18  0.83
2016 Mattenberger F, Sabater-Muñoz B, Hallsworth JE, Fares MA. Glycerol stress in Saccharomyces cerevisiae: Cellular responses and evolved adaptations. Environmental Microbiology. PMID 27871139 DOI: 10.1111/1462-2920.13603  0.736
2016 Mattenberger F, Sabater-Muñoz B, Toft C, Fares MA. The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3 (Bethesda, Md.). PMID 27799339 DOI: 10.1534/G3.116.035329  0.813
2016 Alvarez-Ponce D, Sabater-Muñoz B, Toft C, Ruiz-González MX, Fares MA. Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli. Genome Biology and Evolution. PMID 27566759 DOI: 10.1093/Gbe/Evw205  0.808
2016 Aguilar-Rodríguez J, Sabater-Muñoz B, Montagud-Martínez R, Berlanga V, Alvarez-Ponce D, Wagner A, Fares MA. The molecular chaperone DnaK is a source of mutational robustness. Genome Biology and Evolution. PMID 27497316 DOI: 10.1093/Gbe/Evw176  0.804
2016 Roque E, Fares MA, Yenush L, Rochina MC, Wen J, Mysore KS, Gómez-Mena C, Beltrán JP, Cañas LA. Evolution by gene duplication of Medicago truncatula PISTILLATA-like transcription factors. Journal of Experimental Botany. PMID 26773809 DOI: 10.1093/Jxb/Erv571  0.481
2015 Cluxton CD, Caffrey BE, Kinsella GK, Moynagh PN, Fares MA, Fallon PG. Functional conservation of an ancestral Pellino protein in helminth species. Scientific Reports. 5: 11687. PMID 26120048 DOI: 10.1038/Srep11687  0.362
2015 Sabater-Muñoz B, Prats-Escriche M, Montagud-Martínez R, López-Cerdán A, Toft C, Aguilar-Rodríguez J, Wagner A, Fares MA. Fitness trade-offs determine the role of the molecular chaperonin GroEL in buffering mutations. Molecular Biology and Evolution. PMID 26116858 DOI: 10.1093/Molbev/Msv144  0.788
2015 Fares MA. The origins of mutational robustness. Trends in Genetics : Tig. PMID 26013677 DOI: 10.1016/J.Tig.2015.04.008  0.482
2015 Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, Bertranpetit J, Laayouni H. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. Genome Biology and Evolution. 7: 1141-54. PMID 25840415 DOI: 10.1093/Gbe/Evv055  0.763
2014 Fares MA. Survival and innovation: The role of mutational robustness in evolution. Biochimie. PMID 25447135 DOI: 10.1016/J.Biochi.2014.10.019  0.453
2014 Fares MA. The evolution of protein moonlighting: adaptive traps and promiscuity in the chaperonins. Biochemical Society Transactions. 42: 1709-14. PMID 25399594 DOI: 10.1042/Bst20140225  0.464
2014 Keane OM, Toft C, Carretero-Paulet L, Jones GW, Fares MA. Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. Genome Research. 24: 1830-41. PMID 25149527 DOI: 10.1101/Gr.176792.114  0.834
2014 Hasiów-Jaroszewska B, Fares MA, Elena SF. Molecular evolution of viral multifunctional proteins: the case of potyvirus HC-Pro. Journal of Molecular Evolution. 78: 75-86. PMID 24271857 DOI: 10.1007/S00239-013-9601-0  0.355
2013 Ruiz-González MX, Fares MA. Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L. Bmc Evolutionary Biology. 13: 156. PMID 23875653 DOI: 10.1186/1471-2148-13-156  0.42
2013 Carretero-Paulet L, Albert VA, Fares MA. Molecular evolutionary mechanisms driving functional diversification of the HSP90A family of heat shock proteins in eukaryotes. Molecular Biology and Evolution. 30: 2035-43. PMID 23813917 DOI: 10.1093/Molbev/Mst113  0.414
2013 Henderson B, Fares MA, Lund PA. Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biological Reviews of the Cambridge Philosophical Society. 88: 955-87. PMID 23551966 DOI: 10.1111/Brv.12037  0.402
2013 Fares MA, Keane OM, Toft C, Carretero-Paulet L, Jones GW. The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. Plos Genetics. 9: e1003176. PMID 23300483 DOI: 10.1371/Journal.Pgen.1003176  0.825
2013 Sablok G, Mudunuri SB, Patnana S, Popova M, Fares MA, Porta NL. ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 20: 127-33. PMID 23284085 DOI: 10.1093/Dnares/Dss038  0.395
2012 Alvarez-Ponce D, Fares MA. Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biology and Evolution. 4: 1263-74. PMID 23160177 DOI: 10.1093/Gbe/Evs101  0.756
2012 Sen L, Fares M, Su YJ, Wang T. Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern. Bmc Evolutionary Biology. 12: 145. PMID 22899792 DOI: 10.1186/1471-2148-12-145  0.434
2012 Carretero-Paulet L, Fares MA. Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Molecular Biology and Evolution. 29: 3541-51. PMID 22734049 DOI: 10.1093/Molbev/Mss162  0.53
2012 Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA. Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations. Plos One. 7: e35659. PMID 22563391 DOI: 10.1371/Journal.Pone.0035659  0.825
2012 Rodrigo G, Fares MA. Describing the structural robustness landscape of bacterial small RNAs. Bmc Evolutionary Biology. 12: 52. PMID 22500888 DOI: 10.1186/1471-2148-12-52  0.393
2011 Jiang X, Fares MA. Functional diversification of the twin-arginine translocation pathway mediates the emergence of novel ecological adaptations. Molecular Biology and Evolution. 28: 3183-93. PMID 21673095 DOI: 10.1093/Molbev/Msr154  0.447
2011 Sen L, Fares MA, Liang B, Gao L, Wang B, Wang T, Su YJ. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biology Direct. 6: 29. PMID 21639885 DOI: 10.1186/1745-6150-6-29  0.439
2011 Fares MA, Ruiz-González MX, Labrador JP. Protein coadaptation and the design of novel approaches to identify protein-protein interactions. Iubmb Life. 63: 264-71. PMID 21488148 DOI: 10.1002/Iub.455  0.381
2010 Codoñer FM, Alfonso-Loeches S, Fares MA. Mutational dynamics of murine angiogenin duplicates. Bmc Evolutionary Biology. 10: 310. PMID 20950426 DOI: 10.1186/1471-2148-10-310  0.412
2010 Williams TA, Fares MA. The effect of chaperonin buffering on protein evolution. Genome Biology and Evolution. 2: 609-19. PMID 20660109 DOI: 10.1093/Gbe/Evq045  0.476
2010 Toft C, Fares MA. Structural calibration of the rates of amino acid evolution in a search for Darwin in drifting biological systems. Molecular Biology and Evolution. 27: 2375-85. PMID 20466746 DOI: 10.1093/Molbev/Msq123  0.803
2010 Garceau V, Smith J, Paton IR, Davey M, Fares MA, Sester DP, Burt DW, Hume DA. Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products. Journal of Leukocyte Biology. 87: 753-64. PMID 20051473 DOI: 10.1189/Jlb.0909624  0.347
2010 Williams TA, Codoñer FM, Toft C, Fares MA. Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends in Genetics : Tig. 26: 47-51. PMID 20036437 DOI: 10.1016/J.Tig.2009.11.009  0.829
2009 Reardon W, Fitzpatrick DA, Fares MA, Nugent JM. Evolution of flower shape in Plantago lanceolata. Plant Molecular Biology. 71: 241-50. PMID 19593661 DOI: 10.1007/S11103-009-9520-Z  0.378
2009 Commins J, Toft C, Fares MA. Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. Biological Procedures Online. 11: 52-78. PMID 19495914 DOI: 10.1007/S12575-009-9004-1  0.799
2009 Toft C, Williams TA, Fares MA. Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. Plos Computational Biology. 5: e1000344. PMID 19343224 DOI: 10.1371/Journal.Pcbi.1000344  0.823
2009 Toft C, Fares MA. Selection for translational robustness in Buchnera aphidicola, endosymbiotic bacteria of aphids. Molecular Biology and Evolution. 26: 743-51. PMID 19126868 DOI: 10.1093/Molbev/Msn301  0.841
2009 Williams TA, Wolfe KH, Fares MA. No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Molecular Biology and Evolution. 26: 445-50. PMID 19037009 DOI: 10.1093/Molbev/Msn267  0.609
2009 Tully DC, Fares MA. Shifts in the selection-drift balance drive the evolution and epidemiology of foot-and-mouth disease virus. Journal of Virology. 83: 781-90. PMID 19004952 DOI: 10.1128/Jvi.01500-08  0.464
2009 Fares MA. Looking for Darwin in Endosymbionts The Open Evolution Journal. 3: 31-37. DOI: 10.2174/1874404400903010031  0.428
2008 Codoñer FM, Fares MA. Why should we care about molecular coevolution? Evolutionary Bioinformatics Online. 4: 29-38. PMID 19204805 DOI: 10.4137/Ebo.S0  0.328
2008 Tully DC, Fares MA. The tale of a modern animal plague: tracing the evolutionary history and determining the time-scale for foot and mouth disease virus. Virology. 382: 250-6. PMID 18945462 DOI: 10.1016/J.Virol.2008.09.011  0.319
2008 Llorens C, Fares MA, Moya A. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. Bmc Evolutionary Biology. 8: 276. PMID 18842133 DOI: 10.1186/1471-2148-8-276  0.611
2008 Toft C, Fares MA. The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Molecular Biology and Evolution. 25: 2069-76. PMID 18635679 DOI: 10.1093/Molbev/Msn153  0.839
2008 Codoñer FM, O'Dea S, Fares MA. Reducing the false positive rate in the non-parametric analysis of molecular coevolution. Bmc Evolutionary Biology. 8: 106. PMID 18402697 DOI: 10.1186/1471-2148-8-106  0.392
2007 Travers SA, Tully DC, McCormack GP, Fares MA. A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Molecular Biology and Evolution. 24: 2787-801. PMID 17921487 DOI: 10.1093/Molbev/Msm213  0.347
2007 McNally D, Fares MA. In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae. Bmc Evolutionary Biology. 7: 81. PMID 17519003 DOI: 10.1186/1471-2148-7-81  0.376
2007 Radhakrishnan Y, Fares MA, French FS, Hall SH. Comparative genomic analysis of a mammalian beta-defensin gene cluster. Physiological Genomics. 30: 213-22. PMID 17456736 DOI: 10.1152/Physiolgenomics.00263.2006  0.454
2007 Ruano-Rubio V, Fares MA. Testing the neutral fixation of hetero-oligomerism in the archaeal chaperonin CCT. Molecular Biology and Evolution. 24: 1384-96. PMID 17406022 DOI: 10.1093/Molbev/Msm065  0.457
2007 Ruano-Rubio V, Fares MA. Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly. Systematic Biology. 56: 68-82. PMID 17366138 DOI: 10.1080/10635150601175578  0.316
2007 Travers SA, Fares MA. Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Molecular Biology and Evolution. 24: 1032-44. PMID 17267421 DOI: 10.1093/Molbev/Msm022  0.356
2006 Tully DC, Fares MA. Unravelling selection shifts among foot-and-mouth disease virus (FMDV) serotypes. Evolutionary Bioinformatics Online. 2: 211-25. PMID 19455214 DOI: 10.4137/Ebo.S0  0.395
2006 Fares MA, McNally D. CAPS: coevolution analysis using protein sequences. Bioinformatics (Oxford, England). 22: 2821-2. PMID 17005535 DOI: 10.1093/Bioinformatics/Btl493  0.334
2006 Codoñer FM, Fares MA, Elena SF. Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus. Journal of Virology. 80: 5833-40. PMID 16731922 DOI: 10.1128/Jvi.00122-06  0.39
2006 Toft C, Fares MA. GRAST: a new way of genome reduction analysis using comparative genomics. Bioinformatics (Oxford, England). 22: 1551-61. PMID 16601001 DOI: 10.1093/Bioinformatics/Btl139  0.826
2006 Fares MA, Travers SA. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics. 173: 9-23. PMID 16547113 DOI: 10.1534/Genetics.105.053249  0.381
2006 Fares MA, Byrne KP, Wolfe KH. Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Molecular Biology and Evolution. 23: 245-53. PMID 16207937 DOI: 10.1093/Molbev/Msj027  0.651
2006 Fares M. Computational and Statistical Methods to Explore the Various Dimensions of Protein Evolution Current Bioinformatics. 1: 207-217. DOI: 10.2174/157489306777011950  0.33
2005 Fares MA, Moya A, Barrio E. Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects. Journal of Evolutionary Biology. 18: 651-60. PMID 15842494 DOI: 10.1111/J.1420-9101.2004.00861.X  0.792
2004 Fares MA, Moya A, Barrio E. GroEL and the maintenance of bacterial endosymbiosis. Trends in Genetics : Tig. 20: 413-6. PMID 15313549 DOI: 10.1016/J.Tig.2004.07.001  0.81
2004 Lynn DJ, Higgs R, Gaines S, Tierney J, James T, Lloyd AT, Fares MA, Mulcahy G, O'Farrelly C. Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken. Immunogenetics. 56: 170-7. PMID 15148642 DOI: 10.1007/S00251-004-0675-0  0.385
2004 Fares MA. SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics (Oxford, England). 20: 2867-8. PMID 15130925 DOI: 10.1093/Bioinformatics/Bth303  0.353
2004 Lynn DJ, Lloyd AT, Fares MA, O'Farrelly C. Evidence of positively selected sites in mammalian alpha-defensins. Molecular Biology and Evolution. 21: 819-27. PMID 14963090 DOI: 10.1093/Molbev/Msh084  0.336
2003 Fares MA, Bezemer D, Moya A, Marín I. Selection on coding regions determined Hox7 genes evolution. Molecular Biology and Evolution. 20: 2104-12. PMID 12949154 DOI: 10.1093/Molbev/Msg222  0.673
2003 Fares MA, Wolfe KH. Positive selection and subfunctionalization of duplicated CCT chaperonin subunits. Molecular Biology and Evolution. 20: 1588-97. PMID 12832642 DOI: 10.1093/Molbev/Msg160  0.596
2003 Wong S, Fares MA, Zimmermann W, Butler G, Wolfe KH. Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata. Genome Biology. 4: R10. PMID 12620120 DOI: 10.1186/Gb-2003-4-2-R10  0.595
2002 Fares MA, Elena SF, Ortiz J, Moya A, Barrio E. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. Journal of Molecular Evolution. 55: 509-21. PMID 12399925 DOI: 10.1007/S00239-002-2346-9  0.755
2002 Fares MA, Barrio E, Sabater-Muñoz B, Moya A. The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Molecular Biology and Evolution. 19: 1162-70. PMID 12082135 DOI: 10.1093/Oxfordjournals.Molbev.A004174  0.8
2002 Fares MA, Holmes EC. A revised evolutionary history of hepatitis B virus (HBV). Journal of Molecular Evolution. 54: 807-14. PMID 12029362 DOI: 10.1007/S00239-001-0084-Z  0.31
2002 Fares MA, Ruiz-González MX, Moya A, Elena SF, Barrio E. Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature. 417: 398. PMID 12024205 DOI: 10.1038/417398A  0.792
2001 Fares MA, Moya A, Escarmís C, Baranowski E, Domingo E, Barrio E. Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Molecular Biology and Evolution. 18: 10-21. PMID 11141188 DOI: 10.1093/Oxfordjournals.Molbev.A003715  0.755
2001 Marín I, Fares MA, González-Candelas F, Barrio E, Moya A. Detecting changes in the functional constraints of paralogous genes. Journal of Molecular Evolution. 52: 17-28. PMID 11139291 DOI: 10.1007/S002390010130  0.787
1998 Fares MA, Barrio E, Becerra N, Escarmís C, Domingo E, Moya A. The foot-and-mouth disease RNA virus as a model in experimental phylogenetics. International Microbiology : the Official Journal of the Spanish Society For Microbiology. 1: 311-8. PMID 10943380 DOI: 10.2436/Im.V1I4.34  0.768
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