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  1. Queen Mary University of London
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Publications: DR Alexandre De Mendoza Soler

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Romero Charria P, Navarrete C, Ovchinnikov V, Xu L, Sarre LA, Shabardina V, Ksiezopolska E, Casacuberta E et al. ( 2025 ) . Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes . Nature Genetics1 - 11 .
Gahan JM, Helfrich LW, Wetzel LA, Bhanu NV, Yuan Z-F, Garcia BA, Klose RJ, de Mendoza A et al. ( 2025 ) . Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates . Nature Communications vol. 16 , ( 1 )
Brethouwer T, de Mendoza A, Bogdanovic O ( 2025 ) . Non-CG DNA methylation in animal genomes . Nature Genetics vol. 57 , ( 10 ) 2395 - 2407 .
Piovani L, Gavriouchkina D, Parey E, Sarre LA, Peijnenburg KTCA, Martín-Durán JM, Rokhsar DS, Satoh N et al. ( 2025 ) . The genomic origin of the unique chaetognath body plan . Nature vol. 645 , ( 8082 ) 964 - 973 .
Sarre LA, Peralta GAG, Charria PR, Ovchinnikov V, de Mendoza A ( 2025 ) . Repressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent Eukaryotes . Molecular Biology and Evolution vol. 42 , ( 8 )
Blais C, Colp MJ, Sarre LA, de Mendoza A, Archibald JM ( 2025 ) . Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba . BMC Biology vol. 23 , ( 1 )
Church SH, Abedon RB, Ahuja N, Anthony CJ, Destanović D, Ramirez DA, Rojas LM, Albinsson ME et al. ( 2025 ) . Population genomics of a sailing siphonophore reveals genetic structure in the open ocean . Current Biology vol. 35 , ( 15 ) 3556 - 3569.e6 .
de Mendoza A ( 2025 ) . Genome synteny reveals hidden enhancer conservation . Nature Genetics vol. 57 , ( 6 ) 1328 - 1329 .
Kim IV, Navarrete C, Grau-Bové X, Iglesias M, Elek A, Zolotarov G, Bykov NS, Montgomery SA et al. ( 2025 ) . Chromatin loops are an ancestral hallmark of the animal regulatory genome . Nature vol. 642 , ( 8069 ) 1097 - 1105 .
Richards TA, Eme L, Archibald JM, Leonard G, Coelho SM, de Mendoza A, Dessimoz C, Dolezal P et al. ( 2024 ) . Reconstructing the last common ancestor of all eukaryotes . PLOS Biology vol. 22 , ( 11 ) e3002917 - e3002917 .
Gao Y, Tan DS, Girbig M, Hu H, Zhou X, Xie Q, Yeung SW, Lee KS et al. ( 2024 ) . The emergence of Sox and POU transcription factors predates the origins of animal stem cells . Nature Communications vol. 15 , ( 1 )
Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ et al. ( 2024 ) . Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria . Genome Biology vol. 25 , ( 1 ) 204 - 204 .
Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O ( 2024 ) . DNA methylation enables recurrent endogenization of giant viruses in an animal relative . Science Advances vol. 10 , ( 28 ) eado6406 - eado6406 .
Dossmann L, Emperle M, Dukatz M, de Mendoza A ( 2024 ) . Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons . Communications Biology vol. 7 , ( 1 )
Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Wan W et al. ( 2024 ) . Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences . Nature Ecology & Evolution vol. 8 , ( 3 ) 519 - 535 .
Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A et al. ( 2023 ) . Transient naive reprogramming corrects hiPS cells functionally and epigenetically . Nature vol. 620 , ( 7975 ) 863 - 872 .
de Mendoza A ( 2023 ) . A mammalian DNA methylation landscape . Science vol. 381 , ( 6658 ) 602 - 603 .
Dukatz M, Dittrich M, Adam S, de Mendoza A, Bashtrykov P ( 2022 ) . DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation . Journal of Biological Chemistry vol. 298 , ( 10 )
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Bogdanovic O et al. ( 2022 ) . Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability . Genome Biology vol. 23 , ( 1 )
De Mendoza Soler A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustiennes E et al. ( 2021 ) . The emergence of the brain non-CpG methylation system in vertebrates . Nature Ecology and Evolution
Ross SE, Angeloni A, Geng F-S ( 2020 ) . Developmental remodelling of non-CG methylation at satellite DNA repeats . Nucleic Acids Research vol. 48 , ( 22 )
Ruiz-Trillo I ( 2020 ) . Towards understanding the origin of animal development . Development (Cambridge, England) vol. 147 , ( 23 )
Hadjieconomou D, King G, Gaspar P, Mineo A, Blackie L, Ameku T, Diao F, White BH et al. ( 2020 ) . Enteric neurons increase maternal food intake during reproduction . Nature
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA et al. ( 2020 ) . Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri . Nature Communications vol. 11 , ( 1 )
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Medina P, Alcaina-Caro A et al. ( 2020 ) . Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings . Nature Communications vol. 11 , ( 1 )
Ross SE, Angeloni A, Bogdanovic O ( 2020 ) . Pervasive non-CpG methylation at zebrafish mosaic satellite repeats .
de Mendoza A, Lister R, Bogdanovic O ( 2019 ) . Evolution of DNA Methylome Diversity in Eukaryotes . Journal of Molecular Biology vol. 432 , ( 6 ) 1687 - 1705 .
de Mendoza A, Sebé-Pedrós A ( 2019 ) . Origin and evolution of eukaryotic transcription factors . Current Opinion in Genetics and Development vol. 58-59 , 25 - 32 .
de Mendoza A, Hatleberg WL, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U et al. ( 2019 ) . Convergent evolution of a vertebrate-like methylome in a marine sponge . Nature Ecology and Evolution vol. 3 , ( 10 ) 1464 - 1473 .
de Mendoza A ( 2019 ) . The Protistan Cellular and Genomic Roots of Animal Multicellularity . Old Questions and Young Approaches to Animal Evolution , Springer Nature
De Mendoza A, Pflueger J ( 2019 ) . Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family . Genome Research vol. 29 , ( 8 ) 1277 - 1286 .
De Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Hori K, Pflueger J et al. ( 2018 ) . Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons . Nature Communications vol. 9 , ( 1 )
Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A et al. ( 2017 ) . Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming . Cell Stem Cell vol. 21 , ( 6 ) 834 - 845.e6 .
Ford E, Grimmer MR, Stolzenburg S, Bogdanovic O, de Mendoza A ( 2017 ) . Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation .
de Mendoza A, Jones JW ( 2016 ) . Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family . Scientific Reports vol. 6 , ( 1 )
Gold DA, Grabenstatter J, de Mendoza A, Riesgo A, Ruiz-Trillo I ( 2016 ) . Sterol and genomic analyses validate the sponge biomarker hypothesis . Proceedings of the National Academy of Sciences of the United States of America vol. 113 , ( 10 ) 2684 - 2689 .
de Mendoza A, Suga H, Permanyer J ( 2015 ) . Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals . eLife vol. 4 ,
Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Whipps CM et al. ( 2015 ) . Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi . Current Biology vol. 25 , ( 18 ) 2404 - 2410 .
Sebé-Pedrós A, de Mendoza A ( 2015 ) . Transcription Factors and the Origin of Animal Multicellularity . Evolutionary Transitions to Multicellular Life , vol. 2 , Springer Nature
de Mendoza A ( 2014 ) . Forward genetics for back-in-time questions . eLife vol. 3 ,
de Mendoza A, Sebé-Pedrós A ( 2014 ) . The Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan Multicellularity . Genome Biology and Evolution vol. 6 , ( 3 ) 606 - 619 .
Desvoyes B, de Mendoza A, Ruiz-Trillo I ( 2013 ) . Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division . Journal of Experimental Botany vol. 65 , ( 10 ) 2657 - 2666 .
de Mendoza A, Sebé-Pedrós A, Matejčić M, Domazet-Lošo T ( 2013 ) . Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages . Proceedings of the National Academy of Sciences of the United States of America vol. 110 , ( 50 ) e4858 - e4866 .
Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P et al. ( 2013 ) . The Capsaspora genome reveals a complex unicellular prehistory of animals . Nature Communications vol. 4 , ( 1 )
Martín-Durán JM, de Mendoza A, Sebé-Pedrós A ( 2013 ) . A Broad Genomic Survey Reveals Multiple Origins and Frequent Losses in the Evolution of Respiratory Hemerythrins and Hemocyanins . Genome Biology and Evolution vol. 5 , ( 7 ) 1435 - 1442 .
Suga H, Dacre M, de Mendoza A, Shalchian-Tabrizi K ( 2012 ) . Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases . Science Signaling vol. 5 , ( 222 )
de Mendoza A, Ruiz-Trillo I ( 2011 ) . New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference . EvoDevo vol. 2 , ( 1 )
de Mendoza A ( 2011 ) . The Mysterious Evolutionary Origin for the GNE Gene and the Root of Bilateria . Molecular Biology and Evolution vol. 28 , ( 11 ) 2987 - 2991 .
Sebé-Pedrós A, de Mendoza A, Lang BF, Degnan BM ( 2010 ) . Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki . Molecular Biology and Evolution vol. 28 , ( 3 ) 1241 - 1254 .
de Mendoza A, Suga H ( 2010 ) . Evolution of the MAGUK protein gene family in premetazoan lineages . BMC Ecology and Evolution vol. 10 , ( 1 )
Charria PR, Navarrete C, Ovchinnikov V, Sarre LA, Shabardina V, Casacuberta E, Lara-Astiaso D, Sebé-Pedrós A et al. . Adenine DNA methylation associated to transcription is widespread across eukaryotes .
Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ et al. . Annelid methylomes reveal ancestral developmental and ageing-associated epigenetic erosion across Bilateria .
Sarre LA, Peralta GAG, Charria PR, Ovchinnikov V, de Mendoza A . Cytosine Methylation is a marker of Viral Gene Transfer across the eukaryotes .
Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A . DNA methylation enables recurrent endogenization of giant viruses in an animal relative .
Blais C, Colp MJ, Sarre LA, de Mendoza A, Archibald JM . Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba .
Church SH, Abedon RB, Ahuja N, Anthony CJ, Ramirez DA, Rojas LM, Albinsson ME, Trasobares IÁ et al. . Global genomics of the man-o’-war (Physalia) reveals biodiversity at the ocean surface .
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