Journal publications
Most articles should have open access links associated to them, otherwise many of the PDFs can be found on my Google Scholar, if none of that works, feel free to contact me.
2024
DNA methylation enables recurrent endogenization of giant viruses in an animal relative.
Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. BioRxiv. [pdf] [website]
Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.
Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D’Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Nature Ecology & Evolution. [pdf] [website]
2023
Annelid methylomes reveal ancestral developmental and ageing-associated epigenetic erosion across Bilateria.
Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martin-Zamora FM, Hurd PJ, de Mendoza A, Martin-Duran JM. BioRxiv. [pdf] [website]
Transient naive reprogramming corrects hiPS cells functionally and epigenetically.
Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Nature. [pdf] [website]
A mammalian DNA methylation landscape.
de Mendoza A. Science. 381 (6658):602-603 [pdf] [website]
-
A perspective on the Science paper "DNA methylation networks underlying mammalian traits"
2022
Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Genome Biology. 23:163. [pdf] [website] [dataset]
DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation.
Dukatz M, Dittrich M, Stahl E, Adam S, de Mendoza A, Bashtrykov P, Jeltsch A. Journal of Biological Chemistry. 298(10):102462 [pdf] [website]
2021
The emergence of the brain non-CpG methylation system in vertebrates.
de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gomez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R. Nature Ecology and Evolution. 5:369–378. [pdf] [website] [dataset]
-
Selected by the “Faculty of 1000 ” (score 2).
2020
Towards understanding the origin of animal development.
Ruiz-Trillo I, de Mendoza A. Development. 147: dev192575 [website]
Developmental remodelling of non-CG methylation at satellite DNA repeats.
Ross SE, Angeloni A, Geng FS, de Mendoza A, Bogdanovic O. Nucleic Acids Research. gkaa1135 [website]
Enteric neurons increase maternal food intake during reproduction.
Hadjieconomou D, King G, Gaspar P, Mineo A, Blackie L, Ameku T, Studd C, de Mendoza A, Diao F, White BH, Brown AEX, Plaçais PY, Préat T, Miguel-Aliaga I. Nature. 587(7834):455-459. [website]
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri.
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderon L, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys S. Nature Communications. 11(1):3676. [website] [dataset]
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings.
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marletaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F. Nature Communications. 11(1):2631. [website]
-
Recommended twice by the “Faculty of 1000 ”.
Evolution of DNA methylome diversity in eukaryotes.
de Mendoza A, Lister R, Bogdanovic O. Journal of Molecular Biology. pii: S0022-2836(19)30659-X. [website]
2019
Convergent evolution of a vertebrate-like methylome in a marine sponge.
de Mendoza A, Hatleberg W, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM, Lister R. Nature Ecology and Evolution. 3(10):1464-1473. [pdf] [website] [dataset]
Capture of a functionally active Methyl-CpG Binding Domain by an arthropod retrotransposon family.
de Mendoza A, Pflueger J, Lister R. Genome Research. 29(8):1277-1286. [pdf] [website] [dataset]
Origin and evolution of eukaryotic transcription factors.
de Mendoza A, Sebé-Pedrós A. Current Opinion in Genetics & Development. 26;58-59:25-32. [website]
2018 to 2010
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R. Nature Communications. 9(1):1341. 2018. [website] [dataset]
Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming.
Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R, Polo JM. Cell Stem Cell 21:834-845. 2017. [website] [dataset]
-
Highlighted in a Cell Stem Cell “Preview”.
Sterol and Genomic Analyses Validate the Sponge Biomarker Hypothesis.
Gold DA, Grabenstatter J, de Mendoza A, Riesgo A, Ruiz-Trillo I, Summons RE. Proceedings of the National Academy of Sciences USA (PNAS). 13(10):2684-9. 2016. [website]
Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family.
de Mendoza A, Jones JW, Friedrich M. Scientific Reports. 6:21801. 2016. [website]
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.
de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I. eLife. e08904. 2015. [website] [dataset]
-
Appeared in Nature “Research Highlights”.
Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.
Torruella G*, de Mendoza A*, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I. Current Biology. 25:2404-2410. 2015. [website]
Forward genetics for back-in-time questions.
de Mendoza A, Ruiz Trillo I. eLife. 3: e05218. 2014. [website]
The evolution of the GPCR signalling system in eukaryotes: modularity, conservation and the transition to metazoan multicellularity.
de Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I. Genome Biology and Evolution 6:606-619. 2014. [website]
Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division.
Desvoyes B, de Mendoza A, Ruiz-Trillo I, Gutierrez C. Journal of experimental botany. 65:2657-66. 2014. [website]
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages.
de Mendoza A*, Sebé-Pedrós A*, Sêstak SM, Matejcîc M, Torruella G, Domazet-Lôso T, Ruiz-Trillo I. Proceedings of the National Academy of Sciences USA (PNAS). 110:E4858-66. 2013. [website]
-
Selected by the “Faculty of 1000 ” (score 3).
The Capsaspora genome reveals a complex unicellular prehistory of animals.
Suga H*, Chen Z*, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang FB, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I. Nature Communications. 4:1–9. 2013. [website]
-
Selected by the “Faculty of 1000 ” (score 2).
A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins.
Martín-Durán JM*, de Mendoza A*, Sebé-Pedrós A*, Ruiz-Trillo I, Hejnol A. Genome Biology and Evolution. 5:1435–1442. 2013. [website]
Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases.
Suga H, Dacre M, de Mendoza A, Shalchian-Tabrizi K, Manning G, Ruiz-Trillo I. Science Signaling 5:ra35–ra35. 2012. [website]
The mysterious Evolutionary Origin for the GNE gene and the root of Bilateria.
de Mendoza A, Ruiz-Trillo I. Molecular Biology and Evolution. 28:2987–2991. 2011. [website]
New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference.
de Mendoza A, Ruiz-Trillo I. EvoDevo. 23;2:22. 2011. [website]
Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki.
Sebé-Pedrós A*, de Mendoza A*, Lang BF, Degnan BM, Ruiz-Trillo I. Molecular Biology and Evolution. 28:1241–1254. 2011. [website]
Evolution of the MAGUK protein gene family in premetazoan lineages.
de Mendoza A, Suga H, Ruiz-Trillo I. BMC Evolutionary Biology. 10:93. 2010. [website]
Book Chapters
Transposable Elements: Methods and Protocols
Branco MR, de Mendoza A. Methods in Molecular Biology Series. Humana Press / Springer Nature, ISSN 1064-3745. 2022.
The protistan cellular and genomic roots of animal multicellularity.
de Mendoza A, Sebé-Pedrós A. Book: Old Questions and Young Approaches to Animal Evolution. Springer, ISBN 978-3-030-18202-1. 2019.
Transcription Factors and the Origin of Animal Multicellularity.
Sebé-Pedrós A, de Mendoza A#. Book: Evolutionary Transitions to Multicellular Life, pages 379-394. Springer, ISBN 978-94-017-9641-5. 2015.