Reader in Bioinformatics
Epigenomics, Macroevolution, Protists, DNA methylation, Transposable Elements, Phylogeny
Publications of specific relevance to the Centre for Evolutionary and Functional GenomicsAdenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes.Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellatesNon-CG DNA methylation in animal genomesThe genomic origin of the unique chaetognath body planRepressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent EukaryotesEpigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in AcanthamoebaPopulation genomics of a sailing siphonophore reveals genetic structure in the open oceanGenome synteny reveals hidden enhancer conservationChromatin loops are an ancestral hallmark of the animal regulatory genomeReconstructing the last common ancestor of all eukaryotes.The emergence of Sox and POU transcription factors predates the origins of animal stem cellsAnnelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across BilateriaDNA methylation enables recurrent endogenization of giant viruses in an animal relativeSpecific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposonsHagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequencesTransient naive reprogramming corrects hiPS cells functionally and epigeneticallyA mammalian DNA methylation landscape
DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylationLarge-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stabilityThe emergence of the brain non-CpG methylation system in vertebratesDevelopmental remodelling of non-CG methylation at satellite DNA repeatsTowards understanding the origin of animal developmentEnteric neurons increase maternal food intake during reproductionTracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleriGenomic adaptations to aquatic and aerial life in mayflies and the origin of insect wingsPervasive non-CpG methylation at zebrafish mosaic satellite repeatsEvolution of DNA Methylome Diversity in EukaryotesOrigin and evolution of eukaryotic transcription factorsConvergent evolution of a vertebrate-like methylome in a marine spongeCapture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon familyThe Protistan Cellular and Genomic Roots of Animal MulticellularityRecurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposonsTransient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive ReprogrammingFrequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulationMethuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene familySterol and genomic analyses validate the sponge biomarker hypothesisPhylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and FungiComplex transcriptional regulation and independent evolution of fungal-like traits in a relative of animalsTranscription Factors and the Origin of Animal MulticellularityThe Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan MulticellularityForward genetics for back-in-time questionsNovel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell divisionTranscription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineagesA Broad Genomic Survey Reveals Multiple Origins and Frequent Losses in the Evolution of Respiratory Hemerythrins and HemocyaninsThe Capsaspora genome reveals a complex unicellular prehistory of animalsGenomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine KinasesThe Mysterious Evolutionary Origin for the GNE Gene and the Root of BilateriaNew genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conferenceUnexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzakiEvolution of the MAGUK protein gene family in premetazoan lineagesAdenine DNA methylation associated to transcription is widespread across eukaryotesEpigenetic silencing and host genome evolution determine fate of viral insertions in AcanthamoebaCytosine Methylation is a marker of Viral Gene Transfer across the eukaryotesAnnelid methylomes reveal ancestral developmental and ageing-associated epigenetic erosion across BilateriaDNA methylation enables recurrent endogenization of giant viruses in an animal relativeGlobal genomics of the man-o’-war (Physalia) reveals biodiversity at the ocean surfaceGrants of specific relevance to the Centre for Evolutionary and Functional GenomicsSMALLGIANT MSCA PF 2024 De Mendoza Soler / OlivieraExploring the cooperativity of the POU-SOX stemness regulators during early animal evolutionDeciphering the evolution of cytosine DNA methylation across eukaryotes through experimental and epi - ERC StG 2020 Alex de MendozaAssessing the potential of DNA methylation for intergenerational inheritance in a sea anemone - Alex de MendozaA confocal microscope for multidisciplinary dynamic studies of complex biological systemsDr de Mendoza, Reader in Bioinformatics, has been granted a Wellcome Trust Discovery Award to investigate the role of 6mA DNA methylation in eukaryotes and its potential biotechnological implications. Combining mammalian with unicellular eukaryotes, the project promises to transform our views on the evolution of genome regulation. Congrats, Alex!
An international group of researchers lead by Dr Piovani and Dr Marlétaz at UCL, in collaboration with Dr de Mendoza and Dr Martin-Duran from QMUL, has generated the first chromosome-level genome assembly for a chaetognath (arrow worm), an enigmatic animal group. Combining multiple functional genomic approaches, the researchers identified ... [more]
