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Showing 1–16 of 16 results
Advanced filters: Author: Maria Colomé-Tatché Clear advanced filters

  • Several computational tools have now been developed to identify copy number variations (CNVs) from scRNA-seq data. Here authors benchmark these methods, showing that performance is affected by dataset quality, CNV type and reference dataset, with methods including allelic information being more robust in large datasets.

    • Katharina T. Schmid
    • Aikaterini Symeonidi
    • Maria Colomé-Tatché
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-17

  • 'Here the authors present epiAneufinder, an algorithm for the identification of single-cell copy number alterations from scATAC-seq data, and explore the clonal heterogeneity in cell populations.

    • Akshaya Ramakrishnan
    • Aikaterini Symeonidi
    • Maria Colomé-Tatché
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-10

  • The authors review recent studies into the heritable basis of population epigenomic variation and discuss important challenges when interpreting results from these genetic studies in different species to highlight the state of knowledge regarding how genetic variation can influence differences in chromatin states between individuals.

    • Aaron Taudt
    • Maria Colomé-Tatché
    • Frank Johannes
    Reviews
    Nature Reviews Genetics
    Volume: 17, P: 319-332

  • In cancer, the impact on cellular fitness of copy-number gains affecting collaterally-amplified genes remains poorly understood compared to oncogenes. Here, the authors integrate genomic data from tumours and cell lines and identify a class of ‘Amplification-Related Gain Of Sensitivity’ (ARGOS) genes, with potential therapeutic applications.

    • Veronica Rendo
    • Michael Schubert
    • Floris Foijer
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18

  • The authors present epiScanpy: a computational framework for the analysis of single-cell epigenomic data, both ATAC-seq and DNA methylation data, with examples for clustering, cell type identification, trajectory learning and atlas integration - and show its performance in distinguishing cell types.

    • Anna Danese
    • Maria L. Richter
    • Maria Colomé-Tatché
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-8

  • Long-range cis-regulatory elements play important roles in regulating agronomic traits, but they are largely uncharacterized in crops. This study provides genetic, epigenomic and functional molecular evidence to support their widespread existence in the maize genome.

    • William A. Ricci
    • Zefu Lu
    • Xiaoyu Zhang
    Research
    Nature Plants
    Volume: 5, P: 1237-1249

  • The molecular mechanisms underlying direct neuronal reprogramming are unclear. Here the authors show Ngn2-mediated chromatin remodeling and its binding sites underlying mouse astrocyte-to-neuron reprogramming and identify Yy1, a transcription co-factor, as an important regulator.

    • Allwyn Pereira
    • Jeisimhan Diwakar
    • Magdalena Götz
    ResearchOpen Access
    Nature Neuroscience
    Volume: 27, P: 1260-1273

  • During oogenesis, H3K4 trimethylation is targeted to genomic elements through transcription-dependent and transcription-independent mechanisms, the latter relying on MLL2 recruitment to unmethylated CpG-rich regions.

    • Courtney W. Hanna
    • Aaron Taudt
    • Gavin Kelsey
    Research
    Nature Structural & Molecular Biology
    Volume: 25, P: 73-82

  • Histone H3 lysine 14 is propionylated and butyrylated in vivo in a metabolic-state-dependent manner and these modifications promote high levels of transcription.

    • Adam F Kebede
    • Anna Nieborak
    • Robert Schneider
    Research
    Nature Structural & Molecular Biology
    Volume: 24, P: 1048-1056