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    1. Cancer Biology
    2. Computational and Systems Biology

    Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

    Aurélie Anne-Gaëlle Gabriel, Julien Racle ... David Gfeller
    EPIC-ATAC accurately quantifies cell-type heterogeneity in tumor bulk ATAC-Seq samples using reliable cell-type specific chromatin accessibility markers for the major cell types found in tumor microenvironments.
    1. Genetics and Genomics
    2. Neuroscience

    Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity

    Xinrui L Zhang, William C Spencer ... Evan S Deneris
    Terminal selectors reorganize postmitotic neuronal chromatin to select cis-regulatory elements during 5-HT neuron maturation.
    1. Chromosomes and Gene Expression
    2. Immunology and Inflammation

    Maternal obesity blunts antimicrobial responses in fetal monocytes

    Suhas Sureshchandra, Brianna M Doratt ... Ilhem Messaoudi
    Maternal obesity and high-fat diet present metabolic, signaling, and epigenetic impediments to pathogen recognition in fetal innate immune cells that result in a state of immune paralysis during gestation and at birth.
    1. Cancer Biology
    2. Genetics and Genomics

    Convergent epigenetic evolution drives relapse in acute myeloid leukemia

    Kevin Nuno, Armon Azizi ... Ravindra Majeti
    Integrated analyses of acute myeloid leukemia genetics and epigenetics demonstrate that epigenetic evolution occurs in a convergent manner in the absence of DNA mutations at relapse post-chemotherapy.
    1. Immunology and Inflammation

    Mir221/222 drive synovial hyperplasia and arthritis by targeting cell cycle inhibitors and chromatin remodeling components

    Fani Roumelioti, Christos Tzaferis ... George Kollias
    A novel in vivo role for miRNAs Mir221/222 in arthritogenic synovial fibroblasts and progression of arthritis is presented.
    1. Immunology and Inflammation

    T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells

    Josep Garnica, Patricia Sole ... Pere Santamaria
    T-regulatory type 1 cells inherit a broad repertoire of epigenetic marks from T-follicular helper T-cells, offering new insights into the developmental biology of this subset.
    1. Genetics and Genomics

    Science Forum: The single-cell eQTLGen consortium

    MGP van der Wijst, DH de Vries ... L Franke
    The single-cell eQTLGen consortium aims to pinpoint the cellular contexts in which disease-causing genetic variants affect gene expression and its regulation.
    1. Computational and Systems Biology

    Shared enhancer gene regulatory networks between wound and oncogenic programs

    Swann Floc'hlay, Ramya Balaji ... Stein Aerts
    Single-cell multiomics reveals the gene regulatory networks and enhancer logic underlying two distinct wound response cell states in the Drosophila wing imaginal disc and finds similarities with cell states observed in the Ras-scrib tumor model.
    1. Genetics and Genomics
    2. Neuroscience

    Machine learning sequence prioritization for cell type-specific enhancer design

    Alyssa J Lawler, Easwaran Ramamurthy ... Andreas R Pfenning
    A new cross-species machine learning-based strategy is applied to find enhancers that specifically label parvalbumin neurons in the mouse and macaque.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells

    Jakke Neiro, Divya Sridhar ... Aziz Aboobaker
    Predicted gene regulatory networks active in planarians adult stem cells provide testable hypotheses about the control of pluripotency and differentiation in animals.