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    Frataxin Deficiency Drives a Shift from Mitochondrial Metabolism to Glucose Catabolism, Triggering an Inflammatory Phenotype in Microglia
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    1. EMBOpress 08 May 2024

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    biorxiv.org/content/10.1101/2023.10.18.562916v1
  3. Apr 2024
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    Integrative DNA methylation analysis of pediatric brain tumors reveals tumor type-specific developmental trajectories and epigenetic signatures of malignancy
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    biorxiv.org/content/10.1101/2022.03.14.483566v2
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    pADP-ribosylation Regulates the Cytoplasmic Localization, Cleavage and Pro-apoptotic Function of HuR
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    biorxiv.org/content/10.1101/2023.08.07.552262v1
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    Condensate functionalization with motors directs their nucleation in space and allows manipulating RNA localization
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    biorxiv.org/content/10.1101/2022.07.10.499452v1
  7. Mar 2024
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    The P4-ATPase Drs2 regulates the homeostasis of Atg9
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    biorxiv.org/content/10.1101/2020.12.25.417865v3
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    A YTHDF-PABP axis is required for m6A-mediated organogenesis in plants
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    biorxiv.org/content/10.1101/2023.07.03.547513v2
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    Plant YTHDF proteins are direct effectors of antiviral immunity against an m6A-containing RNA virus
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    biorxiv.org/content/10.1101/2022.10.19.512835v1
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    Circadian Transcriptomic and Epigenomic Remodeling in Response to Lipid Overload and Human Obesity
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    biorxiv.org/content/10.1101/2021.02.23.432336v4
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    Regulation of branched versus linear Arp2/3-generated actin filaments
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    biorxiv.org/content/10.1101/2022.05.06.490861v1
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    Extracellular vesicles and co-isolated endogenous retroviruses differently affect dendritic cells
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    biorxiv.org/content/10.1101/2023.01.27.525863v1
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    Variable PD-1 glycosylation modulates the activity of immune checkpoint inhibitors
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    biorxiv.org/content/10.1101/2023.08.25.554811v1
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    Structural and biochemical insights into heterotetramer formation between human oncogenic K-Ras4BG12V and Rgl2, a RalA/B activator
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    biorxiv.org/content/10.1101/2022.10.10.511529v8
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    The memory of airway epithelium damage in smokers and COPD patients
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    biorxiv.org/content/10.1101/2021.04.21.439437v3
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    Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography
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    1. EMBOpress 05 Mar 2024

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    biorxiv.org/content/10.1101/2023.10.05.560879v1
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    Micronucleus Is Not a Potent Inducer of cGAS-STING Pathway
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    1. EMBOpress 05 Mar 2024

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    biorxiv.org/content/10.1101/2023.10.16.561322v1
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    CLN3 deficiency leads to neurological and metabolic perturbations during early development
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    biorxiv.org/content/10.1101/2023.03.17.533107v1
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    A nuclear signal in prophase determines centrosome positioning and ensures efficient mitotic spindle assembly
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    1. EMBOpress 01 Mar 2024

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    biorxiv.org/content/10.1101/2023.06.14.544905v2
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    The origin, evolution and molecular diversity of the chemokine system
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    1. EMBOpress 01 Mar 2024

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    biorxiv.org/content/10.1101/2023.05.17.541135v2
  22. Feb 2024
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    Cryo-EM structure of lipid embedded human ABCA7 at 3.6 &Aring resolution
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    1. EMBOpress 27 Feb 2024

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    biorxiv.org/content/10.1101/2021.03.01.433448v2
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    Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans
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    biorxiv.org/content/10.1101/2023.04.14.536891v2
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    Histology-associated transcriptomic heterogeneity in ovarian folliculogenesis revealed by quantitative single-cell RNA-sequencing for tissue sections with DRaqL
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    1. EMBOpress 21 Feb 2024

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    biorxiv.org/content/10.1101/2022.12.14.520513v1
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    Pioneer activity distinguishes activating from non-activating pluripotency transcription factor binding sites
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    1. EMBOpress 07 Feb 2024

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    biorxiv.org/content/10.1101/2022.07.27.501606v1
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    CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including the PTEN gene locus mimicking cancer profiles
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    1. EMBOpress 03 Feb 2024

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    biorxiv.org/content/10.1101/2023.04.05.535680v1
  28. Jan 2024
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    Convergent Insulin and TGF-β signalling drives cancer cachexia by promoting aberrant fatbody ECM accumulation in a Drosophila tumour model
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    1. EMBOpress 31 Jan 2024

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    biorxiv.org/content/10.1101/2023.06.10.544444v1
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    Proteomic-based stratification of intermediate-risk prostate cancer patients
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    1. EMBOpress 26 Jan 2024

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    biorxiv.org/content/10.1101/2023.03.03.530910v1
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    Human RAD52 stimulates the RAD51-mediated homology search
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    biorxiv.org/content/10.1101/2022.06.27.497340v1
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    The structural basis for deubiquitination by the fingerless USP-type effector TssM
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    1. EMBOpress 25 Jan 2024

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    biorxiv.org/content/10.1101/2023.08.01.551441v1
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    Changes in searching behaviour of CSL transcription complexes in Notch active conditions
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    biorxiv.org/content/10.1101/2023.08.10.552734v2
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    Human liver organoids model progressive inflammatory and fibrotic injury in non-alcoholic fatty liver disease
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    biorxiv.org/content/10.1101/2022.07.19.500693v2
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    Arp2/3 inhibition switches Eps8’s network associations to favour longer actin filament formation necessary for tunneling nanotubes
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    biorxiv.org/content/10.1101/2022.08.24.504515v2
  36. Dec 2023
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    Monomeric α-Synuclein activates the Plasma Membrane Calcium Pump
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    biorxiv.org/content/10.1101/2022.02.21.481193v2
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    RIF1 ensures the organization of replication factories upon DNA replicative stress.
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    1. EMBOpress 16 Dec 2023

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    biorxiv.org/content/10.1101/669234v3
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    TUMOR ENDOTHELIAL CELL AUTOPHAGY IS A KEY VASCULAR-IMMUNE CHECKPOINT IN MELANOMA
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    1. EMBOpress 16 Dec 2023

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    biorxiv.org/content/10.1101/2023.04.21.537799v2
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    Decline of DNA damage response along with myogenic differentiation
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    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2023.06.27.546688v1
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    Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells
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    biorxiv.org/content/10.1101/2023.10.17.562690v1
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    Structural analysis shows that the BIR2 domain of E3 ligase XIAP binds across the RIP2 kinase dimer interface
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    biorxiv.org/content/10.1101/2022.10.14.512215v1
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    The 5:2 diet does not increase adult hippocampal neurogenesis or enhance spatial memory in mice
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    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2022.10.03.510613v1
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    Adult neural stem cells and neurogenesis are resilient to intermittent fasting
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    biorxiv.org/content/10.1101/2022.07.08.499318v2
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    Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration
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    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2023.05.19.540965v1
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    The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition
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    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2022.12.09.519716v1
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    Molecular view of ER membrane remodeling by the Sec61/TRAP translocon
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    biorxiv.org/content/10.1101/2022.09.30.510141v1
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    Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex
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    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2023.06.06.543957v1
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    Mitochondrial phosphoproteomes are functionally specialized across tissues
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    biorxiv.org/content/10.1101/2022.03.23.485457v1
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    Protein phosphatase 1 regulates core PCP signaling
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    biorxiv.org/content/10.1101/2023.09.12.556998v1
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    Blood flow diverts extracellular vesicles from endothelial degradative compartments to promote angiogenesis
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    biorxiv.org/content/10.1101/2022.12.19.521008v1
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    Circadian oscillation in primary cilium length by clock genes regulate fibroblast cell migration
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    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2023.01.24.525311v2
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    Propylene glycol inactivates respiratory viruses and prevents airborne transmission
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    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2023.02.13.528349v1
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    The nucleolar protein GNL3 prevents resection of stalled replication forks.
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    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2022.10.27.514025v2
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    The Response of the Eukaryotic Replisome to G-quadruplex- and i-motif-forming Sequences
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    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2022.11.18.517070v2
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    Thiol reductive stress activates the hypoxia response pathway
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    Paralog dispensability shapes homozygous deletion patterns in tumor genomes
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    Enucleation of the C. elegans embryo revealed the mechanism of dynein-dependent spacing between microtubule asters
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    Epithelial lumen development requires differential participation of the vertebrate clathrin light chain isoforms with dominance of CLCa in vivo
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    Identification of FAM53C as a suppressive binding protein of a neurodevelopmental disorders-related kinase DYRK1A
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    Modeling of Aberrant Epithelial Reprogramming in Idiopathic Pulmonary Fibrosis using Human Induced Pluripotent Stem Cell-derived Alveolar Organoids
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    Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
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    Downregulation of stromal syntenin sustains AML development
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    Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis
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    Monomeric agonist peptide/MHCII complexes activate T-cells in an autonomous fashion
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    DONSON is required for CMG helicase assembly in the mammalian cell cycle
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    Automated staging of zebrafish embryos with deep learning
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    NRF2 connects Src tyrosine kinase to ferroptosis resistance in glioblastoma
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    MICA: A multi-omics method to predict gene regulatory networks in early human embryos
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    Tetraspanner-based nanodomains modulate BAR domain-induced membrane curvature
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    YAP antagonizes TEAD-mediated AR signaling and prostate cancer growth
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    Expansion microscopy reveals subdomains in C. elegans germ granules
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    A bifunctional kinase-phosphatase module integrates mitotic checkpoint and error-correction signalling to ensure mitotic fidelity
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    SARS-CoV-2 ORF3c suppresses immune activation by inhibiting innate sensing
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    Vimentin intermediate filaments organize organellar architecture in response to ER stress
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    Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2
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    A region-resolved proteomic map of the human brain enabled by high-throughput proteomics
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    Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
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    Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence
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    A network of small RNAs regulates sporulation initiation in C. difficile
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    http://biorxiv.org/cgi/content/short/2021.01.06.425396
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    Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells
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    Revisiting degron motifs in human AURKA required for its targeting by APC/C-FZR1
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    High Resolution Kinetic Characterization and Dynamic Mathematical Modeling of the RIG-I Signaling Pathway and the Antiviral Responses
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    EMBRYO-UTERINE INTERACTION COORDINATES MOUSE EMBRYOGENESIS DURING IMPLANTATION
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    M-CSF induces a coordinated myeloid and NK cell differentiation program protecting against CMV after hematopoietic cell transplantation
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    Caspase-4 dimerisation and D289 auto-processing elicits an interleukin-1β converting enzyme
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    Neuroprotective effects of hepatoma-derived growth factor in models of Huntington's disease
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    Structural evidence for elastic tethers connecting separating chromosomes in crane-fly spermatocytes
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    A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance
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    Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism
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    Mechanisms and physiological function of daily haemoglobin oxidation rhythms in red blood cells
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    PTEN deficiency exposes a requirement for an ARF GTPase module in integrin-dependent invasion in ovarian cancer.
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    Interferon inhibits a model RNA virus via a limited set of inducible effector genes
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    Branched chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast
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    Predictability of the community-function landscape in wine yeast ecosystems
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    A Sterol-PI(4)P exchanger controls the Tel1/ATM axis of the DNA Damage Response
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    Identification of a novel enhancer essential for Satb1 expression in TH2 cells and activated ILC2s.
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    MAP4K3 inhibits Sirtuin-1 to repress LKB1-AMPK to promote amino acid dependent activation of mTORC1
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    Origin and segregation of the human germline
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    Apolipoprotein E intersects with amyloid-β within neurons
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    Distant sequence regions of JBP1 contribute to J-DNA binding
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    IKBKB reduces huntingtin aggregation by phosphorylating Serine 13 via a non-canonical IKK pathway
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    Germinal Centers Convergent Evolution and B cell Recirculation in Human Lymph Nodes
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    Phosphorylation controls spatial and temporal activities of motor-PRC1 complexes to complete mitosis
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    Myddosome clustering in IL-1 receptor signaling regulates the formation of an NF-kB activating signalosome
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    Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
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    A metabolic map of the DNA damage response identifies PRDX1 in nuclear ROS scavenging and aspartate synthesis
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    Targeting CD301+ macrophage inhibits endometrial fibrosis and improves pregnancy outcome
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    Senescent cell death as an aging resistance mechanism in naked mole-rat
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    Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance
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    Synaptotagmin 1 mediates toxicity of botulinum neurotoxin type A
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    The C-terminal tail of CSNAP attenuates the CSN complex
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    Direct observation of coordinated assembly of individual native centromeric nucleosomes
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    Consistency across multi-omics layers in a drug-perturbed gut microbial community
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    ATR inhibition augments the efficacy of lurbinectedin in small cell lung cancer
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    Terminal differentiation of enterocytes is governed by distinct members of Tgfβ superfamily
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    Evolutionary transcriptomics reveals longevity mostly driven by polygenic and indirect selection in mammals
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  130. Jul 2023
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    Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
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    Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20
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    Characterization of the REC114-MEI4-IHO1 complex regulating meiotic DNA double-strand break formation
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    Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression
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    Extracellular matrix sensing via modulation of orientational order of integrins and F-actin in focal adhesions
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    DOT1L bridges transcription and heterochromatin formation at pericentromeres
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    Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase
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    PARK15/FBXO7 is dispensable for PINK1/Parkin-dependent mitophagy in iNeuron and HeLa cell systems
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    MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization
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    Differential roles of CTP synthetases CTPS1 and CTPS2 in cell proliferation
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    The cytochrome b carboxyl-terminal region is necessary for mitochondrial Complex III assembly
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    arfA antisense RNA regulates MscL excretory activity
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    Antibody reliability influences observed mRNA-protein correlations in tumour samples
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    N-terminal proteoforms may engage in different protein complexes
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    PI3P dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase
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    Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes.
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    Centrosome amplification fine-tunes tubulin acetylation to differentially control intracellular organization
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    ENGRAILED-1 transcription factor exerts a paracrine neurotrophic activity on adult spinal cord &#x03B1;-motoneurons.
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    A tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases
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    Accurate genotype-based demultiplexing of single cell RNA sequencing samples from non-human animals
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    HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
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    Structural basis of ubiquitin-independent PP1 complex disassembly by p97
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    Maternal diet and gut microbiome composition modulate early life immune responses
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    Structure-based design and characterization of Parkin activating mutations
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    Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins
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    Upf3a is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells
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    Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases
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    The pro-inflammatory response to influenza A virus infection is fueled by endothelial cells
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    Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
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    biorxiv.org/content/10.1101/2022.12.11.519953v2
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    Multivalent BARD1-nucleosome interactions facilitate H2A ubiquitylation by BRCA1/BARD1
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  163. www.biorxiv.org www.biorxiv.org
    PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid
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    biorxiv.org/content/10.1101/2022.02.23.481593v2
  164. www.biorxiv.org www.biorxiv.org
    Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response
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    biorxiv.org/content/10.1101/2022.12.21.521356v1
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    Updated benchmarking of variant effect predictors using deep mutational scanning
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    Tmem117 in AVP neurons regulates the counterregulatory response to hypoglycemia
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    Pseudomonas aeruginosa mechanosensing controls cell polarity during twitching by activating two antagonistic response regulators
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    Two distinct mechanisms underlie dosage sensitivity in Pumilio1-associated diseases
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    Stable kinetochore-microtubule attachment requires loop-dependent Ndc80-Ndc80 binding
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    Deterministic and probabilistic fate decisions co-exist in a single retinal lineage
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    Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns
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    A case of mistaken identity: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli
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    Highly multiplexed quantitative phosphosite assay for biology and preclinical studies
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    The histone methyltransferase DOT1L regulates chromatin reorganization and gene expression during the postmeiotic differentiation of male germ cells
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    Age-dependent lipid droplet-rich microglia worsen stroke outcome in old mice
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    Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
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  177. May 2023
  178. www.biorxiv.org www.biorxiv.org
    BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer
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    Recursive splicing discovery using lariats in total RNA sequencing
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    Exploratory Meta-Analysis of Hypoxic Transcriptomes Using a Precise Transcript Reference Sequence Set
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    VEGFR3 modulates brain microvessel branching in a mouse model of 22q11.2 deletion syndrome
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    Telescoping bimodal latent Dirichlet allocation to identify expression QTLs across tissues
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    RAS and PP2A activities converge on epigenetic gene regulation
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    Functional substitutions of amino acids that differ between GDF11 and GDF8 impact skeletal development and skeletal muscle.
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    Gapless provides combined scaffolding, gap filling and assembly correction with long reads
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    A quantitative fluorescence-based approach to study mitochondrial protein import
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    Ubiquitination occurs in the mitochondrial matrix by eclipsed components of the ubiquitin machinery
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    The transcriptional regulator Sin3A balances IL-17A and Foxp3 expression in primary CD4 T cells
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    Inhibition of the ATM kinase rescues planarian regeneration after lethal radiation
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    Ubx5-Cdc48 assists the protease Wss1 at DNA-protein crosslink sites in yeast
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    Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain
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    Nirmatrelvir treatment blunts the development of antiviral adaptive immune responses in SARS-CoV-2 infected mice
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    Endothelial FOXC1 and FOXC2 promote intestinal regeneration after ischemia-reperfusion injury
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    eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content
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    Z-Flipon Variants reveal the many roles of Z-DNA and Z-RNA in health and disease
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    A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes
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    Automated assembly of molecular mechanisms at scale from text mining and curated databases
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    Subcutaneous BCG vaccination protects against streptococcal pneumonia via regulating innate immune responses in the lung
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    Transcription factor expression is the main determinant of variability in gene co-activity
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    FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors
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    Mapping single-cell responses to population-level dynamics during antibiotic treatment
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    ROR1 plays a critical role in pancreatic tumor-initiating cells with a partial EMT signature.
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    The piRNA pathway sustains adult neurogenesis by repressing protein synthesis
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    DASH/Dam1 complex mutants stabilize ploidy by weakening kinetochore-microtubule attachments
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    The value of genotype-specific reference for transcriptome analyses
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    Genome-wide CRISPRi screening reveals regulators of Alzheimee's tau pathology shared between exosomal and vesicle-free tau seeds.
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    Small non-coding vault RNA1-2 modulate expression of cell membrane proteins through nascent RNA silencing
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    LuminoCell: a versatile and affordable luminometer platform for monitoring in-cell luciferase-based reporters
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    Caspase-dependent activation of Hedgehog-signalling sustains proliferation and differentiation of ovarian somatic stem cells.
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  210. Apr 2023
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    TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana
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    β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
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      PeerReviewed EMBOPress EMBO Molecular Medicine cancer biology
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    biorxiv.org/content/10.1101/2022.07.07.499249v1
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    UBAP2L-dependent coupling of PLK1 localization and stability during mitosis
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      PeerReviewed EMBOPress EMBO reports cell biology
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    biorxiv.org/content/10.1101/2022.10.24.513562v2
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    An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene
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      PeerReviewed EMBOPress The EMBO Journal cancer biology
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    biorxiv.org/content/10.1101/2021.12.16.472890v3