345 Matching Annotations
  1. May 2025
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    Lipid-driven SRC self-association modulates its transformation capacity
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    biorxiv.org/content/10.1101/2024.11.12.623151v1
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    STAT1 is required to establish but not maintain IFNγ-induced transcriptional memory
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    biorxiv.org/content/10.1101/2022.09.17.508285v1
  4. Dec 2024
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    N-6-methyladenosine (m6A) Promotes the Nuclear Retention of mRNAs with Intact 5' Splice Site Motifs
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    biorxiv.org/content/10.1101/2023.06.20.545713v4
  6. Oct 2024
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    FAM111A regulates replication origin activation and cell fitness
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    biorxiv.org/content/10.1101/2020.04.22.055574v1
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    Differential Modulation of Polycomb-Associated Histone Marks by cBAF, pBAF, and gBAF Complexes
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    biorxiv.org/content/10.1101/2023.09.23.557848v2
  9. May 2024
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    K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific interactors.
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    biorxiv.org/content/10.1101/2024.01.08.574586v1
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    IGHMBP2 deletion suppresses translation and activates the integrated stress response
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    biorxiv.org/content/10.1101/2023.12.11.571166v2
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    http://biorxiv.org/cgi/content/short/2020.10.26.356014
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    biorxiv.org/content/10.1101/2020.10.26.356014v3
  13. docdrop.org docdrop.org
    Video: Biology beyond the genome | Denis Noble (DocDrop)
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    1. stopresetgo 18 May 2024
      four 00:08:25 major common misunderstandings that have infected our understanding of what it is to be a living system

      for - molecular biology - paradigm shift - living system - 4 common misunderstandings - book - Understanding Living Systems - 4 common misunderstandings

      4 common misunderstandings of living systems - 1. The central dogma of molecular biology - one way causation - Genes (DNA) to - proteins to - organism - 2. The Weismann Barrier - 3. DNA as self-replicator - 4. Separation of Replicator (DNA) and Vehicle (Living cell) are completely separate

      molecular biology - paradigm shift - Denis Noble living system - 4 common misunderstandings book - Understanding Living Systems - 4 common misunderstandings
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    docdrop.org/video/bzXFSufDDn8/
  14. Mar 2024
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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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    CLN3 deficiency leads to neurological and metabolic perturbations during early development
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    biorxiv.org/content/10.1101/2023.03.17.533107v1
  17. Feb 2024
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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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    Pioneer activity distinguishes activating from non-activating pluripotency transcription factor binding sites
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    biorxiv.org/content/10.1101/2022.07.27.501606v1
  20. Jan 2024
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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
  22. Dec 2023
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    TUMOR ENDOTHELIAL CELL AUTOPHAGY IS A KEY VASCULAR-IMMUNE CHECKPOINT IN MELANOMA
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    biorxiv.org/content/10.1101/2023.04.21.537799v2
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    The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition
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    biorxiv.org/content/10.1101/2022.12.09.519716v1
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    The nucleolar protein GNL3 prevents resection of stalled replication forks.
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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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    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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    biorxiv.org/content/10.1101/2023.03.06.531274v2
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    Paralog dispensability shapes homozygous deletion patterns in tumor genomes
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    biorxiv.org/content/10.1101/2022.06.20.496722v3
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    Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
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    biorxiv.org/content/10.1101/2022.02.16.480673v2
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    Downregulation of stromal syntenin sustains AML development
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    biorxiv.org/content/10.1101/2023.02.15.527799v1
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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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    biorxiv.org/content/10.1101/2022.10.03.510635v2
  32. Nov 2023
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    Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
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    biorxiv.org/content/10.1101/2023.02.22.529573v2
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    A network of small RNAs regulates sporulation initiation in C. difficile
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    biorxiv.org/content/10.1101/2022.10.17.512509v1
  35. Sep 2023
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    Predictability of the community-function landscape in wine yeast ecosystems
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    biorxiv.org/content/10.1101/2022.12.15.520418v1
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    Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors
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    biorxiv.org/content/10.1101/2022.12.27.521482v1
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    Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
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    biorxiv.org/content/10.1101/2022.12.02.518917v1
  39. Aug 2023
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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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    biorxiv.org/content/10.1101/2022.08.01.500855v1
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    PRMT5 links lipid metabolism to contractile function of skeletal muscles
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    biorxiv.org/content/10.1101/2022.11.04.515165v1
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    Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance
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    biorxiv.org/content/10.1101/2021.05.20.444985v1
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    Consistency across multi-omics layers in a drug-perturbed gut microbial community
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    biorxiv.org/content/10.1101/2023.01.03.519475v1
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    ATR inhibition augments the efficacy of lurbinectedin in small cell lung cancer
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    biorxiv.org/content/10.1101/2022.12.16.520783v1
  45. Jul 2023
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    DOT1L bridges transcription and heterochromatin formation at pericentromeres
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    biorxiv.org/content/10.1101/2021.10.21.465349v1
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    arfA antisense RNA regulates MscL excretory activity
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    biorxiv.org/content/10.1101/2022.11.21.517365v1
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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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    biorxiv.org/content/10.1101/2021.02.16.430825v1
  49. Jun 2023
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    HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
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    biorxiv.org/content/10.1101/2022.10.27.514062v1
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    Updated benchmarking of variant effect predictors using deep mutational scanning
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    biorxiv.org/content/10.1101/2022.11.19.517196v1
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    Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns
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    biorxiv.org/content/10.1101/2022.09.30.509643v2
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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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    biorxiv.org/content/10.1101/738823v4
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    Highly multiplexed quantitative phosphosite assay for biology and preclinical studies
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    biorxiv.org/content/10.1101/2020.12.08.415281v1
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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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    biorxiv.org/content/10.1101/2022.10.17.512530v2
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    Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
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    biorxiv.org/content/10.1101/2022.11.08.515576v1
  57. May 2023
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    BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer
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    biorxiv.org/content/10.1101/2021.07.15.452487v2
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    Ubx5-Cdc48 assists the protease Wss1 at DNA-protein crosslink sites in yeast
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    biorxiv.org/content/10.1101/2022.05.30.493988v1
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    Endothelial FOXC1 and FOXC2 promote intestinal regeneration after ischemia-reperfusion injury
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    biorxiv.org/content/10.1101/2022.03.03.482713v2
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    A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes
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    biorxiv.org/lookup/doi/10.1101/2022.08.11.503561
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    Automated assembly of molecular mechanisms at scale from text mining and curated databases
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    Transcription factor expression is the main determinant of variability in gene co-activity
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    Mapping single-cell responses to population-level dynamics during antibiotic treatment
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    Small non-coding vault RNA1-2 modulate expression of cell membrane proteins through nascent RNA silencing
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    biorxiv.org/content/10.1101/2022.08.12.503724v2
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    LuminoCell: a versatile and affordable luminometer platform for monitoring in-cell luciferase-based reporters
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    biorxiv.org/content/10.1101/2022.01.28.478134v1
  67. Apr 2023
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    β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
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    biorxiv.org/content/10.1101/2022.07.07.499249v1
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    Combined measurements of proteome and cell turnover reveal the influences of tissue context and pathological aging on protein and organelle lifetimes
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    biorxiv.org/content/10.1101/2022.04.24.488979v3
  70. Mar 2023
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    The ADAM17 sheddase complex regulator iTAP/Frmd8 modulates inflammation, epithelial repair, and tumor growth
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    biorxiv.org/content/10.1101/2022.04.11.487842v1
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    Uncoupling from transcription protects polyadenylation site cleavage from inhibition by DNA damage
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    biorxiv.org/content/10.1101/2022.05.26.492040v2
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    Blockade of pro-fibrotic response mediated by the miR-143/-145 cluster prevents targeted therapy-induced phenotypic plasticity and delays resistance in melanoma
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    biorxiv.org/content/10.1101/2021.07.02.450838v1
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    A spatial model of the plant circadian clock reveals design principles for coordinated timing under noisy environments
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    biorxiv.org/content/10.1101/2020.09.13.294785v2
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    Protein Complexes in Bacillus subtilis by AI-assisted structural proteomics
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    biorxiv.org/content/10.1101/2022.07.26.501605v3
  76. Feb 2023
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    TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes
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    biorxiv.org/content/10.1101/2022.08.08.503151v2
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    Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
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    biorxiv.org/content/10.1101/2022.02.17.480899v1
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    Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis
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    biorxiv.org/content/10.1101/2022.01.04.474903v1
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    Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish
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    biorxiv.org/content/10.1101/2021.05.12.443743v1
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    Epigenetic signals that direct cell type specific interferon beta response in mouse cells
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    biorxiv.org/content/10.1101/2022.02.26.481127v1
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    CDK9 and PP2A regulate the link between RNA polymerase II transcription termination and RNA maturation.
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    biorxiv.org/content/10.1101/2021.06.21.449289v3
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    Evolution of genome fragility enables microbial division of labor
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    biorxiv.org/content/10.1101/2021.06.04.447040v5
  84. Jan 2023
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    A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast
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    biorxiv.org/content/10.1101/2022.04.27.489741v1
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    Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival
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    Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells
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    Adaptation of bacterial proteome reveals a key role of the cell envelope in starvation survival
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    Condensin pinches a short negatively supercoiledDNA loop during each round of ATP usage
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    biorxiv.org/content/10.1101/2022.06.03.494647v1
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    A synergistic activation of RARb and RARg nuclear receptors restores cell-types specialization during stem cells differentiation by hijacking RARa-controlled program
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    biorxiv.org/content/10.1101/2022.05.31.494116v2
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    Sibling rivalry among the ZBTB transcription factor family: homo vs. heterodimers
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    biorxiv.org/content/10.1101/2021.12.17.472994v2
  92. Dec 2022
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    Stage-specific gene and transcript dynamics in human male germ cells
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    biorxiv.org/content/10.1101/2022.03.22.485121v1
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    Systematic analysis of ADP-ribose detection reagents and optimisation of sample preparation to detect ADP-ribosylation in vitro and in cells
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    Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines
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    biorxiv.org/content/10.1101/2021.11.02.466992v1
  96. Nov 2022
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    Heterogeneity of the Cancer Cell Line Metabolic Landscape
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    biorxiv.org/content/10.1101/2021.08.19.456093v1
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    A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A
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    biorxiv.org/content/10.1101/2021.12.13.472381v1
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    Bleeding in patients and mice with Alagille syndrome: sex differences and risk factors
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    biorxiv.org/content/10.1101/2021.04.13.439679v2
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    RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA.
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    biorxiv.org/content/10.1101/2022.01.04.474918v1
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    The molecular architecture of cell cycle arrest
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    biorxiv.org/content/10.1101/2022.04.27.489684v1
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    TSG101 Associates with PARP1 and is Essential for PARylation and DNA Damage-induced NF-κB Activation
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    biorxiv.org/content/10.1101/2021.12.07.471537v1
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    Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions
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    biorxiv.org/content/10.1101/2021.12.08.471723v2
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    Growth-mediated negative feedback shapes quantitative antibiotic response
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    biorxiv.org/content/10.1101/2020.12.28.424579v2
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    Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
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    biorxiv.org/content/10.1101/2022.02.03.478981v1
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    Vesalius: Tissue anatomy from spatial transcriptomic data.
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      The several panels show what happens in each cycle. Each cycle consists of a denaturation step at a temperature higher than the melting temperature of the duplex DNA (e.g. 95 oC ), then an annealing step at a temperature below the melting temperature for the primer-template (e.g. 55 oC), followed by extension of the primer by DNA polymerase using dNTPs provided in the reaction. This is done at the temperature optimum for the DNA polymerase (e.g. 70 oC for a thermostable polymerase). Thermocylers are commercially available for carrying out many cycles quickly and reliably
      • Denature
      • Annealing primer
      • Synthesize new DNA with polymerase
      BL2302 Molecular biology techniques
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    Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
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    Phosphoproteomics Reveals a Distinct Mode of Mec1/ATR Signaling in Response to DNA End Hyper-Resection
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    Human POT1 Prevents Severe Telomere Instability Induced by Homology Directed DNA Repair
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    LSD1 inhibitors induce neuronal differentiation of Merkel cell carcinoma by disrupting the LSD1-CoREST complex and activating TGFβ signaling
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