340 Matching Annotations
  1. May 2024
  2. www.biorxiv.org www.biorxiv.org
    K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific interactors.
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    1. EMBOpress 29 May 2024

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    biorxiv.org/content/10.1101/2024.01.08.574586v1
  3. www.biorxiv.org www.biorxiv.org
    IGHMBP2 deletion suppresses translation and activates the integrated stress response
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    1. EMBOpress 29 May 2024

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    biorxiv.org/content/10.1101/2023.12.11.571166v2
  4. www.biorxiv.org www.biorxiv.org
    http://biorxiv.org/cgi/content/short/2020.10.26.356014
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    1. EMBOpress 29 May 2024

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    biorxiv.org/content/10.1101/2020.10.26.356014v3
  5. docdrop.org docdrop.org
    Video: Biology beyond the genome | Denis Noble (DocDrop)
    1
    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/
  6. Mar 2024
  7. www.biorxiv.org www.biorxiv.org
    A YTHDF-PABP axis is required for m6A-mediated organogenesis in plants
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    1. EMBOpress 22 Mar 2024

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    biorxiv.org/content/10.1101/2023.07.03.547513v2
  8. www.biorxiv.org www.biorxiv.org
    CLN3 deficiency leads to neurological and metabolic perturbations during early development
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    1. EMBOpress 05 Mar 2024

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    biorxiv.org/content/10.1101/2023.03.17.533107v1
  9. Feb 2024
  10. www.biorxiv.org www.biorxiv.org
    Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans
    1
    1. EMBOpress 24 Feb 2024

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    biorxiv.org/content/10.1101/2023.04.14.536891v2
  11. www.biorxiv.org www.biorxiv.org
    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
  12. Jan 2024
  13. www.biorxiv.org www.biorxiv.org
    Human liver organoids model progressive inflammatory and fibrotic injury in non-alcoholic fatty liver disease
    1
    1. EMBOpress 17 Jan 2024

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    biorxiv.org/content/10.1101/2022.07.19.500693v2
  14. Dec 2023
  15. www.biorxiv.org www.biorxiv.org
    TUMOR ENDOTHELIAL CELL AUTOPHAGY IS A KEY VASCULAR-IMMUNE CHECKPOINT IN MELANOMA
    1
    1. EMBOpress 16 Dec 2023

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    biorxiv.org/content/10.1101/2023.04.21.537799v2
  16. www.biorxiv.org www.biorxiv.org
    The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition
    1
    1. EMBOpress 15 Dec 2023

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    biorxiv.org/content/10.1101/2022.12.09.519716v1
  17. www.biorxiv.org www.biorxiv.org
    The nucleolar protein GNL3 prevents resection of stalled replication forks.
    1
    1. EMBOpress 13 Dec 2023

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

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    biorxiv.org/content/10.1101/2022.11.18.517070v2
  19. www.biorxiv.org www.biorxiv.org
    Thiol reductive stress activates the hypoxia response pathway
    1
    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2023.03.06.531274v2
  20. www.biorxiv.org www.biorxiv.org
    Paralog dispensability shapes homozygous deletion patterns in tumor genomes
    1
    1. EMBOpress 13 Dec 2023

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    biorxiv.org/content/10.1101/2022.06.20.496722v3
  21. www.biorxiv.org www.biorxiv.org
    Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
    1
    1. EMBOpress 12 Dec 2023

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    biorxiv.org/content/10.1101/2022.02.16.480673v2
  22. www.biorxiv.org www.biorxiv.org
    Downregulation of stromal syntenin sustains AML development
    1
    1. EMBOpress 12 Dec 2023

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    biorxiv.org/content/10.1101/2023.02.15.527799v1
  23. www.biorxiv.org www.biorxiv.org
    Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis
    1
    1. EMBOpress 12 Dec 2023

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    biorxiv.org/content/10.1101/2022.10.03.510635v2
  24. Nov 2023
  25. www.biorxiv.org www.biorxiv.org
    Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
    1
    1. EMBOpress 21 Nov 2023

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    biorxiv.org/content/10.1101/2023.02.22.529573v2
  26. www.biorxiv.org www.biorxiv.org
    A network of small RNAs regulates sporulation initiation in C. difficile
    1
    1. EMBOpress 15 Nov 2023

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    biorxiv.org/content/10.1101/2022.10.17.512509v1
  27. Sep 2023
  28. www.biorxiv.org www.biorxiv.org
    Predictability of the community-function landscape in wine yeast ecosystems
    1
    1. EMBOpress 02 Sep 2023

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    biorxiv.org/content/10.1101/2022.12.15.520418v1
  29. www.biorxiv.org www.biorxiv.org
    Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors
    1
    1. EMBOpress 02 Sep 2023

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    biorxiv.org/content/10.1101/2022.12.27.521482v1
  30. www.biorxiv.org www.biorxiv.org
    Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
    1
    1. EMBOpress 01 Sep 2023

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    biorxiv.org/content/10.1101/2022.12.02.518917v1
  31. Aug 2023
  32. www.biorxiv.org www.biorxiv.org
    A metabolic map of the DNA damage response identifies PRDX1 in nuclear ROS scavenging and aspartate synthesis
    1
    1. EMBOpress 30 Aug 2023

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    biorxiv.org/content/10.1101/2022.08.01.500855v1
  33. www.biorxiv.org www.biorxiv.org
    PRMT5 links lipid metabolism to contractile function of skeletal muscles
    1
    1. EMBOpress 17 Aug 2023

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    biorxiv.org/content/10.1101/2022.11.04.515165v1
  34. www.biorxiv.org www.biorxiv.org
    Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance
    1
    1. EMBOpress 04 Aug 2023

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    biorxiv.org/content/10.1101/2021.05.20.444985v1
  35. www.biorxiv.org www.biorxiv.org
    Consistency across multi-omics layers in a drug-perturbed gut microbial community
    1
    1. EMBOpress 02 Aug 2023

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    biorxiv.org/content/10.1101/2023.01.03.519475v1
  36. www.biorxiv.org www.biorxiv.org
    ATR inhibition augments the efficacy of lurbinectedin in small cell lung cancer
    1
    1. EMBOpress 02 Aug 2023

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    biorxiv.org/content/10.1101/2022.12.16.520783v1
  37. Jul 2023
  38. www.biorxiv.org www.biorxiv.org
    DOT1L bridges transcription and heterochromatin formation at pericentromeres
    1
    1. EMBOpress 20 Jul 2023

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    biorxiv.org/content/10.1101/2021.10.21.465349v1
  39. www.biorxiv.org www.biorxiv.org
    arfA antisense RNA regulates MscL excretory activity
    1
    1. EMBOpress 13 Jul 2023

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    biorxiv.org/content/10.1101/2022.11.21.517365v1
  40. www.biorxiv.org www.biorxiv.org
    A tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases
    1
    1. EMBOpress 07 Jul 2023

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    biorxiv.org/content/10.1101/2021.02.16.430825v1
  41. Jun 2023
  42. www.biorxiv.org www.biorxiv.org
    HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
    1
    1. EMBOpress 29 Jun 2023

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    biorxiv.org/content/10.1101/2022.10.27.514062v1
  43. www.biorxiv.org www.biorxiv.org
    Updated benchmarking of variant effect predictors using deep mutational scanning
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    1. EMBOpress 27 Jun 2023

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    biorxiv.org/content/10.1101/2022.11.19.517196v1
  44. www.biorxiv.org www.biorxiv.org
    Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns
    1
    1. EMBOpress 10 Jun 2023

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    biorxiv.org/content/10.1101/2022.09.30.509643v2
  45. www.biorxiv.org www.biorxiv.org
    A case of mistaken identity: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli
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    1. EMBOpress 10 Jun 2023

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    biorxiv.org/content/10.1101/738823v4
  46. www.biorxiv.org www.biorxiv.org
    Highly multiplexed quantitative phosphosite assay for biology and preclinical studies
    1
    1. EMBOpress 10 Jun 2023

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    biorxiv.org/content/10.1101/2020.12.08.415281v1
  47. www.biorxiv.org www.biorxiv.org
    The histone methyltransferase DOT1L regulates chromatin reorganization and gene expression during the postmeiotic differentiation of male germ cells
    1
    1. EMBOpress 10 Jun 2023

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    biorxiv.org/content/10.1101/2022.10.17.512530v2
  48. www.biorxiv.org www.biorxiv.org
    Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
    1
    1. EMBOpress 02 Jun 2023

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    biorxiv.org/content/10.1101/2022.11.08.515576v1
  49. May 2023
  50. www.biorxiv.org www.biorxiv.org
    BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer
    1
    1. EMBOpress 31 May 2023

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    biorxiv.org/content/10.1101/2021.07.15.452487v2
  51. www.biorxiv.org www.biorxiv.org
    Ubx5-Cdc48 assists the protease Wss1 at DNA-protein crosslink sites in yeast
    1
    1. EMBOpress 25 May 2023

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    biorxiv.org/content/10.1101/2022.05.30.493988v1
  52. www.biorxiv.org www.biorxiv.org
    Endothelial FOXC1 and FOXC2 promote intestinal regeneration after ischemia-reperfusion injury
    1
    1. EMBOpress 25 May 2023

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    biorxiv.org/content/10.1101/2022.03.03.482713v2
  53. www.biorxiv.org www.biorxiv.org
    A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes
    1
    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.08.11.503561
  54. www.biorxiv.org www.biorxiv.org
    Automated assembly of molecular mechanisms at scale from text mining and curated databases
    1
    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.08.30.505688
  55. www.biorxiv.org www.biorxiv.org
    Transcription factor expression is the main determinant of variability in gene co-activity
    1
    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.10.11.511770
  56. www.biorxiv.org www.biorxiv.org
    Mapping single-cell responses to population-level dynamics during antibiotic treatment
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    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.11.18.517151
  57. www.biorxiv.org www.biorxiv.org
    Small non-coding vault RNA1-2 modulate expression of cell membrane proteins through nascent RNA silencing
    1
    1. EMBOpress 11 May 2023

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    biorxiv.org/content/10.1101/2022.08.12.503724v2
  58. www.biorxiv.org www.biorxiv.org
    LuminoCell: a versatile and affordable luminometer platform for monitoring in-cell luciferase-based reporters
    1
    1. EMBOpress 11 May 2023

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    biorxiv.org/content/10.1101/2022.01.28.478134v1
  59. Apr 2023
  60. www.biorxiv.org www.biorxiv.org
    β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
    1
    1. EMBOpress 27 Apr 2023

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    biorxiv.org/content/10.1101/2022.07.07.499249v1
  61. www.biorxiv.org www.biorxiv.org
    Combined measurements of proteome and cell turnover reveal the influences of tissue context and pathological aging on protein and organelle lifetimes
    1
    1. EMBOpress 20 Apr 2023

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    The ADAM17 sheddase complex regulator iTAP/Frmd8 modulates inflammation, epithelial repair, and tumor growth
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    Uncoupling from transcription protects polyadenylation site cleavage from inhibition by DNA damage
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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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    A spatial model of the plant circadian clock reveals design principles for coordinated timing under noisy environments
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    Protein Complexes in Bacillus subtilis by AI-assisted structural proteomics
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    TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes
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    Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
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    Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis
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    Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish
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    Epigenetic signals that direct cell type specific interferon beta response in mouse cells
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    CDK9 and PP2A regulate the link between RNA polymerase II transcription termination and RNA maturation.
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    Evolution of genome fragility enables microbial division of labor
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  76. 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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    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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    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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    Sibling rivalry among the ZBTB transcription factor family: homo vs. heterodimers
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    Stage-specific gene and transcript dynamics in human male germ cells
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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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  88. Nov 2022
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    Heterogeneity of the Cancer Cell Line Metabolic Landscape
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    A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A
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    Bleeding in patients and mice with Alagille syndrome: sex differences and risk factors
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    RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA.
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    The molecular architecture of cell cycle arrest
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    TSG101 Associates with PARP1 and is Essential for PARylation and DNA Damage-induced NF-κB Activation
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    Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions
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    Growth-mediated negative feedback shapes quantitative antibiotic response
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    Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
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    Vesalius: Tissue anatomy from spatial transcriptomic data.
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    CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
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    Quantifying the phenotypic information in mRNA abundance
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    Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes
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    Regulation of mitochondrial proteostasis by the proton gradient
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    Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity
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    Species richness determines C. difficile invasion outcome in synthetic human gut communities
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    Optogenetic actuator/biosensor circuits for large-scale interrogation of ERK dynamics identify sources of MAPK signaling robustness.
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    Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models
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    Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome
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    THEM6-mediated lipid remodelling sustains stress resistance in cancer
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    Growth-dependent heterogeneity in the DNA damage response in Escherichia coli
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    Dynamic human liver proteome atlas reveals functional insights into disease pathways
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    3.5: Polymerase Chain Reaction (PCR)
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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
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      BL2302 Molecular biology techniques
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      • High speed
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    Islet Gene View - a tool to facilitate islet research
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    Drosophila insulator proteins exhibit in-vivo liquid-liquid phase separation properties
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  116. Jul 2022
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    LncRNA RUS shapes the gene expression program towards neurogenesis
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    biorxiv.org/content/10.1101/2022.02.17.480853v1
  118. Jun 2022
  119. www.biorxiv.org www.biorxiv.org
    A RIF1 and KAP1-based, double-bookmarking system generates a toggle switch that stabilises the identities of the active and inactive X chromosomes during random X inactivation in mouse
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    biorxiv.org/content/10.1101/2020.06.04.133512v2
  120. May 2022
  121. www.biorxiv.org www.biorxiv.org
    Diauxic lags explain unexpected coexistence in multi-resource environments
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    biorxiv.org/content/10.1101/2021.08.09.455603v2
  122. www.biorxiv.org www.biorxiv.org
    UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
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    1. EMBOpress 19 May 2022

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    biorxiv.org/content/10.1101/2021.07.07.451444v3
  123. www.biorxiv.org www.biorxiv.org
    Differential impact of TNFRSF co-stimulation on CD8+ T cell cytokine production by feedback control of surface receptor expression
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    1. EMBOpress 07 May 2022

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    biorxiv.org/content/10.1101/2021.07.02.450833v1
  124. www.biorxiv.org www.biorxiv.org
    Single Cell Variability of CRISPR-Cas Interference and Adaptation
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    1. EMBOpress 04 May 2022

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    biorxiv.org/content/10.1101/2021.07.21.453200v1
  125. Apr 2022
  126. www.biorxiv.org www.biorxiv.org
    Unique features of transcription termination and initiation at closely spaced tandem human genes
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    biorxiv.org/content/10.1101/2021.09.10.459726v1
  127. www.biorxiv.org www.biorxiv.org
    A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay
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    1. EMBOpress 22 Apr 2022

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    biorxiv.org/content/10.1101/2021.01.27.428318v2
  128. Mar 2022
  129. www.biorxiv.org www.biorxiv.org
    Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
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    biorxiv.org/content/10.1101/2020.12.22.423933v2
  130. www.biorxiv.org www.biorxiv.org
    A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions
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    1. EMBOpress 22 Mar 2022

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    biorxiv.org/content/10.1101/2021.11.18.469002v1
  131. www.biorxiv.org www.biorxiv.org
    Nonsense-mediated mRNA decay utilizes complementary mechanisms to suppress mRNA and protein accumulation
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    1. EMBOpress 09 Mar 2022

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    biorxiv.org/content/10.1101/2021.05.24.445486v1
  132. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.01.458647
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  133. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.09.459577
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  134. Feb 2022
  135. www.biorxiv.org www.biorxiv.org
    A census of cell types and paracrine interactions in colorectal cancer
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