301 Matching Annotations
  1. Last 7 days
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    Ubx5-Cdc48 assists the protease Wss1 at DNA-protein crosslink sites in yeast
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    1. EMBOpress 25 May 2023

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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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    1. EMBOpress 25 May 2023

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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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    1. EMBOpress 24 May 2023

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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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    1. EMBOpress 24 May 2023

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

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    biorxiv.org/lookup/doi/10.1101/2022.10.11.511770
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    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
  8. May 2023
  9. www.biorxiv.org www.biorxiv.org
    Small non-coding vault RNA1-2 modulate expression of cell membrane proteins through nascent RNA silencing
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    1. EMBOpress 11 May 2023

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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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    1. EMBOpress 11 May 2023

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

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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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    1. EMBOpress 20 Apr 2023

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    biorxiv.org/content/10.1101/2022.04.24.488979v3
  14. Mar 2023
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    The ADAM17 sheddase complex regulator iTAP/Frmd8 modulates inflammation, epithelial repair, and tumor growth
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    1. EMBOpress 15 Mar 2023

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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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    1. EMBOpress 15 Mar 2023

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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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    1. EMBOpress 15 Mar 2023

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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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    1. EMBOpress 15 Mar 2023

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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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    1. EMBOpress 09 Mar 2023

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    biorxiv.org/content/10.1101/2022.07.26.501605v3
  20. Feb 2023
  21. www.biorxiv.org www.biorxiv.org
    TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes
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    1. EMBOpress 17 Feb 2023

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    biorxiv.org/content/10.1101/2022.08.08.503151v2
  22. www.biorxiv.org www.biorxiv.org
    Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
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    1. EMBOpress 17 Feb 2023

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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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    1. EMBOpress 15 Feb 2023

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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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    1. EMBOpress 15 Feb 2023

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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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    1. EMBOpress 14 Feb 2023

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    biorxiv.org/content/10.1101/2022.02.26.481127v1
  26. www.biorxiv.org www.biorxiv.org
    CDK9 and PP2A regulate the link between RNA polymerase II transcription termination and RNA maturation.
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    1. EMBOpress 14 Feb 2023

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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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    1. EMBOpress 14 Feb 2023

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    biorxiv.org/content/10.1101/2021.06.04.447040v5
  28. Jan 2023
  29. www.biorxiv.org www.biorxiv.org
    A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast
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    1. EMBOpress 31 Jan 2023

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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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    1. EMBOpress 28 Jan 2023

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    biorxiv.org/content/10.1101/2021.06.09.447741v1
  31. www.biorxiv.org www.biorxiv.org
    Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells
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    1. EMBOpress 26 Jan 2023

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    biorxiv.org/content/10.1101/2022.09.07.506974v1
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    Adaptation of bacterial proteome reveals a key role of the cell envelope in starvation survival
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    1. EMBOpress 24 Jan 2023

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    biorxiv.org/content/10.1101/2022.05.18.492425v2
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    Condensin pinches a short negatively supercoiledDNA loop during each round of ATP usage
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    1. EMBOpress 24 Jan 2023

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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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    1. EMBOpress 19 Jan 2023

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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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    1. EMBOpress 13 Jan 2023

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    biorxiv.org/content/10.1101/2021.12.17.472994v2
  36. Dec 2022
  37. www.biorxiv.org www.biorxiv.org
    Stage-specific gene and transcript dynamics in human male germ cells
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    1. EMBOpress 30 Dec 2022

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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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    biorxiv.org/content/10.1101/2022.02.22.481411v1
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    Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines
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    1. EMBOpress 01 Dec 2022

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    biorxiv.org/content/10.1101/2021.11.02.466992v1
  40. Nov 2022
  41. www.biorxiv.org www.biorxiv.org
    Heterogeneity of the Cancer Cell Line Metabolic Landscape
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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2020.12.28.424579v2
  49. www.biorxiv.org www.biorxiv.org
    Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.02.03.478981v1
  50. www.biorxiv.org www.biorxiv.org
    Vesalius: Tissue anatomy from spatial transcriptomic data.
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.08.13.456235v3
  51. www.biorxiv.org www.biorxiv.org
    CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.09.01.458524v1
  52. www.biorxiv.org www.biorxiv.org
    Quantifying the phenotypic information in mRNA abundance
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.02.23.481668v1
  53. www.biorxiv.org www.biorxiv.org
    Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.01.03.474504v1
  54. www.biorxiv.org www.biorxiv.org
    Regulation of mitochondrial proteostasis by the proton gradient
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.12.12.470907v1
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    Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.08.20.457118v1
  56. www.biorxiv.org www.biorxiv.org
    Species richness determines C. difficile invasion outcome in synthetic human gut communities
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.03.23.436677v1
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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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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.07.27.453955v2
  58. www.biorxiv.org www.biorxiv.org
    Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models
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    biorxiv.org/content/10.1101/2022.01.15.476442v1
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    Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome
    1
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    biorxiv.org/content/10.1101/2021.04.13.439572v1
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    THEM6-mediated lipid remodelling sustains stress resistance in cancer
    1
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    biorxiv.org/content/10.1101/2021.04.04.438378v1
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    Growth-dependent heterogeneity in the DNA damage response in Escherichia coli
    1
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    biorxiv.org/content/10.1101/2021.05.06.442821v2
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    Dynamic human liver proteome atlas reveals functional insights into disease pathways
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    biorxiv.org/content/10.1101/2022.01.28.478194v1
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    Reproducibility in systems biology modelling
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    biorxiv.org/content/10.1101/2020.08.07.239855v1
  64. bio.libretexts.org bio.libretexts.org
    3.5: Polymerase Chain Reaction (PCR)
    2
    1. owendavies 16 Nov 2022
      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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    bio.libretexts.org/Bookshelves/Genetics/Book:_Working_with_Molecular_Genetics_(Hardison)/Unit_I:_Genes_Nucleic_Acids_Genomes_and_Chromosomes/3:_Isolating_and_Analyzing_Genes/3.05:_Polymerase_Chain_Reaction_(PCR)
  65. Aug 2022
  66. www.biorxiv.org www.biorxiv.org
    Islet Gene View - a tool to facilitate islet research
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    biorxiv.org/content/10.1101/435743v3
  67. www.biorxiv.org www.biorxiv.org
    Drosophila insulator proteins exhibit in-vivo liquid-liquid phase separation properties
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    biorxiv.org/content/10.1101/2022.05.27.493687v1
  68. 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
  70. Jun 2022
  71. 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
    1
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    biorxiv.org/content/10.1101/2020.06.04.133512v2
  72. May 2022
  73. 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
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    UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
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    biorxiv.org/content/10.1101/2021.07.07.451444v3
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    Differential impact of TNFRSF co-stimulation on CD8+ T cell cytokine production by feedback control of surface receptor expression
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    biorxiv.org/content/10.1101/2021.07.02.450833v1
  76. www.biorxiv.org www.biorxiv.org
    Single Cell Variability of CRISPR-Cas Interference and Adaptation
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    biorxiv.org/content/10.1101/2021.07.21.453200v1
  77. Apr 2022
  78. 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
  79. www.biorxiv.org www.biorxiv.org
    A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay
    1
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    biorxiv.org/content/10.1101/2021.01.27.428318v2
  80. Mar 2022
  81. 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
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    A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions
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    biorxiv.org/content/10.1101/2021.11.18.469002v1
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    Nonsense-mediated mRNA decay utilizes complementary mechanisms to suppress mRNA and protein accumulation
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    biorxiv.org/content/10.1101/2021.05.24.445486v1
  84. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.01.458647
    1
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    biorxiv.org/content/10.1101/2021.09.01.458647v1
  85. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.09.459577
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    1. EMBOpress 08 Mar 2022

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    biorxiv.org/content/10.1101/2021.09.09.459577v1
  86. Feb 2022
  87. www.biorxiv.org www.biorxiv.org
    A census of cell types and paracrine interactions in colorectal cancer
    1
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    biorxiv.org/content/10.1101/2020.01.10.901579v3
  88. www.biorxiv.org www.biorxiv.org
    Structured decomposition improves systems serology prediction and interpretation
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    biorxiv.org/content/10.1101/2021.01.03.425138v2
  89. www.biorxiv.org www.biorxiv.org
    Major functional bias for mitochondrial complexes in genome-wide CRISPR screens
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    biorxiv.org/content/10.1101/2020.08.31.273730v1
  90. www.biorxiv.org www.biorxiv.org
    Refining the domain architecture model of the replication origin firing factor Treslin/TICRR
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    biorxiv.org/content/10.1101/2021.07.24.453613v1
  91. www.biorxiv.org www.biorxiv.org
    Ontogeny and function of the circadian clock in intestinal organoids
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    biorxiv.org/content/10.1101/2020.04.22.053223v1
  92. Jan 2022
  93. www.biorxiv.org www.biorxiv.org
    The Sec61 translocon is a therapeutic vulnerability in Multiple Myeloma
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    biorxiv.org/content/10.1101/2021.09.05.459026v1
  94. www.biorxiv.org www.biorxiv.org
    Trade-offs in adaptation to glycolysis and gluconeogenesis result in a preferential flux direction in central metabolism
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    biorxiv.org/content/10.1101/2021.05.07.443112v3
  95. Dec 2021
  96. www.biorxiv.org www.biorxiv.org
    The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation
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    biorxiv.org/content/10.1101/2020.12.09.417709v3
  97. www.biorxiv.org www.biorxiv.org
    Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections
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    biorxiv.org/content/10.1101/2020.12.18.423434v1
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    A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism
    1
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    biorxiv.org/content/10.1101/2021.05.13.443927v1
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    Two redundant ubiquitin-dependent pathways of BRCA1 localization to DNA damage sites
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    biorxiv.org/content/10.1101/2021.07.21.452958v1
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    Physiologically relevant miRNAs in mammalian oocytes are rare and highly abundant.
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    biorxiv.org/content/10.1101/2021.08.08.455568v1
  101. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    https://biorxiv.org/cgi/content/10.1101/2021.01.27.428543
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    ncbi.nlm.nih.gov/pmc/articles/PMC7852273/
  102. Nov 2021
  103. www.biorxiv.org www.biorxiv.org
    Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd
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    biorxiv.org/content/10.1101/2021.03.23.436603v2
  104. Oct 2021
  105. www.biorxiv.org www.biorxiv.org
    Transcriptomic analysis reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes
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    biorxiv.org/lookup/doi/10.1101/2021.01.19.427259
  106. www.biorxiv.org www.biorxiv.org
    Exploring amino acid functions in a deep mutational landscape
    1
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    biorxiv.org/lookup/doi/10.1101/2020.05.26.116756
  107. Sep 2021
  108. www.biorxiv.org www.biorxiv.org
    Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes
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    biorxiv.org/content/10.1101/2020.07.17.208777v1
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    https://biorxiv.org/cgi/content/10.1101/2021.04.01.438087
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    biorxiv.org/content/10.1101/2021.04.01.438087v1
  110. Aug 2021
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    BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state
    1
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    biorxiv.org/content/10.1101/2020.07.03.185843v2
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    Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
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    biorxiv.org/content/10.1101/2020.08.19.255893v1
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    Identification of Covalent Modifications Regulating Immune Signaling Complex Composition and Phenotype
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    biorxiv.org/content/10.1101/2020.11.16.384750v1
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    Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit
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    biorxiv.org/content/10.1101/2020.06.18.158790v1
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    TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes
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    biorxiv.org/content/10.1101/2020.11.16.384297v1
  116. Jul 2021
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    Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots
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    biorxiv.org/lookup/doi/10.1101/2020.07.15.203638
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    HMGB1 as a rheostat of chromatin topology and RNA homeostasis on the path to senescence
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    biorxiv.org/lookup/doi/10.1101/540146
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    A genome-scale yeast library with inducible expression of individual genes
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    biorxiv.org/content/10.1101/2020.12.30.424776v2
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    Diverse natural variants suppress mutations in hundreds of essential genes
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    biorxiv.org/content/10.1101/2020.11.24.395855v2
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    Behavioral fingerprints predict insecticide and anthelmintic mode of action
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    biorxiv.org/content/10.1101/2021.01.27.428391v1
  122. www.biorxiv.org www.biorxiv.org
    JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics
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    biorxiv.org/content/10.1101/2020.09.18.304147v1
  123. www.biorxiv.org www.biorxiv.org
    Primary platinum resistance and immune exclusion in ovarian carcinomas with high expression of the homologous recombination mediator RAD51
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    biorxiv.org/content/10.1101/2020.06.09.137612v1
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    Dynamic association of IκBα to chromatin is regulated by acetylation and cleavage of histone H4
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    biorxiv.org/content/10.1101/2021.02.15.431217v1
  125. www.biorxiv.org www.biorxiv.org
    Targeting the SHP2 phosphatase promotes vascular damage and inhibition of tumor growth
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    biorxiv.org/content/10.1101/2020.10.06.327882v1
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    Quantifying signal persistence in the T cell signaling network using an optically controllable antigen receptor
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    biorxiv.org/content/10.1101/2020.10.30.362194v1
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    A dynamic and spatially periodic micro-pattern of HES5 expression underlies the probability of neuronal differentiation in the mouse spinal cord
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    biorxiv.org/content/10.1101/2020.08.03.234369v2
  128. Jun 2021
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    Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids
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      Zhao, H., Wu, D., Nguyen, A., Li, Y., Adão, R. C., Valkov, E., Patterson, G. H., Piszczek, G., & Schuck, P. (2021). Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. IScience, 24(6), 102523. https://doi.org/10.1016/j.isci.2021.102523

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  130. www.biorxiv.org www.biorxiv.org
    Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription
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    biorxiv.org/content/10.1101/2020.05.04.076190v2
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    Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
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    Pancreatic Cancer Intrinsic PI3Kα Activity accelerates Metastasis and rewires Macrophage Component
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    biorxiv.org/content/10.1101/2020.09.23.307884v1
  133. May 2021
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    Spurious regulatory connections dictate the expression-fitness landscape of translation factors
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    hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
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