322 Matching Annotations
  1. Nov 2023
  2. www.biorxiv.org www.biorxiv.org
    Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
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    1. EMBOpress 21 Nov 2023

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

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

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

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

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

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

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

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

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

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    biorxiv.org/content/10.1101/2022.12.16.520783v1
  14. Jul 2023
  15. 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
  16. 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
  17. 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
  18. Jun 2023
  19. 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
  20. www.biorxiv.org www.biorxiv.org
    Updated benchmarking of variant effect predictors using deep mutational scanning
    1
    1. EMBOpress 27 Jun 2023

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    biorxiv.org/content/10.1101/2022.11.19.517196v1
  21. 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
  22. www.biorxiv.org www.biorxiv.org
    A case of mistaken identity: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli
    1
    1. EMBOpress 10 Jun 2023

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    biorxiv.org/content/10.1101/738823v4
  23. 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
  24. 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
  25. 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
  26. May 2023
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. Apr 2023
  37. 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
  38. 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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    biorxiv.org/content/10.1101/2022.04.24.488979v3
  39. Mar 2023
  40. www.biorxiv.org www.biorxiv.org
    The ADAM17 sheddase complex regulator iTAP/Frmd8 modulates inflammation, epithelial repair, and tumor growth
    1
    1. EMBOpress 15 Mar 2023

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    biorxiv.org/content/10.1101/2022.04.11.487842v1
  41. www.biorxiv.org www.biorxiv.org
    Uncoupling from transcription protects polyadenylation site cleavage from inhibition by DNA damage
    1
    1. EMBOpress 15 Mar 2023

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    biorxiv.org/content/10.1101/2022.05.26.492040v2
  42. www.biorxiv.org www.biorxiv.org
    Blockade of pro-fibrotic response mediated by the miR-143/-145 cluster prevents targeted therapy-induced phenotypic plasticity and delays resistance in melanoma
    1
    1. EMBOpress 15 Mar 2023

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    biorxiv.org/content/10.1101/2021.07.02.450838v1
  43. www.biorxiv.org www.biorxiv.org
    A spatial model of the plant circadian clock reveals design principles for coordinated timing under noisy environments
    1
    1. EMBOpress 15 Mar 2023

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    biorxiv.org/content/10.1101/2020.09.13.294785v2
  44. www.biorxiv.org www.biorxiv.org
    Protein Complexes in Bacillus subtilis by AI-assisted structural proteomics
    1
    1. EMBOpress 09 Mar 2023

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

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

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    biorxiv.org/content/10.1101/2022.02.17.480899v1
  48. www.biorxiv.org www.biorxiv.org
    Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis
    1
    1. EMBOpress 15 Feb 2023

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    biorxiv.org/content/10.1101/2022.01.04.474903v1
  49. www.biorxiv.org www.biorxiv.org
    Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish
    1
    1. EMBOpress 15 Feb 2023

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    biorxiv.org/content/10.1101/2021.05.12.443743v1
  50. www.biorxiv.org www.biorxiv.org
    Epigenetic signals that direct cell type specific interferon beta response in mouse cells
    1
    1. EMBOpress 14 Feb 2023

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

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    biorxiv.org/content/10.1101/2021.06.21.449289v3
  52. www.biorxiv.org www.biorxiv.org
    Evolution of genome fragility enables microbial division of labor
    1
    1. EMBOpress 14 Feb 2023

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

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    biorxiv.org/content/10.1101/2022.04.27.489741v1
  55. www.biorxiv.org www.biorxiv.org
    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
  56. www.biorxiv.org www.biorxiv.org
    Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells
    1
    1. EMBOpress 26 Jan 2023

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

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

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    biorxiv.org/content/10.1101/2022.06.03.494647v1
  59. www.biorxiv.org www.biorxiv.org
    A synergistic activation of RARb and RARg nuclear receptors restores cell-types specialization during stem cells differentiation by hijacking RARa-controlled program
    1
    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
    1
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  61. Dec 2022
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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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  65. 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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    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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    Vesalius: Tissue anatomy from spatial transcriptomic data.
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    biorxiv.org/content/10.1101/2021.08.13.456235v3
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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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    biorxiv.org/content/10.1101/2022.02.23.481668v1
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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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    Reproducibility in systems biology modelling
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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
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      BL2302 Molecular biology techniques
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      • High speed
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  90. Aug 2022
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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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    LncRNA RUS shapes the gene expression program towards neurogenesis
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    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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    Diauxic lags explain unexpected coexistence in multi-resource environments
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    UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
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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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    Single Cell Variability of CRISPR-Cas Interference and Adaptation
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    Unique features of transcription termination and initiation at closely spaced tandem human genes
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    A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay
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  105. Mar 2022
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    Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
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    A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions
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    Nonsense-mediated mRNA decay utilizes complementary mechanisms to suppress mRNA and protein accumulation
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    A census of cell types and paracrine interactions in colorectal cancer
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    Structured decomposition improves systems serology prediction and interpretation
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    Major functional bias for mitochondrial complexes in genome-wide CRISPR screens
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    Refining the domain architecture model of the replication origin firing factor Treslin/TICRR
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    Ontogeny and function of the circadian clock in intestinal organoids
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    The Sec61 translocon is a therapeutic vulnerability in Multiple Myeloma
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    biorxiv.org/content/10.1101/2021.09.05.459026v1
  119. 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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    1. EMBOpress 21 Jan 2022

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    biorxiv.org/content/10.1101/2021.05.07.443112v3
  120. Dec 2021
  121. www.biorxiv.org www.biorxiv.org
    The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation
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    1. EMBOpress 30 Dec 2021

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      PeerReviewed EMBOPress The EMBO Journal molecular biology
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    biorxiv.org/content/10.1101/2020.12.09.417709v3
  122. www.biorxiv.org www.biorxiv.org
    Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections
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    1. EMBOpress 16 Dec 2021

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    biorxiv.org/content/10.1101/2020.12.18.423434v1
  123. www.biorxiv.org www.biorxiv.org
    A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism
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    1. EMBOpress 16 Dec 2021

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    biorxiv.org/content/10.1101/2021.05.13.443927v1
  124. www.biorxiv.org www.biorxiv.org
    Two redundant ubiquitin-dependent pathways of BRCA1 localization to DNA damage sites
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    1. EMBOpress 14 Dec 2021

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      PeerReviewed EMBOPress EMBO reports molecular biology
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    biorxiv.org/content/10.1101/2021.07.21.452958v1
  125. www.biorxiv.org www.biorxiv.org
    Physiologically relevant miRNAs in mammalian oocytes are rare and highly abundant.
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    1. EMBOpress 14 Dec 2021

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    biorxiv.org/content/10.1101/2021.08.08.455568v1
  126. 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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    1. EMBOpress 01 Dec 2021

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    ncbi.nlm.nih.gov/pmc/articles/PMC7852273/
  127. Nov 2021
  128. 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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    1. EMBOpress 30 Nov 2021

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      PeerReviewed EMBOPress Molecular Systems Biology bioinformatics
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    biorxiv.org/content/10.1101/2021.03.23.436603v2
  129. Oct 2021
  130. www.biorxiv.org www.biorxiv.org
    Transcriptomic analysis reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes
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    1. EMBOpress 30 Oct 2021

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      PeerReviewed EMBOPress Life Science Alliance molecular biology
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    biorxiv.org/lookup/doi/10.1101/2021.01.19.427259
  131. www.biorxiv.org www.biorxiv.org
    Exploring amino acid functions in a deep mutational landscape
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    1. EMBOpress 30 Oct 2021

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    biorxiv.org/lookup/doi/10.1101/2020.05.26.116756
  132. Sep 2021
  133. www.biorxiv.org www.biorxiv.org
    Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes
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    1. EMBOpress 30 Sep 2021

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    biorxiv.org/content/10.1101/2020.07.17.208777v1
  134. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.04.01.438087
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    1. EMBOpress 22 Sep 2021

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    biorxiv.org/content/10.1101/2021.04.01.438087v1
  135. Aug 2021
  136. www.biorxiv.org www.biorxiv.org
    BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state
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    1. EMBOpress 24 Aug 2021

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