205 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. Sep 2023
  4. 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
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    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
  6. Aug 2023
  7. 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
  8. 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
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    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
  10. Jul 2023
  11. www.biorxiv.org www.biorxiv.org
    Antibody reliability influences observed mRNA-protein correlations in tumour samples
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    1. EMBOpress 13 Jul 2023

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    biorxiv.org/content/10.1101/2022.12.23.521733v1
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    N-terminal proteoforms may engage in different protein complexes
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    1. EMBOpress 13 Jul 2023

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    biorxiv.org/content/10.1101/2023.01.17.524352v2
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    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
  14. Jun 2023
  15. www.biorxiv.org www.biorxiv.org
    Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
    1
    1. EMBOpress 28 Jun 2023

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    biorxiv.org/content/10.1101/2022.12.11.519953v2
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    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
  17. 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
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    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
  19. 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
  20. May 2023
  21. 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
  22. 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
  23. 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
  24. www.biorxiv.org www.biorxiv.org
    Mapping single-cell responses to population-level dynamics during antibiotic treatment
    1
    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.11.18.517151
  25. Apr 2023
  26. 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
  27. www.biorxiv.org www.biorxiv.org
    Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells
    1
    1. EMBOpress 11 Apr 2023

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    biorxiv.org/content/10.1101/2022.08.15.503960v1
  28. Mar 2023
  29. 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
  30. 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
  31. Feb 2023
  32. 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
  33. www.biorxiv.org www.biorxiv.org
    Constricted migration contributes to persistent 3D genome structure changes associated with an invasive phenotype in melanoma cells
    1
    1. EMBOpress 14 Feb 2023

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    biorxiv.org/content/10.1101/856583v3
  34. 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
  35. Jan 2023
  36. 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
  37. www.biorxiv.org www.biorxiv.org
    Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival
    1
    1. EMBOpress 28 Jan 2023

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    biorxiv.org/content/10.1101/2021.06.09.447741v1
  38. 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
  39. Dec 2022
  40. www.biorxiv.org www.biorxiv.org
    Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines
    1
    1. EMBOpress 01 Dec 2022

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

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    biorxiv.org/content/10.1101/2021.08.19.456093v1
  43. www.biorxiv.org www.biorxiv.org
    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
  44. www.biorxiv.org www.biorxiv.org
    Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.12.08.471723v2
  45. www.biorxiv.org www.biorxiv.org
    Growth-mediated negative feedback shapes quantitative antibiotic response
    1
    1. EMBOpress 21 Nov 2022

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

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

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

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    biorxiv.org/content/10.1101/2021.09.01.458524v1
  49. 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
  50. 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
  51. www.biorxiv.org www.biorxiv.org
    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
  52. www.biorxiv.org www.biorxiv.org
    Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.04.13.439572v1
  53. www.biorxiv.org www.biorxiv.org
    Growth-dependent heterogeneity in the DNA damage response in Escherichia coli
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.05.06.442821v2
  54. www.biorxiv.org www.biorxiv.org
    Dynamic human liver proteome atlas reveals functional insights into disease pathways
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.01.28.478194v1
  55. www.biorxiv.org www.biorxiv.org
    Reproducibility in systems biology modelling
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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2020.08.07.239855v1
  56. May 2022
  57. www.biorxiv.org www.biorxiv.org
    Diauxic lags explain unexpected coexistence in multi-resource environments
    1
    1. EMBOpress 27 May 2022

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    biorxiv.org/content/10.1101/2021.08.09.455603v2
  58. 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
    1
    1. EMBOpress 07 May 2022

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

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    biorxiv.org/content/10.1101/2021.07.21.453200v1
  60. Apr 2022
  61. www.biorxiv.org www.biorxiv.org
    Unique features of transcription termination and initiation at closely spaced tandem human genes
    1
    1. EMBOpress 23 Apr 2022

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    biorxiv.org/content/10.1101/2021.09.10.459726v1
  62. www.biorxiv.org www.biorxiv.org
    Physical and functional interactome atlas of human receptor tyrosine kinases
    1
    1. EMBOpress 22 Apr 2022

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    biorxiv.org/content/10.1101/2021.09.17.460748v1
  63. www.biorxiv.org www.biorxiv.org
    Conserved exchange of paralog proteins during neuronal differentiation
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    1. EMBOpress 08 Apr 2022

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    biorxiv.org/content/10.1101/2021.07.22.453347v1
  64. Mar 2022
  65. www.biorxiv.org www.biorxiv.org
    GROWTH-RATE DEPENDENT AND NUTRIENT-SPECIFIC GENE EXPRESSION RESOURCE ALLOCATION IN FISSION YEAST
    1
    1. EMBOpress 22 Mar 2022

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    biorxiv.org/content/10.1101/2021.03.16.435638v1
  66. 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
  67. 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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    biorxiv.org/content/10.1101/2021.11.18.469002v1
  68. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.01.458647
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    1. EMBOpress 09 Mar 2022

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    biorxiv.org/content/10.1101/2021.09.01.458647v1
  69. Feb 2022
  70. 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
  71. 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
  72. Jan 2022
  73. 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
  74. Dec 2021
  75. www.biorxiv.org www.biorxiv.org
    Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections
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    A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism
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    biorxiv.org/content/10.1101/2021.05.13.443927v1
  77. 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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  78. Nov 2021
  79. 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
  80. Oct 2021
  81. www.biorxiv.org www.biorxiv.org
    Exploring amino acid functions in a deep mutational landscape
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  82. Sep 2021
  83. 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
  84. Aug 2021
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    Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
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  86. www.biorxiv.org www.biorxiv.org
    Identification of Covalent Modifications Regulating Immune Signaling Complex Composition and Phenotype
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    biorxiv.org/content/10.1101/2020.11.16.384750v1
  87. www.biorxiv.org www.biorxiv.org
    Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit
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    biorxiv.org/content/10.1101/2020.06.18.158790v1
  88. www.biorxiv.org www.biorxiv.org
    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
  89. Jul 2021
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    Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots
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  91. www.biorxiv.org www.biorxiv.org
    HMGB1 as a rheostat of chromatin topology and RNA homeostasis on the path to senescence
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  92. www.biorxiv.org www.biorxiv.org
    A genome-scale yeast library with inducible expression of individual genes
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    biorxiv.org/content/10.1101/2020.12.30.424776v2
  93. www.biorxiv.org www.biorxiv.org
    Diverse natural variants suppress mutations in hundreds of essential genes
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    biorxiv.org/content/10.1101/2020.11.24.395855v2
  94. www.biorxiv.org www.biorxiv.org
    Behavioral fingerprints predict insecticide and anthelmintic mode of action
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    biorxiv.org/content/10.1101/2021.01.27.428391v1
  95. 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
  96. www.biorxiv.org www.biorxiv.org
    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
  97. www.biorxiv.org www.biorxiv.org
    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
  98. Jun 2021
  99. www.biorxiv.org www.biorxiv.org
    Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
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    biorxiv.org/content/10.1101/542381v1
  100. May 2021
  101. www.biorxiv.org www.biorxiv.org
    Spurious regulatory connections dictate the expression-fitness landscape of translation factors
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    biorxiv.org/content/10.1101/2020.11.27.400200v1
  102. www.biorxiv.org www.biorxiv.org
    hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
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    biorxiv.org/content/10.1101/2020.09.15.298216v1
  103. www.biorxiv.org www.biorxiv.org
    http://biorxiv.org/cgi/content/short/2020.10.21.348854
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  104. www.biorxiv.org www.biorxiv.org
    Multidimensional Chromatin Regulation of Cell Lineage Differentiation in a Metazoan Embryo
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    biorxiv.org/content/10.1101/2020.05.18.101584v1
  105. www.biorxiv.org www.biorxiv.org
    CODEX, a neural network approach to explore signaling dynamics landscapes
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    biorxiv.org/lookup/doi/10.1101/2020.08.05.237842
  106. www.biorxiv.org www.biorxiv.org
    Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments
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    biorxiv.org/content/10.1101/2020.10.15.340554v1
  107. Apr 2021
  108. www.biorxiv.org www.biorxiv.org
    CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing
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    biorxiv.org/content/10.1101/2020.10.15.340844v1
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    Urinary proteome profiling for stratifying patients with familial Parkinsons disease
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    biorxiv.org/content/10.1101/2020.08.09.243584v1
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    Integrated intra- and intercellular signaling knowledge for multicelullar omics analysis
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    biorxiv.org/content/10.1101/2020.08.03.221242v2
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    Identifying Modules of Cooperating Cancer Drivers
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    biorxiv.org/content/10.1101/2020.06.29.168229v1
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    The genotype-phenotype landscape of an allosteric protein
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    biorxiv.org/content/10.1101/2020.07.10.197574v1
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    The genotype-phenotype landscape of an allosteric protein
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    biorxiv.org/content/10.1101/2020.09.30.320812v1
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    Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
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    biorxiv.org/content/10.1101/2020.01.31.929372v1
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    The circadian oscillator analysed at the single-transcript level
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    biorxiv.org/content/10.1101/2020.08.26.268201v1
  116. www.biorxiv.org www.biorxiv.org
    From Chemoproteomic-Detected Amino Acids to Genomic Coordinates: Insights into Precise Multi-omic Data Integration
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    biorxiv.org/content/10.1101/2020.07.03.186007v2
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    Promoters adopt distinct dynamic manifestations depending on transcription factor context
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    biorxiv.org/content/10.1101/650762v2
  118. www.biorxiv.org www.biorxiv.org
    TATA and paused promoters active in differentiated tissues have distinct expression characteristics
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    biorxiv.org/content/10.1101/2020.07.15.196493v1
  119. Feb 2021
  120. www.biorxiv.org www.biorxiv.org
    Using single-plant -omics in the field to link maize genes to functions and phenotypes
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    biorxiv.org/content/10.1101/2020.04.06.027300v1
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    A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids
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    biorxiv.org/content/10.1101/2020.07.24.219659v1
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    DOMINO: a novel network-based module detection algorithm with reduced rate offalse calls
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    biorxiv.org/content/10.1101/2020.03.10.984963v4
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    Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
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    biorxiv.org/content/10.1101/2020.04.23.057893v1
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    Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models
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    biorxiv.org/content/10.1101/532895v2
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    Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration
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    biorxiv.org/content/10.1101/2020.05.12.090688v1
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    CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators
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    biorxiv.org/content/10.1101/2020.10.03.324715v1
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    Dormancy as a spectrum measuring spore’s proximity to death and to replicative life
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    The transcriptome dynamics of single cells during the cell cycle
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    biorxiv.org/content/10.1101/2019.12.23.887570v1
  129. www.biorxiv.org www.biorxiv.org
    Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression
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    biorxiv.org/content/10.1101/2020.02.10.942276v1
  130. www.biorxiv.org www.biorxiv.org
    Oncogenic mutant RAS activity is rescaled by the ERK/MAPK pathway
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    biorxiv.org/content/10.1101/2020.02.17.952093v1
  131. www.biorxiv.org www.biorxiv.org
    CEN-tools: An integrative platform to identify the contexts of essential genes
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    biorxiv.org/content/10.1101/2020.05.10.087668v2
  132. www.biorxiv.org www.biorxiv.org
    Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function
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    biorxiv.org/content/10.1101/2020.05.03.074815v1
  133. www.biorxiv.org www.biorxiv.org
    Aggregation and Disaggregation Features of the Human Proteome
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    biorxiv.org/content/10.1101/2020.02.05.931675v1
  134. Oct 2020
  135. www.biorxiv.org www.biorxiv.org
    Programmable and portable CRISPR-Cas transcriptional activation in bacteria
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    biorxiv.org/content/10.1101/2020.01.03.882431v2
  136. www.biorxiv.org www.biorxiv.org
    State transitions of a developmental oscillator
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    biorxiv.org/content/10.1101/755421v2
  137. www.biorxiv.org www.biorxiv.org
    Predicting antigen-specificity of single T-cells based on TCR CDR3 regions
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    biorxiv.org/content/10.1101/734053v1
  138. www.biorxiv.org www.biorxiv.org
    Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder
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    biorxiv.org/content/10.1101/2020.01.30.923003v3
  139. doi.org doi.org
    https://doi.org/10.1101/2020.03.31.016048
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