185 Matching Annotations
  1. Mar 2023
  2. www.biorxiv.org www.biorxiv.org
    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
  3. 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
  4. Feb 2023
  5. 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
  6. 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
  7. www.biorxiv.org www.biorxiv.org
    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
  8. Jan 2023
  9. 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
  10. 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
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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
  12. Dec 2022
  13. 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
  14. Nov 2022
  15. 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
  16. www.biorxiv.org www.biorxiv.org
    The molecular architecture of cell cycle arrest
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.04.27.489684v1
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. www.biorxiv.org www.biorxiv.org
    Quantifying the phenotypic information in mRNA abundance
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2022.02.23.481668v1
  23. www.biorxiv.org www.biorxiv.org
    Species richness determines C. difficile invasion outcome in synthetic human gut communities
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.03.23.436677v1
  24. 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
  25. 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
  26. 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
  27. 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
  28. www.biorxiv.org www.biorxiv.org
    Reproducibility in systems biology modelling
    1
    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2020.08.07.239855v1
  29. May 2022
  30. 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
  31. 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
  32. 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
  33. Apr 2022
  34. 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
  35. www.biorxiv.org www.biorxiv.org
    Physical and functional interactome atlas of human receptor tyrosine kinases
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    1. EMBOpress 22 Apr 2022

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

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      PeerReviewed EMBOPress Life Science Alliance systems biology
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    biorxiv.org/content/10.1101/2021.07.22.453347v1
  37. Mar 2022
  38. 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
  39. www.biorxiv.org www.biorxiv.org
    Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
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    1. EMBOpress 22 Mar 2022

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    biorxiv.org/content/10.1101/2020.12.22.423933v2
  40. www.biorxiv.org www.biorxiv.org
    A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions
    1
    1. EMBOpress 22 Mar 2022

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    biorxiv.org/content/10.1101/2021.11.18.469002v1
  41. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.01.458647
    1
    1. EMBOpress 09 Mar 2022

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    biorxiv.org/content/10.1101/2021.09.01.458647v1
  42. Feb 2022
  43. www.biorxiv.org www.biorxiv.org
    Structured decomposition improves systems serology prediction and interpretation
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    1. EMBOpress 19 Feb 2022

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    biorxiv.org/content/10.1101/2021.01.03.425138v2
  44. www.biorxiv.org www.biorxiv.org
    Major functional bias for mitochondrial complexes in genome-wide CRISPR screens
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    1. EMBOpress 19 Feb 2022

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    biorxiv.org/content/10.1101/2020.08.31.273730v1
  45. Jan 2022
  46. www.biorxiv.org www.biorxiv.org
    Trade-offs in adaptation to glycolysis and gluconeogenesis result in a preferential flux direction in central metabolism
    1
    1. EMBOpress 21 Jan 2022

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    biorxiv.org/content/10.1101/2021.05.07.443112v3
  47. Dec 2021
  48. 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
  49. www.biorxiv.org www.biorxiv.org
    A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism
    1
    1. EMBOpress 16 Dec 2021

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    biorxiv.org/content/10.1101/2021.05.13.443927v1
  50. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    https://biorxiv.org/cgi/content/10.1101/2021.01.27.428543
    1
    1. EMBOpress 01 Dec 2021

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    ncbi.nlm.nih.gov/pmc/articles/PMC7852273/
  51. Nov 2021
  52. 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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    biorxiv.org/content/10.1101/2021.03.23.436603v2
  53. Oct 2021
  54. 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
  55. Sep 2021
  56. www.biorxiv.org www.biorxiv.org
    Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes
    1
    1. EMBOpress 30 Sep 2021

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    biorxiv.org/content/10.1101/2020.07.17.208777v1
  57. Aug 2021
  58. www.biorxiv.org www.biorxiv.org
    Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
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    1. EMBOpress 13 Aug 2021

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    biorxiv.org/content/10.1101/2020.08.19.255893v1
  59. www.biorxiv.org www.biorxiv.org
    Identification of Covalent Modifications Regulating Immune Signaling Complex Composition and Phenotype
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    1. EMBOpress 13 Aug 2021

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    biorxiv.org/content/10.1101/2020.11.16.384750v1
  60. www.biorxiv.org www.biorxiv.org
    Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit
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    1. EMBOpress 13 Aug 2021

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    biorxiv.org/content/10.1101/2020.06.18.158790v1
  61. www.biorxiv.org www.biorxiv.org
    TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes
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    1. EMBOpress 13 Aug 2021

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    biorxiv.org/content/10.1101/2020.11.16.384297v1
  62. Jul 2021
  63. www.biorxiv.org www.biorxiv.org
    Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots
    1
    1. EMBOpress 28 Jul 2021

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    biorxiv.org/lookup/doi/10.1101/2020.07.15.203638
  64. 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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    1. EMBOpress 28 Jul 2021

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    biorxiv.org/lookup/doi/10.1101/540146
  65. www.biorxiv.org www.biorxiv.org
    A genome-scale yeast library with inducible expression of individual genes
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    1. EMBOpress 20 Jul 2021

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    biorxiv.org/content/10.1101/2020.12.30.424776v2
  66. www.biorxiv.org www.biorxiv.org
    Diverse natural variants suppress mutations in hundreds of essential genes
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    1. EMBOpress 17 Jul 2021

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    biorxiv.org/content/10.1101/2020.11.24.395855v2
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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
  71. Jun 2021
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  73. May 2021
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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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    http://biorxiv.org/cgi/content/short/2020.10.21.348854
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    CODEX, a neural network approach to explore signaling dynamics landscapes
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  80. Apr 2021
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    The genotype-phenotype landscape of an allosteric protein
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    The genotype-phenotype landscape of an allosteric protein
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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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    The circadian oscillator analysed at the single-transcript level
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    From Chemoproteomic-Detected Amino Acids to Genomic Coordinates: Insights into Precise Multi-omic Data Integration
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    Promoters adopt distinct dynamic manifestations depending on transcription factor context
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    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
  92. Feb 2021
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    A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids
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    DOMINO: a novel network-based module detection algorithm with reduced rate offalse calls
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    Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models
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    Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration
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    CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators
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    Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression
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    Oncogenic mutant RAS activity is rescaled by the ERK/MAPK pathway
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    CEN-tools: An integrative platform to identify the contexts of essential genes
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    Aggregation and Disaggregation Features of the Human Proteome
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  107. Oct 2020
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    Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder
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    Hormonal dysregulation after prolonged HPA axis activation can be explained by changes of adrenal and corticotroph masses
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  116. Jul 2020
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    STAT3-dependent systems-level analysis reveals PDK4 as an independent predictor of biochemical recurrence in prostate cancer
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    Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation
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    Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor
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    Digitalizing heterologous gene expression in Gram-negative bacteria with a portable on/off module
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    biorxiv.org/content/10.1101/783506v1
  127. www.biorxiv.org www.biorxiv.org
    Machine characterization of rat toxin responses identifies disease states, tolerance mechanisms and organ to whole-body communication
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    The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
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  129. www.biorxiv.org www.biorxiv.org
    Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency
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  130. www.biorxiv.org www.biorxiv.org
    Robust and conserved stochastic self-assembly mechanism for dynamic ParB-parS partition complexes on bacterial chromosomes and plasmids
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    Temporal perturbation of Erk dynamics reveals network architecture of FGF2-MAPK signaling
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  132. Jun 2020
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    A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth
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    Regulatory kinase genetic interaction profiles differ between environmental conditions and cellular states
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