215 Matching Annotations
  1. Oct 2025
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    Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions
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    biorxiv.org/lookup/doi/10.1101/2024.11.27.625594
  3. Dec 2024
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    Transcriptional regulators ensuring specific gene expression and decision making at high TGFβ doses
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    biorxiv.org/content/10.1101/2024.04.23.590740v1
  5. Jul 2024
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    A large-scale cancer-specific protein-DNA interaction network
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    biorxiv.org/content/10.1101/2024.01.24.577099v1
  7. May 2024
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    http://biorxiv.org/cgi/content/short/2020.10.26.356014
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    biorxiv.org/content/10.1101/2020.10.26.356014v3
  9. docdrop.org docdrop.org
    Video: Biology beyond the genome | Denis Noble (DocDrop)
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    1. stopresetgo 18 May 2024
      four 00:08:25 major common misunderstandings that have infected our understanding of what it is to be a living system

      for - molecular biology - paradigm shift - living system - 4 common misunderstandings - book - Understanding Living Systems - 4 common misunderstandings

      4 common misunderstandings of living systems - 1. The central dogma of molecular biology - one way causation - Genes (DNA) to - proteins to - organism - 2. The Weismann Barrier - 3. DNA as self-replicator - 4. Separation of Replicator (DNA) and Vehicle (Living cell) are completely separate

      molecular biology - paradigm shift - Denis Noble living system - 4 common misunderstandings book - Understanding Living Systems - 4 common misunderstandings
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    docdrop.org/video/bzXFSufDDn8/
  10. Feb 2024
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    Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans
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    biorxiv.org/content/10.1101/2023.04.14.536891v2
  12. Dec 2023
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    Paralog dispensability shapes homozygous deletion patterns in tumor genomes
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    biorxiv.org/content/10.1101/2022.06.20.496722v3
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    Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
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    biorxiv.org/content/10.1101/2022.02.16.480673v2
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    Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis
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    biorxiv.org/content/10.1101/2022.10.03.510635v2
  16. Nov 2023
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    Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
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    biorxiv.org/content/10.1101/2023.02.22.529573v2
  18. Sep 2023
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    Predictability of the community-function landscape in wine yeast ecosystems
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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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    biorxiv.org/content/10.1101/2022.12.02.518917v1
  21. Aug 2023
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    A metabolic map of the DNA damage response identifies PRDX1 in nuclear ROS scavenging and aspartate synthesis
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    biorxiv.org/content/10.1101/2022.08.01.500855v1
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    Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance
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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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    biorxiv.org/content/10.1101/2023.01.03.519475v1
  25. Jul 2023
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    Antibody reliability influences observed mRNA-protein correlations in tumour samples
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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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    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
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    biorxiv.org/content/10.1101/2021.02.16.430825v1
  29. Jun 2023
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    Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
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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
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    biorxiv.org/content/10.1101/2022.11.19.517196v1
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    A case of mistaken identity: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli
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    biorxiv.org/content/10.1101/738823v4
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    Highly multiplexed quantitative phosphosite assay for biology and preclinical studies
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    biorxiv.org/content/10.1101/2020.12.08.415281v1
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    Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
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    biorxiv.org/content/10.1101/2022.11.08.515576v1
  35. May 2023
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    A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes
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    Automated assembly of molecular mechanisms at scale from text mining and curated databases
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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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    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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    biorxiv.org/lookup/doi/10.1101/2022.11.18.517151
  40. Apr 2023
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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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    biorxiv.org/content/10.1101/2022.04.24.488979v3
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    Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells
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    biorxiv.org/content/10.1101/2022.08.15.503960v1
  43. Mar 2023
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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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    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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    biorxiv.org/content/10.1101/2022.07.26.501605v3
  46. Feb 2023
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    Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
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    biorxiv.org/content/10.1101/2022.02.17.480899v1
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    Constricted migration contributes to persistent 3D genome structure changes associated with an invasive phenotype in melanoma cells
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    biorxiv.org/content/10.1101/856583v3
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    Evolution of genome fragility enables microbial division of labor
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    biorxiv.org/content/10.1101/2021.06.04.447040v5
  50. Jan 2023
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    A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast
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    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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    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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    biorxiv.org/content/10.1101/2022.05.18.492425v2
  54. Dec 2022
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    Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines
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    biorxiv.org/content/10.1101/2021.11.02.466992v1
  56. Nov 2022
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    Heterogeneity of the Cancer Cell Line Metabolic Landscape
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    biorxiv.org/content/10.1101/2021.08.19.456093v1
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    The molecular architecture of cell cycle arrest
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    biorxiv.org/content/10.1101/2022.04.27.489684v1
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    Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions
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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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    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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    biorxiv.org/content/10.1101/2022.02.03.478981v1
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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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    biorxiv.org/content/10.1101/2021.09.01.458524v1
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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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    Species richness determines C. difficile invasion outcome in synthetic human gut communities
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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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    biorxiv.org/content/10.1101/2021.07.27.453955v2
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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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    biorxiv.org/content/10.1101/2021.04.13.439572v1
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    Growth-dependent heterogeneity in the DNA damage response in Escherichia coli
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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
  71. May 2022
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    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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    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
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    Single Cell Variability of CRISPR-Cas Interference and Adaptation
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    biorxiv.org/content/10.1101/2021.07.21.453200v1
  75. Apr 2022
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    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
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    Physical and functional interactome atlas of human receptor tyrosine kinases
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    biorxiv.org/content/10.1101/2021.09.17.460748v1
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    Conserved exchange of paralog proteins during neuronal differentiation
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    biorxiv.org/content/10.1101/2021.07.22.453347v1
  79. Mar 2022
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    GROWTH-RATE DEPENDENT AND NUTRIENT-SPECIFIC GENE EXPRESSION RESOURCE ALLOCATION IN FISSION YEAST
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    biorxiv.org/content/10.1101/2021.03.16.435638v1
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    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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    https://biorxiv.org/cgi/content/10.1101/2021.09.01.458647
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    biorxiv.org/content/10.1101/2021.09.01.458647v1
  84. Feb 2022
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    Structured decomposition improves systems serology prediction and interpretation
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    biorxiv.org/content/10.1101/2021.01.03.425138v2
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    Major functional bias for mitochondrial complexes in genome-wide CRISPR screens
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    biorxiv.org/content/10.1101/2020.08.31.273730v1
  87. Jan 2022
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    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
  89. Dec 2021
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    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
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    biorxiv.org/content/10.1101/2021.05.13.443927v1
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    https://biorxiv.org/cgi/content/10.1101/2021.01.27.428543
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    ncbi.nlm.nih.gov/pmc/articles/PMC7852273/
  93. Nov 2021
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    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
  95. Oct 2021
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    Exploring amino acid functions in a deep mutational landscape
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    biorxiv.org/lookup/doi/10.1101/2020.05.26.116756
  97. Sep 2021
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    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
  99. Aug 2021
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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
  104. 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
  108. 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
  109. 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
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    JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics
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    biorxiv.org/content/10.1101/2020.09.18.304147v1
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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
  113. Jun 2021
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    Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
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    biorxiv.org/content/10.1101/542381v1
  115. May 2021
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    Spurious regulatory connections dictate the expression-fitness landscape of translation factors
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    biorxiv.org/content/10.1101/2020.11.27.400200v1
  117. 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
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      A final word: when we do not understand something, it does not look like there is anything to be understood at all - it just looks like random noise. Just because it looks like noise does not mean there is no hidden structure.

      Excellent statement! Could this be the guiding principle of the current big data boom in biology?

      noise systems biology big data
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    MODELING SIGNALING-DEPENDENT PLURIPOTENT CELL STATES WITH BOOLEAN LOGIC CAN PREDICT CELL FATE TRANSITIONS
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    biorxiv.org/content/10.1101/115683v2
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    Genome-wide phenotypic analysis of growth, cell morphogenesis and cellcycle events in Escherichia coli.
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    biorxiv.org/content/10.1101/101832v3
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    A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes
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    biorxiv.org/content/10.1101/092361v1
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    A two-state photoconversion model predicts the spectral response dynamics of optogenetic systems
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    Unraveling mitotic protein networks by 3D multiplexed epitope drug screening
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    Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics
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    Redesigning chromosomes to optimize conformation capture (Hi-C) assays
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    Deciphering microbial interactions in synthetic human gut microbiome communities
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    Expression variation and covariation impair analog and enable binary signaling control
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    Timing of gene expression in a cell-fate decision system
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    Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
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    A Map Of Genetic Interactions In Cancer Cells
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    Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics
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    Assigning Function To Natural Allelic Variation Via Dynamic Modeling Of Gene Network Induction
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    Expanding the Atlas of Functional Missense Variation for Human Genes
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    Resolving Drug Effects In Patient-Derived Cancer Cells Links Organoid Responses To Genome Alterations
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    biorxiv.org/content/10.1101/124446v1
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    The Landscape Of Human Mutually Exclusive Splicing
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    From word models to executable models of signaling networks using automated assembly
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    biorxiv.org/content/10.1101/119834v3