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  1. Last 7 days
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    Transcriptional regulators ensuring specific gene expression and decision making at high TGFβ doses
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    1. EMBOpress 03 Dec 2024

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    biorxiv.org/content/10.1101/2024.04.23.590740v1
  3. Jul 2024
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    A large-scale cancer-specific protein-DNA interaction network
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    1. EMBOpress 30 Jul 2024

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    biorxiv.org/content/10.1101/2024.01.24.577099v1
  5. 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
  7. 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
    2. stopresetgo 18 May 2024
      biology Beyond The 00:00:19 genome

      for - book - Biology Beyond the Genome - author - scientist - biologist - Denis Noble - book - Understanding Living Systems

      Denis Noble book - Biology Beyond the Genome book - Understanding Living Systems
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    docdrop.org/video/bzXFSufDDn8/
  8. Feb 2024
  9. www.biorxiv.org www.biorxiv.org
    Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans
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    1. EMBOpress 24 Feb 2024

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    biorxiv.org/content/10.1101/2023.04.14.536891v2
  10. Dec 2023
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    Paralog dispensability shapes homozygous deletion patterns in tumor genomes
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    1. EMBOpress 13 Dec 2023

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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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    1. EMBOpress 12 Dec 2023

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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
  14. Nov 2023
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    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
  16. 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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    1. EMBOpress 01 Sep 2023

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    biorxiv.org/content/10.1101/2022.12.02.518917v1
  19. 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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    1. EMBOpress 30 Aug 2023

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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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    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
  23. Jul 2023
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    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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    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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    1. EMBOpress 07 Jul 2023

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    biorxiv.org/content/10.1101/2021.02.16.430825v1
  27. 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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    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
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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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    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
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    1. EMBOpress 10 Jun 2023

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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
  33. 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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    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.08.11.503561
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    Automated assembly of molecular mechanisms at scale from text mining and curated databases
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    1. EMBOpress 24 May 2023

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

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    biorxiv.org/lookup/doi/10.1101/2022.10.11.511770
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    Mapping single-cell responses to population-level dynamics during antibiotic treatment
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    1. EMBOpress 24 May 2023

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    biorxiv.org/lookup/doi/10.1101/2022.11.18.517151
  38. Apr 2023
  39. 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
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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
  41. 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
  44. 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
  48. Jan 2023
  49. www.biorxiv.org www.biorxiv.org
    A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast
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    1. EMBOpress 31 Jan 2023

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    biorxiv.org/content/10.1101/2022.04.27.489741v1
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    Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival
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    1. EMBOpress 28 Jan 2023

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    biorxiv.org/content/10.1101/2021.06.09.447741v1
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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
  52. Dec 2022
  53. www.biorxiv.org www.biorxiv.org
    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
  54. 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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    1. EMBOpress 21 Nov 2022

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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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    1. EMBOpress 21 Nov 2022

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    biorxiv.org/content/10.1101/2021.03.23.436677v1
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    Optogenetic actuator/biosensor circuits for large-scale interrogation of ERK dynamics identify sources of MAPK signaling robustness.
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    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
  67. www.biorxiv.org www.biorxiv.org
    Dynamic human liver proteome atlas reveals functional insights into disease pathways
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    biorxiv.org/content/10.1101/2022.01.28.478194v1
  68. www.biorxiv.org www.biorxiv.org
    Reproducibility in systems biology modelling
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    biorxiv.org/content/10.1101/2020.08.07.239855v1
  69. May 2022
  70. www.biorxiv.org www.biorxiv.org
    Diauxic lags explain unexpected coexistence in multi-resource environments
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    biorxiv.org/content/10.1101/2021.08.09.455603v2
  71. 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
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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
  73. Apr 2022
  74. www.biorxiv.org www.biorxiv.org
    Unique features of transcription termination and initiation at closely spaced tandem human genes
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    biorxiv.org/content/10.1101/2021.09.10.459726v1
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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
  77. Mar 2022
  78. www.biorxiv.org www.biorxiv.org
    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
  82. Feb 2022
  83. 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
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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
  85. 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
  87. Dec 2021
  88. www.biorxiv.org www.biorxiv.org
    Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections
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    biorxiv.org/content/10.1101/2020.12.18.423434v1
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    A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism
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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/
  91. Nov 2021
  92. 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
  93. 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
  95. Sep 2021
  96. 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
  97. 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
  100. 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
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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
  102. 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
  105. 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
  106. 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
  107. 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
  108. 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
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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
  111. 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
  113. May 2021
  114. 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
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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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    biorxiv.org/content/10.1101/2020.09.15.298216v1
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    http://biorxiv.org/cgi/content/short/2020.10.21.348854
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    Multidimensional Chromatin Regulation of Cell Lineage Differentiation in a Metazoan Embryo
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    biorxiv.org/content/10.1101/2020.05.18.101584v1
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    CODEX, a neural network approach to explore signaling dynamics landscapes
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    biorxiv.org/lookup/doi/10.1101/2020.08.05.237842
  119. 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
  120. Apr 2021
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    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
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    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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    TATA and paused promoters active in differentiated tissues have distinct expression characteristics
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  132. Feb 2021
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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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    Aggregation and Disaggregation Features of the Human Proteome
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  147. Oct 2020
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    Programmable and portable CRISPR-Cas transcriptional activation in bacteria
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    Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder
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  152. doi.org doi.org
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    The protein architecture of the endocytic coat analyzed by FRET
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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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  156. 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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  172. Jun 2020
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  180. May 2020
  181. journals.plos.org journals.plos.org
    Flocking in complex environments—Attention trade-offs in collective information processing
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      Rahmani P, Peruani F, Romanczuk P (2020) Flocking in complex environments—Attention trade-offs in collective information processing. PLoS Comput Biol 16(4): e1007697. https://doi.org/10.1371/journal.pcbi.1007697

      is:preprint lang:en behavioral science collective behavior response interaction cognitive science social systems biology attention processing
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  182. Jan 2020
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    Book Review: Design Principles of Biological Circuits - LessWrong 2.0
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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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  184. Nov 2019
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    Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions
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    An integrated workflow for cross-linking/mass spectrometry
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  191. Sep 2019
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    Hierarchical organization of the human cell from a cancer coessentiality network
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    An integrative machine learning approach for prediction of toxicity-related drug safety
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    Co-existing feedback loops generate tissue-specific circadian rhythms
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    Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
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    Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO)
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    Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system
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    Absolute quantification of translational regulation and burden using combined sequencing approaches
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    Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory networks
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    The fitness cost and benefit of phase separated protein deposits
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    Defining the RNA Interactome by Total RNA-Associated Protein Purification
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    Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy
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    Evidence that the cell cycle is a series of uncoupled, memoryless phases
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    netDx: Patient classification using integrated patient similarity networks
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    De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization
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    Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues
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    A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
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    Widespread inter-individual gene expression variability in Arabidopsis thaliana
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    Complex-centric proteome profiling by SEC-SWATH-MS
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    High-resolution mapping of cancer cell networks using co-functional interactions
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    Functional Compensation Between Hematopoietic Stem Cells In Vivo
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    Synthesis and degradation of FtsZ determines the first cell division in starved bacteria
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    Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming
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    Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations
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    Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis
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    Ratiometric Distribution Of OCT4 During Stem Cell Division Controls The Balance Between Self-Renewal And Differentiation
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    Multi-Omics factor analysis disentangles heterogeneity in blood cancer
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    Fibroblast state switching orchestrates dermal maturation and wound healing
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    Genomics of cellular proliferation under periodic stress
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    MODELING SIGNALING-DEPENDENT PLURIPOTENT CELL STATES WITH BOOLEAN LOGIC CAN PREDICT CELL FATE TRANSITIONS
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    Genome-wide phenotypic analysis of growth, cell morphogenesis and cellcycle events in Escherichia coli.
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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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    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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    Expression variation and covariation impair analog and enable binary signaling control
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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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    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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