68 Matching Annotations
  1. Jan 2020
  2. www.lesswrong.com www.lesswrong.com
    Book Review: Design Principles of Biological Circuits - LessWrong 2.0
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    1. pbk1 06 Jan 2020
      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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    lesswrong.com/posts/bNXdnRTpSXk9p4zmi/book-review-design-principles-of-biological-circuits
  3. Nov 2019
  4. www.biorxiv.org www.biorxiv.org
    Sufficiency analysis of estrogen responsive enhancers using synthetic activators
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    1. EMBOpress 26 Nov 2019

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    biorxiv.org/content/10.1101/479709v2
  5. www.biorxiv.org www.biorxiv.org
    Combinatorial prediction of gene-marker panels from single-cell transcriptomic data.
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    1. EMBOpress 26 Nov 2019

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    biorxiv.org/content/10.1101/655753v2
  6. www.biorxiv.org www.biorxiv.org
    Estrogen receptor alpha controls gene expression via translational offsetting
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    1. EMBOpress 26 Nov 2019

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      PeerReviewed EMBOPress The EMBO Journal systems biology
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    biorxiv.org/content/10.1101/507574v1
  7. www.biorxiv.org www.biorxiv.org
    Paralog dependency indirectly affects the robustness of human cells
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    1. EMBOpress 26 Nov 2019

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    biorxiv.org/content/10.1101/552208v3
  8. www.biorxiv.org www.biorxiv.org
    Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions
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    1. EMBOpress 26 Nov 2019

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    biorxiv.org/content/10.1101/299073v3
  9. www.biorxiv.org www.biorxiv.org
    An integrated workflow for cross-linking/mass spectrometry
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    1. EMBOpress 26 Nov 2019

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      PeerReviewed EMBOPress Molecular Systems Biology biochemistry
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    biorxiv.org/content/10.1101/355396v2
  10. Sep 2019
  11. www.biorxiv.org www.biorxiv.org
    Hierarchical organization of the human cell from a cancer coessentiality network
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/328880v1
  12. www.biorxiv.org www.biorxiv.org
    An integrative machine learning approach for prediction of toxicity-related drug safety
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/455667v1
  13. www.biorxiv.org www.biorxiv.org
    Co-existing feedback loops generate tissue-specific circadian rhythms
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/304451v1
  14. www.biorxiv.org www.biorxiv.org
    Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/250167v1
  15. www.biorxiv.org www.biorxiv.org
    Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO)
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/368282v1
  16. www.biorxiv.org www.biorxiv.org
    Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system
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    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology ecology
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    biorxiv.org/content/10.1101/361584v1
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    Absolute quantification of translational regulation and burden using combined sequencing approaches
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/338939v2
  18. www.biorxiv.org www.biorxiv.org
    Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory networks
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/184325v2
  19. www.biorxiv.org www.biorxiv.org
    The fitness cost and benefit of phase separated protein deposits
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/574657v2
  20. www.biorxiv.org www.biorxiv.org
    Defining the RNA Interactome by Total RNA-Associated Protein Purification
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    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology cell biology
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    biorxiv.org/content/10.1101/436253v1
  21. www.biorxiv.org www.biorxiv.org
    Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/284240v2
  22. www.biorxiv.org www.biorxiv.org
    Evidence that the cell cycle is a series of uncoupled, memoryless phases
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/283614v1
  23. www.biorxiv.org www.biorxiv.org
    netDx: Patient classification using integrated patient similarity networks
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/084418v4
  24. www.biorxiv.org www.biorxiv.org
    De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/367003v1
  25. www.biorxiv.org www.biorxiv.org
    Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/353763v1
  26. www.biorxiv.org www.biorxiv.org
    A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/357137v1
  27. www.biorxiv.org www.biorxiv.org
    Widespread inter-individual gene expression variability in Arabidopsis thaliana
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    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology plant biology
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    biorxiv.org/content/10.1101/335380v2
  28. www.biorxiv.org www.biorxiv.org
    Complex-centric proteome profiling by SEC-SWATH-MS
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/323683v2
  29. www.biorxiv.org www.biorxiv.org
    High-resolution mapping of cancer cell networks using co-functional interactions
    1
    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology genomics
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    biorxiv.org/content/10.1101/369751v1
  30. www.biorxiv.org www.biorxiv.org
    Functional Compensation Between Hematopoietic Stem Cells In Vivo
    1
    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress EMBO reports systems biology
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    biorxiv.org/content/10.1101/236398v1
  31. www.biorxiv.org www.biorxiv.org
    Synthesis and degradation of FtsZ determines the first cell division in starved bacteria
    1
    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology microbiology
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    biorxiv.org/content/10.1101/314922v1
  32. www.biorxiv.org www.biorxiv.org
    Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming
    1
    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology cancer biology
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    biorxiv.org/content/10.1101/197376v1
  33. www.biorxiv.org www.biorxiv.org
    Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/191338v1
  34. www.biorxiv.org www.biorxiv.org
    Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis
    1
    1. EMBOpress 22 Sep 2019

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      PeerReviewed EMBOPress Molecular Systems Biology developmental biology
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    biorxiv.org/content/10.1101/280834v1
  35. www.biorxiv.org www.biorxiv.org
    Ratiometric Distribution Of OCT4 During Stem Cell Division Controls The Balance Between Self-Renewal And Differentiation
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/137299v2
  36. www.biorxiv.org www.biorxiv.org
    Multi-Omics factor analysis disentangles heterogeneity in blood cancer
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/217554v2
  37. www.biorxiv.org www.biorxiv.org
    Fibroblast state switching orchestrates dermal maturation and wound healing
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/236232v2
  38. www.biorxiv.org www.biorxiv.org
    Genomics of cellular proliferation under periodic stress
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/129163v1
  39. www.biorxiv.org www.biorxiv.org
    MODELING SIGNALING-DEPENDENT PLURIPOTENT CELL STATES WITH BOOLEAN LOGIC CAN PREDICT CELL FATE TRANSITIONS
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/115683v2
  40. www.biorxiv.org www.biorxiv.org
    Genome-wide phenotypic analysis of growth, cell morphogenesis and cellcycle events in Escherichia coli.
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/101832v3
  41. www.biorxiv.org www.biorxiv.org
    A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes
    1
    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/092361v1
  42. www.biorxiv.org www.biorxiv.org
    A two-state photoconversion model predicts the spectral response dynamics of optogenetic systems
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/081430v1
  43. www.biorxiv.org www.biorxiv.org
    Unraveling mitotic protein networks by 3D multiplexed epitope drug screening
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/231779v2
  44. www.biorxiv.org www.biorxiv.org
    Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/181750v2
  45. www.biorxiv.org www.biorxiv.org
    Redesigning chromosomes to optimize conformation capture (Hi-C) assays
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/169847v2
  46. www.biorxiv.org www.biorxiv.org
    Deciphering microbial interactions in synthetic human gut microbiome communities
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/228395v1
  47. www.biorxiv.org www.biorxiv.org
    Expression variation and covariation impair analog and enable binary signaling control
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/244236v1
  48. www.biorxiv.org www.biorxiv.org
    Timing of gene expression in a cell-fate decision system
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/197103v1
  49. www.biorxiv.org www.biorxiv.org
    Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/182071v1
  50. www.biorxiv.org www.biorxiv.org
    A Map Of Genetic Interactions In Cancer Cells
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/120964v2
  51. www.biorxiv.org www.biorxiv.org
    Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/187237v1
  52. www.biorxiv.org www.biorxiv.org
    Assigning Function To Natural Allelic Variation Via Dynamic Modeling Of Gene Network Induction
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/140467v1
  53. www.biorxiv.org www.biorxiv.org
    Expanding the Atlas of Functional Missense Variation for Human Genes
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/166595v2
  54. www.biorxiv.org www.biorxiv.org
    Resolving Drug Effects In Patient-Derived Cancer Cells Links Organoid Responses To Genome Alterations
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/124446v1
  55. www.biorxiv.org www.biorxiv.org
    The Landscape Of Human Mutually Exclusive Splicing
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/133215v1
  56. www.biorxiv.org www.biorxiv.org
    From word models to executable models of signaling networks using automated assembly
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/119834v3
  57. www.biorxiv.org www.biorxiv.org
    CRISPR/Cas9 screening using unique molecular identifiers
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    biorxiv.org/content/10.1101/114355v2
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    In Situ Genotyping Of A Pooled Strain Library After Characterizing Complex Phenotypes
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    biorxiv.org/content/10.1101/142729v1
  59. www.biorxiv.org www.biorxiv.org
    A Theory That Predicts Behaviors Of Disordered Cytoskeletal Networks
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  60. www.biorxiv.org www.biorxiv.org
    High-throughput CRISPRi phenotyping in Streptococcus pneumoniae identifies new essential genes involved in cell wall synthesis and competence development
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    biorxiv.org/content/10.1101/088336v1
  61. www.biorxiv.org www.biorxiv.org
    A living vector field reveals constraints on galactose network induction in yeast
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    Distinct Cellular States Determine Calcium Signaling Response
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    An Atlas of Human Kinase Regulation
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    A population-based temporal logic gate for timing and recording chemical events
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    Determinants of RNA metabolism in the Schizosaccharomyces pombe genome
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    Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
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    Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria
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    Measuring error rates in genomic perturbation screens: gold standards for human functional genomics
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  69. Feb 2019
  70. dougengelbart.org dougengelbart.org
    Augmenting Human Intellect: A Conceptual Framework - 1962 (AUGMENT,3906,) - Doug Engelbart Institute
    1
    1. Gardener 14 Feb 2019
      The Two Sides of the H-LAM/T System

      When I view this diagram, I am reminded of Robert Rosen's Modeling Relation, an image of which is here The Modeling Relation grew out of research in Relational Biology which was the first mathematical biology to recognize that relations among organism components and between those components and the environment are key to understanding complex adaptive systems.

      Complex Adaptive Systems Relational Biology Modeling Relation
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  71. Jan 2019
  72. www.quora.com www.quora.com
    (1) How can I start learning about systems biology? - Quora
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    1. Maciej_Motyka 09 Jan 2019
      In my opinion if you can get enrolled into a degree program for systems biology then that would be best. However, if you are just exploring the field on your own I would recommend going through these resources.Video lectures by Uri AlonVideo Lectures by Jeff GorePrinciples of Synthetic Biology (at edx)Coursera specialization on systems biology.If you are looking for mathematical intensive start with first 2 and if you are looking for biologically intensive begin with last 2. Either way go through all 4 of them as they provide diverse perspective on systems biology which is very important. As you will move through these materials all the necessary supplementary information like books, papers and softwares will be informed within these materials itself.Hope this helps!
      bioinformatics online learning systems biology
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  73. Dec 2017
  74. www.nature.com www.nature.com
    Statistical and integrative system-level analysis of DNA methylation data
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    1. rschulz 14 Dec 2017
      Statistical and integrative system-level analysis of DNA methylation data
      DNA-methylation systems-biology epigenetics review data-analysis
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    nature.com/articles/nrg.2017.86