91 Matching Annotations
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    Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens
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    biorxiv.org/content/10.1101/2020.01.14.905729v1
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    Using deep mutational scanning data to benchmark computational phenotype predictors and identify pathogenic missense mutations
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    biorxiv.org/content/10.1101/855957v2
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    Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
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    biorxiv.org/content/10.1101/577478v3
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    Exploring endocytic compartment morphology with systematic genetics and single cell image analysis
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    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/724989v1
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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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    biorxiv.org/content/10.1101/770701v1
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    Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch
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    biorxiv.org/content/10.1101/849711v1
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    CRISPR-TAPE: protein-centric CRISPR guide design for targeted proteome engineering
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    biorxiv.org/content/10.1101/2020.02.26.965889v1
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    Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation
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    biorxiv.org/content/10.1101/741314v2
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    Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor
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    biorxiv.org/content/10.1101/682302v1
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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
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    Machine characterization of rat toxin responses identifies disease states, tolerance mechanisms and organ to whole-body communication
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    biorxiv.org/content/10.1101/322446v1
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    The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
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    biorxiv.org/content/10.1101/487439v1
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    Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency
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    biorxiv.org/content/10.1101/679449v1
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    Robust and conserved stochastic self-assembly mechanism for dynamic ParB-parS partition complexes on bacterial chromosomes and plasmids
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    biorxiv.org/content/10.1101/345066v1
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    Temporal perturbation of Erk dynamics reveals network architecture of FGF2-MAPK signaling
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    biorxiv.org/content/10.1101/629287v1
  17. Jun 2020
  18. www.biorxiv.org www.biorxiv.org
    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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    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/770768v1
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    Regulatory kinase genetic interaction profiles differ between environmental conditions and cellular states
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    biorxiv.org/content/10.1101/735720v1
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    Impact of C-terminal amino acid composition on protein expression in bacteria
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    biorxiv.org/content/10.1101/751305v1
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    Translational efficiency across healthy and tumor tissues is proliferation-related
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    biorxiv.org/content/10.1101/782227v1
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    Time-resolved genome-scale profiling reveals a causal expression network
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    biorxiv.org/content/10.1101/619577v2
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    Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
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    biorxiv.org/content/10.1101/422998v1
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    Mammalian gene expression variability is explained by underlying cell state
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    biorxiv.org/content/10.1101/626424v1
  25. May 2020
  26. journals.plos.org journals.plos.org
    Flocking in complex environments—Attention trade-offs in collective information processing
    1
    1. edampf 29 May 2020

      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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    journals.plos.org/ploscompbiol/article
  27. Jan 2020
  28. 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
  29. Nov 2019
  30. www.biorxiv.org www.biorxiv.org
    Sufficiency analysis of estrogen responsive enhancers using synthetic activators
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    biorxiv.org/content/10.1101/479709v2
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    Combinatorial prediction of gene-marker panels from single-cell transcriptomic data.
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    biorxiv.org/content/10.1101/655753v2
  32. www.biorxiv.org www.biorxiv.org
    Estrogen receptor alpha controls gene expression via translational offsetting
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    biorxiv.org/content/10.1101/507574v1
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    Paralog dependency indirectly affects the robustness of human cells
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    biorxiv.org/content/10.1101/552208v3
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    Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions
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    biorxiv.org/content/10.1101/299073v3
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    An integrated workflow for cross-linking/mass spectrometry
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    biorxiv.org/content/10.1101/355396v2
  36. Sep 2019
  37. www.biorxiv.org www.biorxiv.org
    Hierarchical organization of the human cell from a cancer coessentiality network
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    biorxiv.org/content/10.1101/328880v1
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    An integrative machine learning approach for prediction of toxicity-related drug safety
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    biorxiv.org/content/10.1101/455667v1
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    Co-existing feedback loops generate tissue-specific circadian rhythms
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    biorxiv.org/content/10.1101/304451v1
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    Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
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    biorxiv.org/content/10.1101/250167v1
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    Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO)
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    biorxiv.org/content/10.1101/368282v1
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    Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system
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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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    biorxiv.org/content/10.1101/338939v2
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    Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory networks
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    biorxiv.org/content/10.1101/184325v2
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    The fitness cost and benefit of phase separated protein deposits
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    biorxiv.org/content/10.1101/574657v2
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    Defining the RNA Interactome by Total RNA-Associated Protein Purification
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    biorxiv.org/content/10.1101/436253v1
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    Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy
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    biorxiv.org/content/10.1101/284240v2
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    Evidence that the cell cycle is a series of uncoupled, memoryless phases
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    biorxiv.org/content/10.1101/283614v1
  49. www.biorxiv.org www.biorxiv.org
    netDx: Patient classification using integrated patient similarity networks
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    biorxiv.org/content/10.1101/084418v4
  50. 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
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    Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues
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    biorxiv.org/content/10.1101/353763v1
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    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
  53. 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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    biorxiv.org/content/10.1101/335380v2
  54. 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
  55. 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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    biorxiv.org/content/10.1101/369751v1
  56. www.biorxiv.org www.biorxiv.org
    Functional Compensation Between Hematopoietic Stem Cells In Vivo
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/236398v1
  57. 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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    biorxiv.org/content/10.1101/314922v1
  58. www.biorxiv.org www.biorxiv.org
    Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming
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    1. EMBOpress 22 Sep 2019

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    biorxiv.org/content/10.1101/197376v1
  59. www.biorxiv.org www.biorxiv.org
    Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations
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    1. EMBOpress 22 Sep 2019

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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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    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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    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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    High-throughput CRISPRi phenotyping in Streptococcus pneumoniae identifies new essential genes involved in cell wall synthesis and competence development
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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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  95. Feb 2019
  96. dougengelbart.org dougengelbart.org
    Augmenting Human Intellect: A Conceptual Framework - 1962 (AUGMENT,3906,) - Doug Engelbart Institute
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    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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  97. Jan 2019
  98. 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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  99. Dec 2017
  100. www.nature.com www.nature.com
    Statistical and integrative system-level analysis of DNA methylation data
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      Statistical and integrative system-level analysis of DNA methylation data
      DNA-methylation systems-biology epigenetics review data-analysis
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