113 Matching Annotations
  1. Feb 2021
  2. www.biorxiv.org www.biorxiv.org
    Using single-plant -omics in the field to link maize genes to functions and phenotypes
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    biorxiv.org/content/10.1101/2020.04.06.027300v1
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    A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids
    1
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    biorxiv.org/content/10.1101/2020.07.24.219659v1
  4. www.biorxiv.org www.biorxiv.org
    DOMINO: a novel network-based module detection algorithm with reduced rate offalse calls
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    biorxiv.org/content/10.1101/2020.03.10.984963v4
  5. www.biorxiv.org www.biorxiv.org
    Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
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    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.04.23.057893v1
  6. www.biorxiv.org www.biorxiv.org
    Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models
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    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/532895v2
  7. www.biorxiv.org www.biorxiv.org
    Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration
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    1. EMBOpress 25 Feb 2021

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      PeerReviewed EMBOPress Molecular Systems Biology neuroscience
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    biorxiv.org/content/10.1101/2020.05.12.090688v1
  8. www.biorxiv.org www.biorxiv.org
    CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.10.03.324715v1
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    Dormancy as a spectrum measuring spore’s proximity to death and to replicative life
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    biorxiv.org/content/10.1101/747766v2
  10. www.biorxiv.org www.biorxiv.org
    The transcriptome dynamics of single cells during the cell cycle
    1
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    biorxiv.org/content/10.1101/2019.12.23.887570v1
  11. www.biorxiv.org www.biorxiv.org
    Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.02.10.942276v1
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    Oncogenic mutant RAS activity is rescaled by the ERK/MAPK pathway
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.02.17.952093v1
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    CEN-tools: An integrative platform to identify the contexts of essential genes
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.05.10.087668v2
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    Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.05.03.074815v1
  15. www.biorxiv.org www.biorxiv.org
    Aggregation and Disaggregation Features of the Human Proteome
    1
    1. EMBOpress 25 Feb 2021

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    biorxiv.org/content/10.1101/2020.02.05.931675v1
  16. Oct 2020
  17. www.biorxiv.org www.biorxiv.org
    Programmable and portable CRISPR-Cas transcriptional activation in bacteria
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/2020.01.03.882431v2
  18. www.biorxiv.org www.biorxiv.org
    State transitions of a developmental oscillator
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/755421v2
  19. www.biorxiv.org www.biorxiv.org
    Predicting antigen-specificity of single T-cells based on TCR CDR3 regions
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/734053v1
  20. www.biorxiv.org www.biorxiv.org
    Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder
    1
    1. EMBOpress 06 Oct 2020

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      PeerReviewed EMBOPress Molecular Systems Biology cell biology
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    biorxiv.org/content/10.1101/2020.01.30.923003v3
  21. www.biorxiv.org www.biorxiv.org
    https://doi.org/10.1101/2020.03.31.016048
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/2020.03.31.016048v2
  22. www.biorxiv.org www.biorxiv.org
    The protein architecture of the endocytic coat analyzed by FRET
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/480996v1
  23. www.biorxiv.org www.biorxiv.org
    Multiplexing cell-cell communication
    1
    1. EMBOpress 06 Oct 2020

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    biorxiv.org/content/10.1101/584664v1
  24. www.biorxiv.org www.biorxiv.org
    Hormonal dysregulation after prolonged HPA axis activation can be explained by changes of adrenal and corticotroph masses
    1
    1. EMBOpress 06 Oct 2020

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      PeerReviewed EMBOPress Molecular Systems Biology physiology
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    biorxiv.org/content/10.1101/2020.01.01.892596v2
  25. Jul 2020
  26. www.biorxiv.org www.biorxiv.org
    Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/2020.01.14.905729v1
  27. www.biorxiv.org www.biorxiv.org
    Using deep mutational scanning data to benchmark computational phenotype predictors and identify pathogenic missense mutations
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/855957v2
  28. www.biorxiv.org www.biorxiv.org
    Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/577478v3
  29. www.biorxiv.org www.biorxiv.org
    Exploring endocytic compartment morphology with systematic genetics and single cell image analysis
    1
    1. EMBOpress 15 Jul 2020

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      PeerReviewed EMBOPress Molecular Systems Biology cell biology
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    biorxiv.org/content/10.1101/724989v1
  30. www.biorxiv.org www.biorxiv.org
    STAT3-dependent systems-level analysis reveals PDK4 as an independent predictor of biochemical recurrence in prostate cancer
    1
    1. EMBOpress 15 Jul 2020

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      PeerReviewed EMBOPress Molecular Systems Biology cancer biology
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    biorxiv.org/content/10.1101/770701v1
  31. www.biorxiv.org www.biorxiv.org
    Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/849711v1
  32. www.biorxiv.org www.biorxiv.org
    CRISPR-TAPE: protein-centric CRISPR guide design for targeted proteome engineering
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/2020.02.26.965889v1
  33. www.biorxiv.org www.biorxiv.org
    Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation
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    1. EMBOpress 15 Jul 2020

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      PeerReviewed EMBOPress Molecular Systems Biology plant biology
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    biorxiv.org/content/10.1101/741314v2
  34. www.biorxiv.org www.biorxiv.org
    Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/682302v1
  35. www.biorxiv.org www.biorxiv.org
    Digitalizing heterologous gene expression in Gram-negative bacteria with a portable on/off module
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/783506v1
  36. www.biorxiv.org www.biorxiv.org
    Machine characterization of rat toxin responses identifies disease states, tolerance mechanisms and organ to whole-body communication
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/322446v1
  37. www.biorxiv.org www.biorxiv.org
    The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/487439v1
  38. www.biorxiv.org www.biorxiv.org
    Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency
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    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/679449v1
  39. www.biorxiv.org www.biorxiv.org
    Robust and conserved stochastic self-assembly mechanism for dynamic ParB-parS partition complexes on bacterial chromosomes and plasmids
    1
    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/345066v1
  40. www.biorxiv.org www.biorxiv.org
    Temporal perturbation of Erk dynamics reveals network architecture of FGF2-MAPK signaling
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    1. EMBOpress 15 Jul 2020

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    biorxiv.org/content/10.1101/629287v1
  41. Jun 2020
  42. 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
    1
    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/770768v1
  43. www.biorxiv.org www.biorxiv.org
    Regulatory kinase genetic interaction profiles differ between environmental conditions and cellular states
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    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/735720v1
  44. www.biorxiv.org www.biorxiv.org
    Impact of C-terminal amino acid composition on protein expression in bacteria
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    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/751305v1
  45. www.biorxiv.org www.biorxiv.org
    Translational efficiency across healthy and tumor tissues is proliferation-related
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    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/782227v1
  46. www.biorxiv.org www.biorxiv.org
    Time-resolved genome-scale profiling reveals a causal expression network
    1
    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/619577v2
  47. www.biorxiv.org www.biorxiv.org
    Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
    1
    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/422998v1
  48. www.biorxiv.org www.biorxiv.org
    Mammalian gene expression variability is explained by underlying cell state
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    1. EMBOpress 04 Jun 2020

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    biorxiv.org/content/10.1101/626424v1
  49. May 2020
  50. 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
  51. Jan 2020
  52. www.lesswrong.com www.lesswrong.com
    Book Review: Design Principles of Biological Circuits - LessWrong 2.0
    1
    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
  53. Nov 2019
  54. www.biorxiv.org www.biorxiv.org
    Sufficiency analysis of estrogen responsive enhancers using synthetic activators
    1
    1. EMBOpress 26 Nov 2019

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      PeerReviewed EMBOPress Life Science Alliance systems biology
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    biorxiv.org/content/10.1101/479709v2
  55. 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
  56. www.biorxiv.org www.biorxiv.org
    Estrogen receptor alpha controls gene expression via translational offsetting
    1
    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
  57. 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
  58. 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
  59. www.biorxiv.org www.biorxiv.org
    An integrated workflow for cross-linking/mass spectrometry
    1
    1. EMBOpress 26 Nov 2019

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  60. 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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    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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    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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    CRISPR/Cas9 screening using unique molecular identifiers
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    In Situ Genotyping Of A Pooled Strain Library After Characterizing Complex Phenotypes
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    A Theory That Predicts Behaviors Of Disordered Cytoskeletal Networks
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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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    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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    biorxiv.org/content/10.1101/029967v1
  115. www.biorxiv.org www.biorxiv.org
    Determinants of RNA metabolism in the Schizosaccharomyces pombe genome
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    biorxiv.org/content/10.1101/025585v1
  116. www.biorxiv.org www.biorxiv.org
    Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
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    biorxiv.org/content/10.1101/032797v1
  117. www.biorxiv.org www.biorxiv.org
    Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria
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    biorxiv.org/content/10.1101/001008v3
  118. www.biorxiv.org www.biorxiv.org
    Measuring error rates in genomic perturbation screens: gold standards for human functional genomics
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  119. Feb 2019
  120. 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