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  1. Mapping parameter spaces of biological switches

    Publication
    Since the seminal 1961 paper of Monod and Jacob, mathematical models of biomolecular circuits have guided our understanding of cell regulation. Model-based exploration of the functional capabilities …

  2. Mapping parameter spaces of biological switches

    Publication
    Since the seminal 1961 paper of Monod and Jacob, mathematical models of biomolecular circuits have guided our understanding of cell regulation. Model-based exploration of the functional capabilities …

  3. From heterogeneous datasets to predictive models of embryonic development

    Publication
    Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing, and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these …

  4. Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability

    Publication
    Adhesion-mediated cell sorting has long been considered an organizing principle in developmental biology. While most computational models have emphasized the dynamics of segregation to fully sorted structures …

  5. From heterogeneous datasets to predictive models of embryonic development

    Publication
    Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing, and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these …

  6. An “individualist” model of an active genome in a developing embryo

    Publication
    The early Drosophila embryo provides unique experimental advantages for addressing fundamental questions of gene regulation at multiple levels of organization, from individual gene loci to the whole genome …

  7. Mechanics of a multilayer epithelium instruct tumour architecture and function

    Publication
    Loss of normal tissue architecture is a hallmark of oncogenic transformation1. In developing organisms, tissues architectures are sculpted by mechanical forces during morphogenesis2. However, the origins and consequences …

  8. Template-based mapping of dynamic motifs in tissue morphogenesis

    Publication
    Tissue morphogenesis relies on repeated use of dynamic behaviors at the levels of intracellular structures, individual cells, and cell groups. Rapidly accumulating live imaging datasets make it increasingly …

  9. Template-based mapping of dynamic motifs in tissue morphogenesis

    Publication
    Tissue morphogenesis relies on repeated use of dynamic behaviors at the levels of intracellular structures, individual cells, and cell groups. Rapidly accumulating live imaging datasets make it increasingly …

  10. Optogenetic Rescue of a Patterning Mutant

    Publication
    Animal embryos are patterned by a handful of highly conserved inductive signals. Yet, in most cases, it is unknown which pattern features (i.e., spatial gradients or temporal …

  11. Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes

    Publication
    The famous Arrhenius equation is well motivated to describe the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how …

  12. Excess dNTPs Trigger Oscillatory Surface Flow in the Early Drosophila Embryo

    Publication
    During the first 2 hours of Drosophila development, precisely orchestrated nuclear cleavages, cytoskeletal rearrangements, and directed membrane growth lead to the formation of an epithelial sheet around the …

  13. Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua

    Publication
    Optogenetic perturbations, live imaging, and time-resolved ChIP-seq assays in Drosophila embryos were used to dissect the ERK-dependent control of the HMG-box repressor Capicua (Cic …

  14. Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations

    Publication
    Multisite protein phosphorylation plays a critical role in cell regulation [1, 2, 3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order …

  15. Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations

    Publication
    Multisite protein phosphorylation plays a critical role in cell regulation [1, 2, 3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order …

  16. The design and logic of terminal patterning in Drosophila

    Publication
    Terminal regions of the early Drosophila embryo are patterned by the highly conserved ERK cascade, giving rise to the nonsegmented terminal structures of the future larva. In less …

  17. Activation-induced substrate engagement in ERK signaling

    Publication
    The extracellular signal-regulated kinase (ERK) pathway is an essential component of developmental signaling in metazoans. Previous models of pathway activation suggested that dissociation of activated dually phosphorylated …