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One or more keywords matched the following properties of Reinitz, John
overview My laboratory is engaged in a long term project to understand how DNA sequence specifies biological form. We are interested not only in the specification of typical form by a typical genome, but also in the effects of variability. Such variability might take the form of genetic variation in a population or intrinsic fluctuations in an individual. These problems touch on issues central to developmental and evolutionary biology, and efforts to solve them have previously led to the development of new branches of mathematics. We consider these issues in the specific context of segment determination in the fruit fly Drosophila melanogaster, but actively seek collaborations with investigators working on other organisms or with pure theoreticians. The starting point for our own investigations are quantitative data on gene expression, extracted from images of confocally scanned fixed or living embryos. We use this numerical information to find parameter sets for specific models of fundamental processes of gene regulation and pattern formation by means of large scale optimization procedures performed on parallel computers. These models may be specified in terms of DNA sequence or be more coarse-grained. They might take the form of a dynamical system, deterministic or stochastic, or simply be a complex but explicit mathematical function. Our goal is to use every tool in the toolbox—wet experiments, statistics, computational science, and mathematics—to solve a well focused scientific problem: how does a fly go from DNA sequence to a fate map of presumptive segments at single cell resolution?
One or more keywords matched the following items that are connected to Reinitz, John
Item TypeName
Concept Models, Molecular
Concept Models, Genetic
Concept Models, Theoretical
Concept Models, Statistical
Concept Models, Biological
Academic Article Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity.
Academic Article Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback.
Academic Article Automated assay of gene expression at cellular resolution.
Academic Article Spatio-temporal registration of the expression patterns of Drosophila segmentation genes.
Academic Article Dynamic control of positional information in the early Drosophila embryo.
Academic Article Reverse engineering the gap gene network of Drosophila melanogaster.
Academic Article Turing centenary: Pattern formation.
Academic Article Stripe forming architecture of the gap gene system.
Academic Article Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors.
Academic Article [Studies of stability mechanisms of early embryonal development of fruit fly Drosophila].
Academic Article Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
Academic Article Mechanisms of gap gene expression canalization in the Drosophila blastoderm.
Academic Article Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation.
Academic Article Size regulation in the segmentation of Drosophila: interacting interfaces between localized domains of gene expression ensure robust spatial patterning.
Academic Article Modeling of gap gene expression in Drosophila Kruppel mutants.
Academic Article A connectionist model of development.
Academic Article Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster.
Academic Article Developmental biology: a ten per cent solution.
Academic Article [A model with asymptotically stable dynamics for the network of Drosophila gap genes].
Academic Article Drosophila blastoderm patterning.
Academic Article Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.
Academic Article A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design.
Academic Article Gene regulation and noise reduction by coupling of stochastic processes.
Academic Article Punctuated evolution and robustness in morphogenesis.
Academic Article Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.
Academic Article The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.
Academic Article DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.
Academic Article A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.
Academic Article Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.
Academic Article An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.
Academic Article Fully interpretable deep learning model of transcriptional control.
Grant Physiological Model of Gene Regulation in Drosophila
Grant Physiological Model of Gene Regulation in Drosophila
Academic Article The effect of mutational robustness on the evolvability of multicellular organisms and eukaryotic cells.
Academic Article Evolution of biological cooperation: an algorithmic approach.
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