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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 Allosteric Regulation
Concept Genes, Homeobox
Concept Genes, Regulator
Concept Lac Operon
Concept Gene Expression Regulation
Concept Genes, Switch
Concept Genes
Concept Multigene Family
Concept Genome
Concept Gene Rearrangement
Concept Gene Expression
Concept Genes, Reporter
Concept Gene Expression Regulation, Developmental
Concept Gene Regulatory Networks
Concept Gene Expression Profiling
Concept Gene Silencing
Concept Gene Dosage
Concept Transcriptome
Concept Gene Expression Regulation, Neoplastic
Concept Genes, Insect
Concept Genetic Loci
Academic Article Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity.
Academic Article Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila.
Academic Article Mechanism of eve stripe formation.
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 Registration of the expression patterns of Drosophila segmentation genes by two independent methods.
Academic Article Spatio-temporal registration of the expression patterns of Drosophila segmentation genes.
Academic Article Prediction of mutant expression patterns using gene circuits.
Academic Article Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient.
Academic Article Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila.
Academic Article HOX Pro: a specialized database for clusters and networks of homeobox genes.
Academic Article Characterization of the Drosophila segment determination morphome.
Academic Article Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method.
Academic Article Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins.
Academic Article Dynamic control of positional information in the early Drosophila embryo.
Academic Article A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ.
Academic Article A high-throughput method for quantifying gene expression data from early Drosophila embryos.
Academic Article A database for management of gene expression data in situ.
Academic Article Reverse engineering the gap gene network of Drosophila melanogaster.
Academic Article Removal of background signal from in situ data on the expression of segmentation genes in Drosophila.
Academic Article Stripe forming architecture of the gap gene system.
Academic Article Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila.
Academic Article Thoracic patterning by the Drosophila gap gene hunchback.
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 Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images.
Academic Article Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
Academic Article On the dynamic nature of positional information.
Academic Article Mechanisms of gap gene expression canalization in the Drosophila blastoderm.
Academic Article [Methods for acquisition of quantitative from confocal images of gene expression in situ].
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 Preparation of Drosophila embryos for quantitative imaging of gene expression.
Academic Article Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants.
Academic Article Modeling of gap gene expression in Drosophila Kruppel mutants.
Academic Article Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic.
Academic Article Quantitative imaging of gene expression in Drosophila embryos.
Academic Article A connectionist model of development.
Academic Article Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns.
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 FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution.
Academic Article GCPReg package for registration of the segmentation gene expression data in Drosophila.
Academic Article Drosophila blastoderm patterning.
Academic Article A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.
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 Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster.
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 Methods for Acquisition of Quantitative Data from Confocal Images of Gene Expression in situ.
Academic Article How gap genes make their domains: An analytical study based on data driven approximations.
Academic Article Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation.
Academic Article Physical implications of so(2, 1) symmetry in exact solutions for a self-repressing gene.
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
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