ArticleeLife2013
Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Article in eLife, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Hybrid deep learning-mechanistic modeling of cellular dynamics from a spatiotemporal single-cell atlas.bioRxiv : the preprint server for biology · 2025Article
- Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development.Genetics · 2025Article
- From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation.Frontiers in cell and developmental biology · 2025Article
- Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes.Development (Cambridge, England) · 2024Article
- Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.Mathematical biosciences · 2021Article
- Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks.Nucleic acids research · 2021Article
- Enhancer grammar in development, evolution, and disease: dependencies and interplay.Developmental cell · 2021Review
- Fully interpretable deep learning model of transcriptional control.Bioinformatics (Oxford, England) · 2020Article
- Multimodal transcriptional control of pattern formation in embryonic development.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of FiveG3 (Bethesda, Md.) · 2019Article
- Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.PLoS genetics · 2018Article
- Allele-specific expression elucidates cis-regulatory logic.PLoS genetics · 2018Article
- Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos.PLoS genetics · 2018Article
- Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.Cell reports · 2017Article
- Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors.Nature genetics · 2016Article
- Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration.PLoS computational biology · 2015Article
- A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate.Development (Cambridge, England) · 2015Article
- Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications.Frontiers in cell and developmental biology · 2015Article
- Estimating binding properties of transcription factors from genome-wide binding profiles.Nucleic acids research · 2015Article
Corrections and comments
- Commented on by
Authors and funding
5 authors.
Funding
Abstract
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve's complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI:http://dx.doi.org/10.7554/eLife.00522.001.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.