ArticleCell2014
De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis.
Article in Cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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
51 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE.bioRxiv : the preprint server for biology · 2025Article
- Vacuolar HeLife · 2024Article
- A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.Nature communications · 2024Article
- Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development.PLoS computational biology · 2023Article
- Visualizing Phagocytic Cargo In Vivo from Engulfment to Resolution in Caenorhabditis elegans.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Deep distributed computing to reconstruct extremely large lineage trees.Nature biotechnology · 2022Article
- Delineating the mechanisms and design principles ofComputational and structural biotechnology journal · 2022Review
- A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis.Nature methods · 2021Article
- Disabling the Fanconi Anemia Pathway in Stem Cells Leads to Radioresistance and Genomic Instability.Cancer research · 2021Article
- Single-cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos.Molecular systems biology · 2021Article
- Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types.iScience · 2020Article
- Tools and Concepts for Interrogating and Defining Cellular Identity.Cell stem cell · 2020Review
- Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network ofFrontiers in cell and developmental biology · 2020Review
- Data-mining Techniques for Image-based Plant Phenotypic Traits Identification and Classification.Scientific reports · 2019Article
- Using deep reinforcement learning to speed up collective cell migration.BMC bioinformatics · 2019Article
- Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans.Lab animal · 2019Review
- Lineage context switches the function of aDevelopment (Cambridge, England) · 2019Article
- A high-content imaging approach to profileDevelopment (Cambridge, England) · 2019Article
- 'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networks.Genes & development · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Elucidation of complex phenotypes for mechanistic insights presents a significant challenge in systems biology. We report a strategy to automatically infer mechanistic models of cell fate differentiation based on live-imaging data. We use cell lineage tracing and combinations of tissue-specific marker expression to assay progenitor cell fate and detect fate changes upon genetic perturbation. Based on the cellular phenotypes, we further construct a model for how fate differentiation progresses in progenitor cells and predict cell-specific gene modules and cell-to-cell signaling events that regulate the series of fate choices. We validate our approach in C. elegans embryogenesis by perturbing 20 genes in over 300 embryos. The result not only recapitulates current knowledge but also provides insights into gene function and regulated fate choice, including an unexpected self-renewal. Our study provides a powerful approach for automated and quantitative interpretation of complex in vivo information.
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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.