ArticleG3 (Bethesda, Md.)2013
A high-fidelity cell lineage tracing method for obtaining systematic spatiotemporal gene expression patterns in Caenorhabditis elegans.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Article
- Extensive programmed centriole elimination unveiled inScience advances · 2023Article
- Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy.Genetics · 2022Review
- The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo.PLoS genetics · 2022Article
- An Exact Hypergraph Matching algorithm for posture identification in embryonic C. elegans.PloS one · 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
- Tools and Concepts for Interrogating and Defining Cellular Identity.Cell stem cell · 2020Review
- Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans.Lab animal · 2019Review
- Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time.Genesis (New York, N.Y. : 2000) · 2016Review
- Overlapping cell population expression profiling and regulatory inference in C. elegans.BMC genomics · 2016Article
- WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.BMC bioinformatics · 2015Article
- The Bicoid class homeodomain factors ceh-36/OTX and unc-30/PITX cooperate in C. elegans embryonic progenitor cells to regulate robust development.PLoS genetics · 2015Article
- Identification of genes driving lineage divergence from single-cell gene expression data in C. elegans.Developmental biology · 2014Article
- Article
- A semi-local neighborhood-based framework for probabilistic cell lineage tracing.BMC bioinformatics · 2014Article
- Article
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5 authors.
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Abstract
Advances in microscopy and fluorescent reporters have allowed us to detect the onset of gene expression on a cell-by-cell basis in a systemic fashion. This information, however, is often encoded in large repositories of images, and developing ways to extract this spatiotemporal expression data is a difficult problem that often uses complex domain-specific methods for each individual data set. We present a more unified approach that incorporates general previous information into a hierarchical probabilistic model to extract spatiotemporal gene expression from 4D confocal microscopy images of developing Caenorhabditis elegans embryos. This approach reduces the overall error rate of our automated lineage tracing pipeline by 3.8-fold, allowing us to routinely follow the C. elegans lineage to later stages of development, where individual neuronal subspecification becomes apparent. Unlike previous methods that often use custom approaches that are organism specific, our method uses generalized linear models and extensions of standard reversible jump Markov chain Monte Carlo methods that can be readily extended to other organisms for a variety of biological inference problems relating to cell fate specification. This modeling approach is flexible and provides tractable avenues for incorporating additional previous information into the model for similar difficult high-fidelity/low error tolerance image analysis problems for systematically applied genomic experiments.
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