Publications (113)1065.78 Total impact
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Article: A High Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns in Caenorhabditis elegans.
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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 methods to extract this spatiotemporal expression data is a difficult problem that often employs complex domain specific methods for each individual data set. We present a more unified approach that incorporates general prior 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 sub-specification becomes apparent. Unlike previous methods that often use custom approaches that are organism specific, our method employs 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 prior information into the model for similar difficult high-fidelity/low error tolerance image analysis problems for systematically applied genomic experiments.G3 (Bethesda, Md.). 03/2013; -
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Institutions
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2003–2013
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University of Washington Seattle
- Department of Genome Sciences
Seattle, WA, USA
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2009
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Lawrence Berkeley National Laboratory
Berkeley, CA, USA
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2000–2005
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Washington University in St. Louis
- Department of Genetics
Saint Louis, MO, USA
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2001–2003
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Howard Hughes Medical Institute
Chevy Chase, MD, USA
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1997–2003
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Cold Spring Harbor Laboratory
Cold Spring Harbor, NY, USA
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