ArticleBioinformatics (Oxford, England)2010
SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 37 citations in OpenAlex.
- Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis.IEEE transactions on big data · 2020Article
- Predicting gene regulatory interactions based on spatial gene expression data and deep learning.PLoS computational biology · 2019Article
- New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images.PLoS computational biology · 2018Article
- A geometric method for contour extraction of Drosophila embryos.BMC systems biology · 2017Article
- TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples.Statistics in biosciences · 2017Article
- Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.Integrative biology : quantitative biosciences from nano to macro · 2015Article
- High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.Nature biotechnology · 2015Article
- myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos.Bioinformatics (Oxford, England) · 2014Article
- BIOCAT: a pattern recognition platform for customizable biological image classification and annotation.BMC bioinformatics · 2013Article
- A methodology to infer gene networks from spatial patterns of expression--an application to fluorescence in situ hybridization images.Molecular bioSystems · 2013Article
- Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.Bioinformatics (Oxford, England) · 2013Article
- GINI: from ISH images to gene interaction networks.PLoS computational biology · 2013Article
- Joint stage recognition and anatomical annotation of Drosophila gene expression patterns.Bioinformatics (Oxford, England) · 2012Article
- Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval.BMC bioinformatics · 2012Article
- Localizing genes to cerebellar layers by classifying ISH images.PLoS computational biology · 2012Article
- Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.PloS one · 2012Article
- Automatic annotation of spatial expression patterns via sparse Bayesian factor models.PLoS computational biology · 2011Article
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3 authors at 1 institution in 1 country.
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Abstract
motivationMicroarray profiling of mRNA abundance is often ill suited for temporal-spatial analysis of gene expressions in multicellular organisms such as Drosophila. Recent progress in image-based genome-scale profiling of whole-body mRNA patterns via in situ hybridization (ISH) calls for development of accurate and automatic image analysis systems to facilitate efficient mining of complex temporal-spatial mRNA patterns, which will be essential for functional genomics and network inference in higher organisms.
resultsWe present SPEX(2), an automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos. Our pipeline for gene expression pattern extraction outputs the precise spatial locations and strengths of the gene expression. We performed experiments on the largest publicly available collection of Drosophila ISH images, and show that our method achieves excellent performance in automatic image annotation, and also finds clusters that are significantly enriched, both for gene ontology functional annotations, and for annotation terms from a controlled vocabulary used by human curators to describe these images. AVAILABILITY: Software will be available at http://www.sailing.cs.cmu.edu/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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