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Automated annotation of Drosophila gene expression patterns using a controlled vocabulary

Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, Jieping Ye
2008 Computer applications in the biosciences : CABIOS  
An atlas for the gene expression patterns of fruit fly Drosophila melanogaster has been created by whole-mount in situ hybridization, and it documents the dynamic changes of gene expression pattern during  ...  We propose to extract invariant features from images, and construct pyramid match kernels to measure the similarity between sets of patterns.  ...  for help with access to the gene expression data.  ... 
doi:10.1093/bioinformatics/btn347 pmid:18632750 pmcid:PMC2519157 fatcat:cgpbgo2ifbeztazd7t7plb3j7u

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models

Iulian Pruteanu-Malinici, Daniel L. Mace, Uwe Ohler, Joel S. Bader
2011 PLoS Computational Biology  
We have developed a sparse Bayesian factor analysis model in which the observed expression diversity of among a large set of high-dimensional images is modeled by a small number of hidden common factors  ...  We apply this approach on embryonic expression patterns from a Drosophila RNA in situ image database, and show that the automatically inferred factors provide for a meaningful decomposition and represent  ...  Acknowledgments We thank Erwin Frise for assistance with the data used in this paper. We also thank Pavel Tomancak and Manonmani Arunachalam for helpful comments. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002098 pmid:21814502 pmcid:PMC3140966 fatcat:mi7otvvznfdzvc4jqxlpmxuld4

A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development

Stefano Ceolin, Monika Hanf, Marta Bozek, Andrea Ennio Storti, Nicolas Gompel, Ulrich Unnerstall, Christophe Jung, Ulrike Gaul
2020 Communications Biology  
We derive enhancer activity from the reporter fluorescence dynamics with high spatial and temporal resolution, using a robust reconstruction algorithm.  ...  The rapid temporal dynamics of gene expression during early stages of development, however, are difficult to track with standard techniques.  ...  Acknowledgements We dedicate this publication to the memory of Prof. Ulrike Gaul who passed away after a long illness during the review of the manuscript.  ... 
doi:10.1038/s42003-020-01375-5 pmid:33184447 fatcat:yycadif6r5bjhhqwoqnydyldty

Bioimage Informatics in the context of Drosophila research

Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
2014 Methods  
Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes.  ...  The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging  ...  Quantitative analysis of the data was facilitated by registering all acquired 3D images into a composite Virtual Embryo using a reference gene expression pattern common to all embryos.  ... 
doi:10.1016/j.ymeth.2014.04.004 pmid:24732429 fatcat:trrhw3bzyjaoljxp7ockcnkdeu

From whole-mount to single-cell spatial assessment of gene expression in 3D

Lisa N. Waylen, Hieu T. Nim, Luciano G. Martelotto, Mirana Ramialison
2020 Communications Biology  
Unravelling spatio-temporal patterns of gene expression is crucial to understanding core biological principles from embryogenesis to disease.  ...  These approaches digitally reconstruct patterns of embryonic expression in three dimensions, and have successfully identified novel domains of expression, cell types, and tissue features.  ...  The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government.  ... 
doi:10.1038/s42003-020-01341-1 pmid:33097816 fatcat:zdbbtgfiufhihc7nldbcxgnoxm

Development, evolution, and corroboration

Daniel Janies, Rob DeSalle
1999 The Anatomical Record  
Expression data have become technical commonplace in analysis of mutants of Drosophila melanogaster and a handful of other genetic model systems.  ...  Second, we examine epistemological issues surrounding the descriptive visualization of gene expression patterns.  ...  In short, a particular set of end-points constituting the pattern do not unambiguously designate the dynamic processes that generated the pattern.  ... 
doi:10.1002/(sici)1097-0185(19990215)257:1<6::aid-ar4>;2-i pmid:10333399 fatcat:t25q4cr47rfvna626o7r3yw2yy

Growth zone segmentation in the milkweed bug Oncopeltus fasciatus sheds light on the evolution of insect segmentation

Tzach Auman, Ariel D. Chipman
2018 BMC Evolutionary Biology  
We present a detailed analysis of the segmentation cascade of the milkweed bug Oncopletus fasciatus, an insect with a more primitive segmentation mode, as a comparison to Drosophila, with the aim of reconstructing  ...  This pattern is carried anteriorly by a series of secondary pair-rule genes, expressed in the transition between the growth zone and the segmented germband.  ...  Funding This work was funded by a grant from the NSF / BSF IOS program: BSF 2012763, and by an Israel Science Foundation grant #120/16.  ... 
doi:10.1186/s12862-018-1293-z pmid:30486779 fatcat:2ksq5va6wvbanim22v7jv3oxni

Automatic image analysis for gene expression patterns of fly embryos

Hanchuan Peng, Fuhui Long, Jie Zhou, Garmay Leung, Michael B Eisen, Eugene W Myers
2007 BMC Cell Biology  
Results We have developed algorithms and associated software that extracts a feature representation of a gene expression pattern from an ISH image, that clusters genes sharing the same spatio-temporal  ...  regions that express a gene given a training set of annotations.  ...  Acknowledgements We thank BDGP for providing the data used in this study.  ... 
doi:10.1186/1471-2121-8-s1-s7 pmid:17634097 pmcid:PMC1924512 fatcat:lwt5bamftfezdiattp4ir44cpq

Towards 3D in silico modeling of the sea urchin embryonic development

Barbara Rizzi, Nadine Peyrieras
2013 Journal of chemical biology  
The latter includes the effect of high-level phenotypic features, such as tissue biomechanics on biochemical processes and on the regulation of gene expression.  ...  We discuss here the progress that has been made in this direction, starting with the reconstruction over time of three-dimensional digital embryos from in toto time-lapse imaging.  ...  Acknowledgments We thank Louise Duloquin for the time-lapse imaging of live sea urchin embryos and our collaborators at the BioEmergences platform for their contribution.  ... 
doi:10.1007/s12154-013-0101-x pmid:24386014 pmcid:PMC3877407 fatcat:bfpdzurerzebdih7cdvstnjpbm

Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

Jeremy B. Rothschild, Panagiotis Tsimiklis, Eric D. Siggia, Paul François, Claude Desplan
2016 PLoS Genetics  
The expression pattern of gap genes has evolved between Drosophila (fly) and Anopheles (mosquito), yet one of their targets, eve, has remained invariant.  ...  We use an evolutionary algorithm to reconstruct and predict dynamics of genes controlling stripes in the last common ancestor of fly and mosquito.  ...  Acknowledgments We thank Erik Clark for help with the literature on AP patterning mutants and Michael Akam and Eric Weischaus for discussions. Author Contributions  ... 
doi:10.1371/journal.pgen.1006052 pmid:27227405 pmcid:PMC4882032 fatcat:5izv5c23tfb65jb56luu5rncbq

Reconstructing regulatory network transitions

Jalean J. Petricka, Philip N. Benfey
2011 Trends in Cell Biology  
A transition from a stem cell to differentiated cell state, for example, may occur in response to gene expression changes induced by a transcription factor, or signaling cascades triggered by a hormone  ...  We describe recent regulatory network reconstructions in a variety of organisms and discuss the success they share in identifying new regulatory components as well as shared relationships and phenotypic  ...  A genetic regulatory network was then reconstructed in which connections denoted genes sharing similar genetic interaction profiles or a common set of genetic interactions.  ... 
doi:10.1016/j.tcb.2011.05.001 pmid:21632251 pmcid:PMC3149721 fatcat:7bi7tdqt2rhtzdzo2r7jlyt6cm

A combinatorial code of transcription factors specifies subtypes of visual motion-sensing neurons in Drosophila

Nikolai Hoermann, Tabea Schilling, Aicha Haji Ali, Etienne Serbe, Christian Mayer, Alexander Borst, Jesús Pujol-Martí
2020 Development  
projection pattern.  ...  This revealed a simple and stable combinatorial code of transcription factors defining the four T4/T5 subtypes during their development.  ...  Desplan, A. Garces, the Bloomington Drosophila Stock Center, the Vienna Drosophila Stock Center and the Developmental Studies Hybridoma Bank for flies and antibodies. We also thank M.  ... 
doi:10.1242/dev.186296 pmid:32238425 pmcid:PMC7240302 fatcat:2nkv3sgxozhirg6udrty4hnkha

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

Zixuan Cang, Qing Nie
2020 Nature Communications  
We present SpaOTsc, a method relying on structured optimal transport to recover spatial properties of scRNA-seq data by utilizing spatial measurements of a relatively small number of genes.  ...  Four datasets are employed for cross-validation of spatial gene expression prediction and comparison to known cell-cell communications.  ...  Acknowledgements This work was supported by an NIH grant U01AR073159, an NSF grant DMS1763272, and a grant from the Simons Foundation (594598, QN).  ... 
doi:10.1038/s41467-020-15968-5 pmid:32350282 fatcat:aricuh3k6rgeldbm6boqyysp5y

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

Daniel J. McKay, Jason D. Lieb
2013 Developmental Cell  
Bautch for providing the infrastructure for Drosophila work and for commenting on the manuscript. This work was supported in part by a grant from the National Institutes of Health (F32GM090759).  ...  Struhl, and A. Laughon for sharing reagents, P. Giresi, J. Simon, and S. Pott for technical assistance, and B. Duronio, M. Peifer, G. Matera, and V.  ...  Moreover, the Drosophila appendage master regulators share a common evolutionary origin with the master regulators of vertebrate limb development (Mann and Carroll, 2002) , suggesting that the concept  ... 
doi:10.1016/j.devcel.2013.10.009 pmid:24229644 pmcid:PMC3866527 fatcat:v6gk7ayr5bhgrjlwq6gdrvl5qu

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

Carlos Castro-González, Miguel A. Luengo-Oroz, Louise Duloquin, Thierry Savy, Barbara Rizzi, Sophie Desnoulez, René Doursat, Yannick L. Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, Andrés Santos (+1 others)
2014 PLoS Computational Biology  
With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates  ...  This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization  ...  Acknowledgments The authors would like to thank CC-IN2P3, Pascal Calvat and Jean-Yves Nief for support with data transfer, data storage, hosting and maintenance of the BioEmergences workflow, Ingrid Colin  ... 
doi:10.1371/journal.pcbi.1003670 pmid:24945246 pmcid:PMC4063669 fatcat:e6w7c4hikbbjfghtlisru7dj7e
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