Literature DB >> 22923306

Exploring spatial patterns of gene expression from fruit fly embryogenesis on the iPhone.

Sudhir Kumar1, Kelly Boccia, Michael McCutchan, Jieping Ye.   

Abstract

UNLABELLED: Mobile technologies provide unique opportunities for ubiquitous distribution of scientific information through user-friendly interfaces. Therefore, we have developed a new FlyExpress mobile application that makes available a growing collection (>100 000) of standardized in situ hybridization images containing spatial patterns of gene expression from Drosophila melanogaster (fruit fly) embryogenesis. Using this application, scientists can visualize and compare expression patterns of >4000 developmentally relevant genes. The FlyExpress app displays the expression patterns of the selected gene for different visual projections (e.g. lateral) and displays them according to their developmental stages, which shows a gene's progression of spatial expression over developmental time. Ultimately, we envision the use of FlyExpress app in the laboratory where scientists may wish to immediately conduct a visual comparison of a known expression pattern with the one observed on the bench top or to display expression patterns of interest during scientific discussions at large. AVAILABILITY: Search "FlyExpress" on the Apple iTunes store.

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Year:  2012        PMID: 22923306      PMCID: PMC3476331          DOI: 10.1093/bioinformatics/bts518

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  6 in total

1.  FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.

Authors:  Sudhir Kumar; Charlotte Konikoff; Bernard Van Emden; Christopher Busick; Kailah T Davis; Shuiwang Ji; Lin-Wei Wu; Hector Ramos; Thomas Brody; Sethuraman Panchanathan; Jieping Ye; Timothy L Karr; Kristyn Gerold; Michael McCutchan; Stuart J Newfeld
Journal:  Bioinformatics       Date:  2011-10-12       Impact factor: 6.937

2.  The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool.

Authors:  Regis A James; Mitchell M Rao; Edward S Chen; Margaret A Goodell; Chad A Shaw
Journal:  Bioinformatics       Date:  2012-05-09       Impact factor: 6.937

3.  Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

Authors:  Eric Lécuyer; Hideki Yoshida; Neela Parthasarathy; Christina Alm; Tomas Babak; Tanja Cerovina; Timothy R Hughes; Pavel Tomancak; Henry M Krause
Journal:  Cell       Date:  2007-10-05       Impact factor: 41.582

4.  TimeTree2: species divergence times on the iPhone.

Authors:  Sudhir Kumar; S Blair Hedges
Journal:  Bioinformatics       Date:  2011-05-26       Impact factor: 6.937

5.  Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence.

Authors:  Charlotte E Konikoff; Timothy L Karr; Michael McCutchan; Stuart J Newfeld; Sudhir Kumar
Journal:  Dev Dyn       Date:  2011-09-29       Impact factor: 3.780

6.  Systematic determination of patterns of gene expression during Drosophila embryogenesis.

Authors:  Pavel Tomancak; Amy Beaton; Richard Weiszmann; Elaine Kwan; ShengQiang Shu; Suzanna E Lewis; Stephen Richards; Michael Ashburner; Volker Hartenstein; Susan E Celniker; Gerald M Rubin
Journal:  Genome Biol       Date:  2002-12-23       Impact factor: 13.583

  6 in total
  2 in total

1.  Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression.

Authors:  Lei Yuan; Cheng Pan; Shuiwang Ji; Michael McCutchan; Zhi-Hua Zhou; Stuart J Newfeld; Sudhir Kumar; Jieping Ye
Journal:  Bioinformatics       Date:  2013-12-03       Impact factor: 6.937

2.  Predicting gene regulatory interactions based on spatial gene expression data and deep learning.

Authors:  Yang Yang; Qingwei Fang; Hong-Bin Shen
Journal:  PLoS Comput Biol       Date:  2019-09-17       Impact factor: 4.475

  2 in total

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