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Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.

Pruteanu-Malinici I, Majoros WH, Ohler U.

Bioinformatics. 2013 Jul 1;29(13):i27-35. doi: 10.1093/bioinformatics/btt206.


Automatic annotation of spatial expression patterns via sparse Bayesian factor models.

Pruteanu-Malinici I, Mace DL, Ohler U.

PLoS Comput Biol. 2011 Jul;7(7):e1002098. doi: 10.1371/journal.pcbi.1002098. Epub 2011 Jul 21.


Automatic image analysis for gene expression patterns of fly embryos.

Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW.

BMC Cell Biol. 2007 Jul 10;8 Suppl 1:S7.


SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images.

Puniyani K, Faloutsos C, Xing EP.

Bioinformatics. 2010 Jun 15;26(12):i47-56. doi: 10.1093/bioinformatics/btq172.


Joint stage recognition and anatomical annotation of Drosophila gene expression patterns.

Cai X, Wang H, Huang H, Ding C.

Bioinformatics. 2012 Jun 15;28(12):i16-24. doi: 10.1093/bioinformatics/bts220.


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

Yuan L, Pan C, Ji S, McCutchan M, Zhou ZH, Newfeld SJ, Kumar S, Ye J.

Bioinformatics. 2014 Jan 15;30(2):266-73. doi: 10.1093/bioinformatics/btt648. Epub 2013 Dec 3.


GINI: from ISH images to gene interaction networks.

Puniyani K, Xing EP.

PLoS Comput Biol. 2013;9(10):e1003227. doi: 10.1371/journal.pcbi.1003227. Epub 2013 Oct 10.


Image-level and group-level models for Drosophila gene expression pattern annotation.

Sun Q, Muckatira S, Yuan L, Ji S, Newfeld S, Kumar S, Ye J.

BMC Bioinformatics. 2013 Dec 3;14:350. doi: 10.1186/1471-2105-14-350.


A bag-of-words approach for Drosophila gene expression pattern annotation.

Ji S, Li YX, Zhou ZH, Kumar S, Ye J.

BMC Bioinformatics. 2009 Apr 21;10:119. doi: 10.1186/1471-2105-10-119.


Automated annotation of Drosophila gene expression patterns using a controlled vocabulary.

Ji S, Sun L, Jin R, Kumar S, Ye J.

Bioinformatics. 2008 Sep 1;24(17):1881-8. doi: 10.1093/bioinformatics/btn347. Epub 2008 Jul 16.


Automatic recognition and annotation of gene expression patterns of fly embryos.

Zhou J, Peng H.

Bioinformatics. 2007 Mar 1;23(5):589-96. Epub 2007 Jan 19. Erratum in: Bioinformatics. 2007 Jun;23(12):1571-2..


Automatically identifying and annotating mouse embryo gene expression patterns.

Han L, van Hemert JI, Baldock RA.

Bioinformatics. 2011 Apr 15;27(8):1101-7. doi: 10.1093/bioinformatics/btr105. Epub 2011 Feb 25.


Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.

Crombach A, Cicin-Sain D, Wotton KR, Jaeger J.

PLoS One. 2012;7(9):e46658. doi: 10.1371/journal.pone.0046658. Epub 2012 Sep 28.


A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis.

Zhang W, Feng D, Li R, Chernikov A, Chrisochoides N, Osgood C, Konikoff C, Newfeld S, Kumar S, Ji S.

BMC Bioinformatics. 2013 Dec 28;14:372. doi: 10.1186/1471-2105-14-372.


A methodology to infer gene networks from spatial patterns of expression--an application to fluorescence in situ hybridization images.

Campiteli MG, Comin CH, Costa Lda F, Babu MM, Cesar RM.

Mol Biosyst. 2013 Jul;9(7):1926-30. doi: 10.1039/c3mb25475e. Epub 2013 Apr 17.


Phenotype recognition with combined features and random subspace classifier ensemble.

Zhang B, Pham TD.

BMC Bioinformatics. 2011 Apr 30;12:128. doi: 10.1186/1471-2105-12-128.


A mixture model with random-effects components for clustering correlated gene-expression profiles.

Ng SK, McLachlan GJ, Wang K, Ben-Tovim Jones L, Ng SW.

Bioinformatics. 2006 Jul 15;22(14):1745-52. Epub 2006 May 3.

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