A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

Zhijin Wu; Rafael A Irizarry; Robert Gentleman; Francisco Martinez-Murillo; Forrest Spencer

doi:10.1198/016214504000000683

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

Journal of the American Statistical Association ◽

10.1198/016214504000000683 ◽

2004 ◽

Vol 99 (468) ◽

pp. 909-917 ◽

Cited By ~ 1043

Author(s):

Zhijin Wu ◽

Rafael A Irizarry ◽

Robert Gentleman ◽

Francisco Martinez-Murillo ◽

Forrest Spencer

Keyword(s):

Expression Arrays ◽

Model Based ◽

Background Adjustment

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Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology

Nucleic Acids Research ◽

10.1093/nar/gkn234 ◽

2008 ◽

Vol 36 (10) ◽

pp. e58-e58 ◽

Cited By ~ 43

Author(s):

Liang-Hao Ding ◽

Yang Xie ◽

Seongmi Park ◽

Guanghua Xiao ◽

Michael D. Story

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Background Correction ◽

Whole Genome ◽

Expression Arrays ◽

Biological Validation ◽

Model Based ◽

Genome Expression ◽

Differential Gene ◽

Whole Genome Expression

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Representation, abstraction, and simple-minded sophisticates

Behavioral and Brain Sciences ◽

10.1017/s0140525x19002942 ◽

2020 ◽

Vol 43 ◽

Author(s):

Peter Dayan

Keyword(s):

Decision Theory ◽

Predictive Coding ◽

Bayesian Decision Theory ◽

Bayesian Decision ◽

Model Based ◽

Model Free

Abstract Bayesian decision theory provides a simple formal elucidation of some of the ways that representation and representational abstraction are involved with, and exploit, both prediction and its rather distant cousin, predictive coding. Both model-free and model-based methods are involved.

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Quantitative Model-Based Image Analysis of NuMa Distribution Links Nuclear Organization with Cell Phenotype

Microscopy and Microanalysis ◽

10.1017/s1431927600028968 ◽

2001 ◽

Vol 7 (S2) ◽

pp. 578-579

Author(s):

David W. Knowles ◽

Sophie A. Lelièvre ◽

Carlos Ortiz de Solόrzano ◽

Stephen J. Lockett ◽

Mina J. Bissell ◽

...

Keyword(s):

Image Analysis ◽

Mammary Epithelial Cells ◽

Nuclear Organization ◽

Critical Role ◽

Quantitative Model ◽

Mammary Epithelial ◽

Cell Phenotype ◽

Proliferating Cells ◽

Mitotic Apparatus ◽

Model Based

The extracellular matrix (ECM) plays a critical role in directing cell behaviour and morphogenesis by regulating gene expression and nuclear organization. Using non-malignant (S1) human mammary epithelial cells (HMECs), it was previously shown that ECM-induced morphogenesis is accompanied by the redistribution of nuclear mitotic apparatus (NuMA) protein from a diffuse pattern in proliferating cells, to a multi-focal pattern as HMECs growth arrested and completed morphogenesis . A process taking 10 to 14 days.To further investigate the link between NuMA distribution and the growth stage of HMECs, we have investigated the distribution of NuMA in non-malignant S1 cells and their malignant, T4, counter-part using a novel model-based image analysis technique. This technique, based on a multi-scale Gaussian blur analysis (Figure 1), quantifies the size of punctate features in an image. Cells were cultured in the presence and absence of a reconstituted basement membrane (rBM) and imaged in 3D using confocal microscopy, for fluorescently labeled monoclonal antibodies to NuMA (fαNuMA) and fluorescently labeled total DNA.

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