Computational strategies for analyzing data in gene expression microarray experiments (Q30950304)

27 June 2017

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title

Computational strategies for analyzing data in gene expression microarray experiments (English)

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27 June 2017

Riitta Lahesmaa

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27 June 2017

Tero Aittokallio

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27 June 2017

Markus Kurki

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27 June 2017

Olli Nevalainen

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27 June 2017

Tuomas Nikula

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27 June 2017

Anne West

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27 June 2017

publication date

1 October 2003

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Journal of Bioinformatics and Computational Biology

27 June 2017

published in

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27 June 2017

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27 June 2017

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27 June 2017

page(s)

541-586

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Options available--from start to finish--for obtaining expression data by microarray.

27 June 2017

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21 January 2018

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Ratio statistics of gene expression levels and applications to microarray data analysis

21 January 2018

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Making sense of microarray data distributions

21 January 2018

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Quantitative noise analysis for gene expression microarray experiments

21 January 2018

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Normalization strategies for cDNA microarrays

21 January 2018

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Analysis of variance for gene expression microarray data

21 January 2018

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A variance-stabilizing transformation for gene-expression microarray data

21 January 2018

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Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects

21 January 2018

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Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

21 January 2018

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Adjustments and measures of differential expression for microarray data

21 January 2018

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Binary analysis and optimization-based normalization of gene expression data

21 January 2018

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Variance stabilization applied to microarray data calibration and to the quantification of differential expression

21 January 2018

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Microarray data normalization and transformation

21 January 2018

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Robust Locally Weighted Regression and Smoothing Scatterplots

21 January 2018

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Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale

21 January 2018

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Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data

21 January 2018

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Transcript imaging of the development of human T helper cells using oligonucleotide arrays

21 January 2018

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Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations

21 January 2018

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An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles

21 January 2018

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A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments

21 January 2018

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Multivariate approach for selecting sets of differentially expressed genes.

21 January 2018

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Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments

21 January 2018

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Nonparametric methods for identifying differentially expressed genes in microarray data

21 January 2018

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Analysis of high density expression microarrays with signed-rank call algorithms

21 January 2018

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On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data

21 January 2018

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A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

21 January 2018

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Significance analysis of microarrays applied to the ionizing radiation response

21 January 2018

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Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines

21 January 2018

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Cluster analysis and display of genome-wide expression patterns

21 January 2018

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Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation

21 January 2018

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Model-based clustering and data transformations for gene expression data

21 January 2018

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Mixture modelling of gene expression data from microarray experiments

21 January 2018

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A mixture model-based approach to the clustering of microarray expression data.

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Validating clustering for gene expression data.

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

A cluster validity framework for genome expression data

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Statistical estimation of cluster boundaries in gene expression profile data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Large-scale clustering of cDNA-fingerprinting data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Judging the quality of gene expression-based clustering methods using gene annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Knowledge-based analysis of microarray gene expression data by using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Deriving quantitative conclusions from microarray expression data

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Diagnosis of multiple cancer types by shrunken centroids of gene expression

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Support vector machine classification and validation of cancer tissue samples using microarray expression data

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Multi-class cancer classification via partial least squares with gene expression profiles

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Gene expression data analysis

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Approaches to the automatic discovery of patterns in biosequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Information content of binding sites on nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Sequence logos: a new way to display consensus sequences

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Identifying protein-binding sites from unaligned DNA fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

An algorithm for finding signals of unknown length in DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Discovery of novel transcription factor binding sites by statistical overrepresentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Regulatory element detection using correlation with expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Computational prediction of eukaryotic protein-coding genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Network motifs in the transcriptional regulation network of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Extracting functional information from microarrays: a challenge for functional genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Fundamental patterns underlying gene expression profiles: simplicity from complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Singular value decomposition for genome-wide expression data processing and modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Reverse engineering gene networks using singular value decomposition and robust regression

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Transitive functional annotation by shortest-path analysis of gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Building and analysing genome-wide gene disruption networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Genetic network inference: from co-expression clustering to reverse engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Using Bayesian networks to analyze expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling.

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

A duplication growth model of gene expression networks

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

From patterns to pathways: gene expression data analysis comes of age.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Fundamentals of experimental design for cDNA microarrays

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Determination of minimum sample size and discriminatory expression patterns in microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Modelling regulatory pathways in E. coli from time series expression profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Aligning gene expression time series with time warping algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

21 January 2018

Visualization of data

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Principal component analysis for clustering gene expression data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Correspondence analysis applied to microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Discovering regulatory and signalling circuits in molecular interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

Use of keyword hierarchies to interpret gene expression patterns.

21 January 2018

1 reference

https://api.crossref.org/works/10.1142%2FS0219720003000319

At the interfaces of epidemiology, genetics and genomics

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Linking gene expression data with patient survival times using partial least squares

21 January 2018

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https://api.crossref.org/works/10.1142%2FS0219720003000319

Empirical Bayes Analysis of a Microarray Experiment

21 January 2018

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10.1142/S0219720003000319

21 January 2018

Identifiers

DOI

1 reference

journals/jbcb/AittokallioKNNWL03

27 June 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference