DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Biotechnology progress (Print)

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1021/bp0400240PMID 15458312
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• DNA microarrays and pharmacogenomics.

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  2003cited by this paper
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  2002influential reference
• Microarray data normalization and transformation

  2002cited by this paper
• From patterns to pathways: gene expression data analysis comes of age

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• Whole-Genome Analysis of Genes Regulated by the Bacillus subtilis Competence Transcription Factor ComK

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• expression: towards the regulome

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• A common reference for cDNA microarray hybridizations.

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

  2002cited by this paper
• Computational analysis of microarray gene expression profiles: clustering, classification, and beyond

  2002cited by this paper
• Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response.

  2002cited by this paper
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• Transcriptome Analysis of Acetate Metabolism in Corynebacterium glutamicum Using a Newly Developed Metabolic Array

  2002cited by this paper
• Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein.

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  2002cited by this paper
• Design issues for cDNA microarray experiments

  2002cited by this paper
• Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803.

  2002influential reference
• A Two-Component Mn2+-Sensing System Negatively Regulates Expression of the mntCAB Operon in Synechocystis

  2002cited by this paper
• Functional and comparative genomics of pathogenic bacteria.

  2002cited by this paper
• Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.

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• Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative σ factor, SigH

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• Microarray analysis of the Bacillus subtilis K‐state: genome‐wide expression changes dependent on ComK

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• Transcriptome analysis of all two‐component regulatory system mutants of Escherichia coli K‐12

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• Functional Analysis of the Bacillus subtilis Zur Regulon

  2002cited by this paper
• A Biologist’s Guide to Analysis of DNA Microarray Data.

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• DNA Microarray for Microbial Biotechnology: Gene Expression Profiles in Escherichia coli during Protein Overexpression

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• Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data

  2002cited by this paper
• Global Transcriptional Response of Bacillus subtilis to Heat Shock

  2001cited by this paper
• Quantitative assessment of DNA microarrays--comparison with Northern blot analyses.

  2001cited by this paper
• On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data

  2001cited by this paper
• Gene expression in Pseudomonas aeruginosa biofilms

  2001cited by this paper
• Evolutionary genomics of Staphylococcus aureus: Insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic

  2001cited by this paper
• Bacterial cell cycle: seeing the big picture with microarrays.

  2001cited by this paper
• Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis.

  2001cited by this paper
• Statistical design and the analysis of gene expression microarray data.

  2001cited by this paper
• Pasteurella multocida Gene Expression in Response to Iron Limitation

  2001cited by this paper
• A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

  2001cited by this paper

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