DNA microarray technology in toxicogenomics of aquatic models: methods and applications.

[1]  Z. Ju,et al.  Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. , 2007, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[2]  David E. Williams,et al.  Use of a rainbow trout oligonucleotide microarray to determine transcriptional patterns in aflatoxin B1-induced hepatocellular carcinoma compared to adjacent liver. , 2005, Toxicological sciences : an official journal of the Society of Toxicology.

[3]  G. van den Thillart,et al.  Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. , 2005, American journal of physiology. Regulatory, integrative and comparative physiology.

[4]  M. Toyota,et al.  Epigenetic changes in solid and hematopoietic tumors. , 2005, Seminars in oncology.

[5]  Hisanori Kato,et al.  A nutrigenomics database – integrated repository for publications and associated microarray data in nutrigenomics research , 2005, British Journal of Nutrition.

[6]  B. Koop,et al.  Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray , 2005, BMC Genomics.

[7]  H. Burtscher,et al.  cRNA target preparation for microarrays: comparison of gene expression profiles generated with different amplification procedures. , 2005, Analytical biochemistry.

[8]  D. Kang,et al.  Design issues in toxicogenomics using DNA microarray experiment. , 2005, Toxicology and Applied Pharmacology.

[9]  Don Simone Daly,et al.  Automated Microarray Image Analysis Toolbox for MATLAB , 2005, Bioinform..

[10]  B. Naudts,et al.  Development and application of a brain-specific cDNA microarray for effect evaluation of neuro-active pharmaceuticals in zebrafish (Danio rerio). , 2005, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[11]  R. Lotan,et al.  Global detection of molecular changes reveals concurrent alteration of several biological pathways in nonsmall cell lung cancer cells , 2005, Molecular Genetics and Genomics.

[12]  P. Sanna,et al.  Gene profiling of laser-microdissected brain regions and sub-regions. , 2005, Brain research. Brain research protocols.

[13]  Y. Baba,et al.  Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. , 2005, Genomics.

[14]  Martin T. Wells,et al.  Bayesian Normalization and Identification for Differential Gene Expression Data , 2005, J. Comput. Biol..

[15]  E. J. Neves,et al.  Gene expression arrays in cancer research: methods and applications. , 2005, Critical reviews in oncology/hematology.

[16]  Anna N Stepanova,et al.  Arabidopsis Ethylene Signaling Pathway , 2005, Science's STKE.

[17]  Julie A. Dickerson,et al.  BarleyExpress: a web-based submission tool for enriched microarray database annotations , 2005, Bioinform..

[18]  M. Viant,et al.  Metabolic changes in Japanese medaka (Oryzias latipes) during embryogenesis and hypoxia as determined by in vivo 31P NMR. , 2005, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[19]  D. Crawford,et al.  Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus , 2005, Nature Genetics.

[20]  C. Rexroad,et al.  Gene expression in the brain and kidney of rainbow trout in response to handling stress , 2005, BMC Genomics.

[21]  G. Churchill,et al.  A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. , 2004, Journal of biomolecular techniques : JBT.

[22]  Sanjit K. Mitra,et al.  Optimized LOWESS normalization parameter selection for DNA microarray data , 2004, BMC Bioinformatics.

[23]  J. Rogers,et al.  Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Patrick S. Schnable,et al.  Picky: oligo microarray design for large genomes , 2004, Bioinform..

[25]  Peng Li,et al.  Gene expression analysis of peroxisome proliferators- and phenytoin-induced hepatotoxicity using cDNA microarray. , 2004, The Journal of veterinary medical science.

[26]  P. Zimmermann,et al.  GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] , 2004, Plant Physiology.

[27]  M. P. Beaudet,et al.  Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. , 2004, Analytical biochemistry.

[28]  G. Churchill Using ANOVA to analyze microarray data. , 2004, BioTechniques.

[29]  A. Oikari,et al.  Response of rainbow trout transcriptome to model chemical contaminants. , 2004, Biochemical and biophysical research communications.

[30]  Hans A Hofmann,et al.  Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray , 2004, BMC Genomics.

[31]  Y. Kohara,et al.  Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics , 2004, Mechanisms of Development.

[32]  Jizhong Zhou,et al.  Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.

[33]  J. Schein,et al.  Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. , 2004, Genome research.

[34]  Neil D. Lawrence,et al.  Reducing the variability in cDNA microarray image processing by Bayesian inference , 2004, Bioinform..

[35]  Richard S Paules,et al.  Application of Toxicogenomics to Toxicology: Basic Concepts in the Analysis of Microarray Data , 2004, Toxicologic pathology.

[36]  Nadim W. Alkharouf,et al.  SGMD: the Soybean Genomics and Microarray Database , 2004, Nucleic Acids Res..

[37]  T. Barrette,et al.  ONCOMINE: a cancer microarray database and integrated data-mining platform. , 2004, Neoplasia.

[38]  T. Joshi,et al.  Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. , 2004, Omics : a journal of integrative biology.

[39]  K. Coombes,et al.  A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays , 2004, BMC Genomics.

[40]  P. Coussens,et al.  Development of a porcine brain cDNA library, EST database, and microarray resource. , 2003, Physiological genomics.

[41]  A. Miracle,et al.  The Path from Molecular Indicators of Exposure to Describing Dynamic Biological Systems in an Aquatic Organism: Microarrays and the Fathead Minnow , 2003, Ecotoxicology.

[42]  R. O. Stuart,et al.  Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development. , 2003, Kidney international.

[43]  G. Sagerer,et al.  Methods for automatic microarray image segmentation , 2003, IEEE Transactions on NanoBioscience.

[44]  G. Magoulas,et al.  Improved processing of microarray data using image reconstruction techniques , 2003, IEEE Transactions on NanoBioscience.

[45]  S. Minchin,et al.  A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). , 2003, Aquatic toxicology.

[46]  Makoto Ohnishi,et al.  Identification of potential biomarkers of lymph node metastasis in oral squamous cell carcinoma by cDNA microarray analysis , 2003, International journal of cancer.

[47]  C. Ton,et al.  Gene expression profile of zebrafish exposed to hypoxia during development. , 2003, Physiological genomics.

[48]  James J. Chen,et al.  Normalization Methods for Analysis of Microarray Gene-Expression Data , 2003, Journal of biopharmaceutical statistics.

[49]  Chang-Woo Song,et al.  cDNA microarray gene expression profiling of hydroxyurea, paclitaxel, and p‐anisidine, genotoxic compounds with differing tumorigenicity results , 2003, Environmental and molecular mutagenesis.

[50]  Lucila Ohno-Machado,et al.  A neural network-based similarity index for clustering DNA microarray data , 2003, Comput. Biol. Medicine.

[51]  Shadan Ali,et al.  Direct comparison of microarray gene expression profiles between non-amplification and a modified cDNA amplification procedure applicable for needle biopsy tissues. , 2003, Cancer detection and prevention.

[52]  Jill Duncan,et al.  Analyzing microarray data using cluster analysis. , 2003, Pharmacogenomics.

[53]  Ying Zhang,et al.  Block principal component analysis with application to gene microarray data classification , 2002, Statistics in medicine.

[54]  G. Churchill,et al.  Variation in gene expression within and among natural populations , 2002, Nature Genetics.

[55]  L. Folmar,et al.  Array technology as a tool to monitor exposure of fish to xenoestrogens. , 2002, Marine environmental research.

[56]  Zhanjiang Liu,et al.  Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation , 2002, Molecular Genetics and Genomics.

[57]  W. Pennie,et al.  Toxicogenomics; transcript profiling and potential application to chemical allergy. , 2002, Toxicology in vitro : an international journal published in association with BIBRA.

[58]  Shigeo Yoshida,et al.  Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays. , 2002, Molecular vision.

[59]  Leif E. Peterson,et al.  Screening of gene expression profiles in gastric epithelial cells induced by Helicobacter pylori using microarray analysis , 2002, Alimentary pharmacology & therapeutics.

[60]  Jonathan Pevsner,et al.  Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. , 2002, BioTechniques.

[61]  D. Hittel,et al.  Differential expression of adipose- and heart-type fatty acid binding proteins in hibernating ground squirrels. , 2001, Biochimica et biophysica acta.

[62]  Samuel S. Wu,et al.  A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. , 2001, Physiological genomics.

[63]  X. Wang,et al.  Quantitative quality control in microarray image processing and data acquisition. , 2001, Nucleic acids research.

[64]  Jin Hyuk KIm,et al.  A novel method using edge detection for signal extraction from cDNA microarray image analysis , 2001, Experimental & Molecular Medicine.

[65]  Pierre Baldi,et al.  A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes , 2001, Bioinform..

[66]  D. Crawford,et al.  Utility of Natural Populations for Microarray Analyses: Isolation of Genes Necessary for Functional Genomic Studies , 2001, Marine Biotechnology.

[67]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[69]  S W Burchiel,et al.  Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. , 2001, Toxicological sciences : an official journal of the Society of Toxicology.

[70]  P. Brown,et al.  Genomic views of the immune system*. , 2000, Annual review of immunology.

[71]  J. Barrett,et al.  Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. , 1999, Cancer research.

[72]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[73]  P. Törönen,et al.  Analysis of gene expression data using self‐organizing maps , 1999, FEBS letters.

[74]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[75]  S. Gallinger,et al.  Molecular biology of colorectal cancer. , 1997, Current problems in cancer.

[76]  L. Phillips,et al.  Muscle wasting in insulinopenic rats results from activation of the ATP-dependent, ubiquitin-proteasome proteolytic pathway by a mechanism including gene transcription. , 1996, The Journal of clinical investigation.

[77]  U. Göbel,et al.  Comparison of 16S rRNA sequences from the family Pasteurellaceae: phylogenetic relatedness by cluster analysis. , 1988, Journal of general microbiology.