Published in Nat Genet on January 01, 1999
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol (2009) 7.47
Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol (2001) 7.01
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res (2002) 6.70
Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc Natl Acad Sci U S A (2001) 6.68
Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell (2002) 6.03
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res (2004) 5.82
Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A (2001) 5.57
High-throughput variation detection and genotyping using microarrays. Genome Res (2001) 5.24
Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol (2002) 5.04
Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A (2000) 5.01
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res (2003) 4.64
RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc (2010) 4.35
A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19
Biomarker identification by feature wrappers. Genome Res (2001) 3.93
Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci U S A (2001) 3.91
Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell (2003) 3.69
Classifying gene expression profiles from pairwise mRNA comparisons. Stat Appl Genet Mol Biol (2004) 3.45
Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol (2001) 3.43
Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci U S A (2003) 3.31
In vitro cartilage formation by human adult stem cells from bone marrow stroma defines the sequence of cellular and molecular events during chondrogenesis. Proc Natl Acad Sci U S A (2002) 3.28
Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci U S A (2001) 3.01
Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res (1999) 2.98
Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci U S A (2003) 2.95
Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A (2004) 2.94
Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res (2000) 2.79
Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res (2002) 2.77
Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev (2000) 2.64
Microarray analysis of developing Arabidopsis seeds. Plant Physiol (2000) 2.62
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol (2007) 2.56
High-resolution global genomic survey of 178 gliomas reveals novel regions of copy number alteration and allelic imbalances. Cancer Res (2006) 2.56
Analysis of the transcriptional program induced by Raf in epithelial cells. Genes Dev (2001) 2.56
The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res (2004) 2.54
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics (2004) 2.52
Comprehensive comparison of six microarray technologies. Nucleic Acids Res (2004) 2.50
Insights from gene arrays on the development and growth regulation of uterine leiomyomata. Fertil Steril (2002) 2.48
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Res (2000) 2.46
Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res (2009) 2.42
Evaluation of non-formalin tissue fixation for molecular profiling studies. Am J Pathol (2002) 2.38
An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res (2002) 2.37
Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res (2002) 2.34
Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly. Biophys J (2000) 2.34
Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics (2007) 2.32
High-resolution mutation mapping reveals parallel experimental evolution in yeast. PLoS Biol (2006) 2.32
Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics (2002) 2.31
Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A (2001) 2.28
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res (2001) 2.23
Gene expression analysis of the Streptococcus pneumoniae competence regulons by use of DNA microarrays. J Bacteriol (2000) 2.21
Fluorescence spectral properties of cyanine dye-labeled DNA oligomers on surfaces coated with silver particles. Anal Biochem (2003) 2.21
Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res (2004) 2.17
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics (2006) 2.13
Effects of environmental enrichment on gene expression in the brain. Proc Natl Acad Sci U S A (2000) 2.13
Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J Clin Microbiol (2002) 2.12
Predicting splice variant from DNA chip expression data. Genome Res (2001) 2.09
Group A Streptococcus transcriptome dynamics during growth in human blood reveals bacterial adaptive and survival strategies. Am J Pathol (2005) 2.05
Mutational analysis using oligonucleotide microarrays. J Med Genet (1999) 2.05
Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J Mol Diagn (2007) 2.04
Universality and flexibility in gene expression from bacteria to human. Proc Natl Acad Sci U S A (2004) 2.03
Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J Mol Diagn (2003) 1.99
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res (2009) 1.98
The transcriptional repressor Gfi1 affects development of early, uncommitted c-Kit+ T cell progenitors and CD4/CD8 lineage decision in the thymus. J Exp Med (2003) 1.96
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res (2006) 1.95
Brassinosteroid-regulated gene expression. Plant Physiol (2002) 1.95
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol (2003) 1.94
Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics (2005) 1.91
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
mRNA of placental origin is readily detectable in maternal plasma. Proc Natl Acad Sci U S A (2003) 1.89
Correlation test to assess low-level processing of high-density oligonucleotide microarray data. BMC Bioinformatics (2005) 1.86
Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus. J Clin Microbiol (2003) 1.85
High-throughput microarray detection of olfactory receptor gene expression in the mouse. Proc Natl Acad Sci U S A (2004) 1.82
Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics (2003) 1.77
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics (2007) 1.77
Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J Clin Microbiol (2006) 1.76
Reproducibility of oligonucleotide arrays using small samples. BMC Genomics (2003) 1.75
SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci U S A (2000) 1.74
Relationship between gene expression and observed intensities in DNA microarrays--a modeling study. Nucleic Acids Res (2006) 1.74
The gene expression fingerprint of human heart failure. Proc Natl Acad Sci U S A (2002) 1.73
Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics (2006) 1.73
The effects of aging on gene expression in the hypothalamus and cortex of mice. Proc Natl Acad Sci U S A (2001) 1.72
Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei. Proc Natl Acad Sci U S A (2001) 1.67
Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol (2004) 1.67
Reduced dermatopontin expression is a molecular link between uterine leiomyomas and keloids. Genes Chromosomes Cancer (2004) 1.65
Radiative decay engineering: the role of photonic mode density in biotechnology. J Phys D Appl Phys (2003) 1.64
Advances in Bioconjugation. Curr Org Chem (2010) 1.60
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res (2003) 1.59
In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Res (2003) 1.58
Using DNA microarrays to study host-microbe interactions. Emerg Infect Dis (2000) 1.55
Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS One (2009) 1.55
Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes. J Biol Chem (2008) 1.55
Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities. Nucleic Acids Res (2009) 1.54
A new approach for filtering noise from high-density oligonucleotide microarray datasets. Nucleic Acids Res (2001) 1.54
A non-redundant microarray of genes for two related bacteria. Nucleic Acids Res (2003) 1.53
Design optimization methods for genomic DNA tiling arrays. Genome Res (2005) 1.53
A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res (2004) 1.51
A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics (2003) 1.51
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol (2003) 1.50
The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys J (2003) 1.50
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25
Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol (1997) 27.78
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science (2001) 15.54
Accessing genetic information with high-density DNA arrays. Science (1996) 13.89
Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell (2000) 13.44
Computer programs for the assembly of DNA sequences. Nucleic Acids Res (1979) 13.36
Using oligonucleotide probe arrays to access genetic diversity. Biotechniques (1995) 12.18
Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A (1994) 9.59
Steps toward computer analysis of nucleotide sequences. Science (1980) 8.73
Mitotic misregulation and human aging. Science (2000) 8.47
Replication dynamics of the yeast genome. Science (2001) 7.56
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36
Direct allelic variation scanning of the yeast genome. Science (1998) 5.90
Transcriptional regulation and function during the human cell cycle. Nat Genet (2001) 5.89
Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci U S A (1990) 5.85
Nucleotide sequences from the adenovirus-2 genome. J Biol Chem (1982) 5.76
Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A (2001) 5.57
Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med (1996) 5.35
Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A (2000) 5.01
Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet (1999) 4.79
Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat Genet (1996) 4.19
Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol (1999) 3.87
Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase. J Exp Med (2001) 3.75
Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc Natl Acad Sci U S A (1989) 3.56
Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science (1998) 3.53
Comparing genomes within the species Mycobacterium tuberculosis. Genome Res (2001) 3.40
Evolutionarily conserved sequences on human chromosome 21. Genome Res (2001) 2.95
The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene. Nucleic Acids Res (1983) 2.94
Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res (2000) 2.79
Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J Clin Microbiol (1999) 2.65
Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J Med Chem (1994) 2.56
Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Res (2000) 2.46
A semi-automated method for the reading of nucleic acid sequencing gels. Nucleic Acids Res (1982) 2.44
Nucleic acid amplification in vitro: detection of sequences with low copy numbers and application to diagnosis of human immunodeficiency virus type 1 infection. Clin Microbiol Rev (1989) 2.43
A computer assisted method for the determination of restriction enzyme recognifion sites. Nucleic Acids Res (1978) 2.32
Functional genomics. Proc Natl Acad Sci U S A (1999) 2.29
Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. Genome Res (1998) 2.17
Effects of environmental enrichment on gene expression in the brain. Proc Natl Acad Sci U S A (2000) 2.13
Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res (2000) 2.13
Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells. J Virol (1990) 2.11
Cloned restriction/modification system from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A (1983) 2.05
Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J Med Chem (1994) 2.04
Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Res (1985) 2.00
Myoseverin, a microtubule-binding molecule with novel cellular effects. Nat Biotechnol (2000) 1.97
Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nat Genet (1998) 1.90
Discrimination of DNA hybridization using chemical force microscopy. Biophys J (1999) 1.86
Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Res (1981) 1.84
Hybridization properties of immobilized nucleic acids. Nucleic Acids Res (1987) 1.81
Reduced HIV-1 infectability of CD4+ lymphocytes from exposed-uninfected individuals: association with low expression of CCR5 and high production of beta-chemokines. Virology (1998) 1.76
Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches. Nucleic Acids Res (2001) 1.71
Expression of the lacZ gene from two methanol-regulated promoters in Pichia pastoris. Nucleic Acids Res (1987) 1.57
Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res (2001) 1.55
The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proc Natl Acad Sci U S A (2000) 1.53
The pharmacological chaperone 1-deoxygalactonojirimycin increases alpha-galactosidase A levels in Fabry patient cell lines. J Inherit Metab Dis (2009) 1.50
A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum. J Mol Biol (1978) 1.48
Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. Mol Cell Biol (1985) 1.48
Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci U S A (1998) 1.48
ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris. Nucleic Acids Res (1982) 1.45
Calculation of electrostatic effects at the amino terminus of an alpha helix. Biophys J (1994) 1.43
Mutation detection by ligation to complete n-mer DNA arrays. Genome Res (1998) 1.41
Determination and analysis of adenovirus-2 DNA sequences which may include signals for late messenger RNA processing. J Mol Biol (1979) 1.28
An unnatural biopolymer. Science (1993) 1.23
Bacteriorhodopsin's M412 intermediate contains a 13-cis, 14-s-trans, 15-anti-retinal Schiff base chromophore. Biochemistry (1989) 1.17
Blunt-end and single-strand ligations by Escherichia coli ligase: influence on an in vitro amplification scheme. Gene (1990) 1.16
Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res (1998) 1.11
Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells. Proc Natl Acad Sci U S A (1986) 1.10
Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res (1998) 1.05
Combinatorial chemistry--applications of light-directed chemical synthesis. Trends Biotechnol (1994) 1.00
Imaging biomolecule arrays by atomic force microscopy. Biophys J (1995) 1.00
Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR. PCR Methods Appl (1991) 1.00
Mutant yeast on drugs. Nat Med (1998) 0.97
Defining subsets of naive and memory B cells based on the ability of their progeny to somatically mutate in vitro. Immunity (1995) 0.97
Arrays of arrays for high-throughput gene expression profiling. Genome Res (2001) 0.95
Halorhodopsin and sensory rhodopsin contain a C6-C7 s-trans retinal chromophore. Biophys J (1989) 0.93
Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol (2006) 0.91
Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harb Symp Quant Biol (2006) 0.91
Emergence of dual resistance to zidovudine and lamivudine in HIV-1-infected patients treated with zidovudine plus lamivudine as initial therapy. J Acquir Immune Defic Syndr (2000) 0.91
Expression profiling of neural cells reveals specific patterns of ethanol-responsive gene expression. Mol Pharmacol (2000) 0.89
HIV-1 infectability of CD4+ lymphocytes with relation to beta-chemokines and the CCR5 coreceptor. Immunol Lett (1999) 0.89
Resonance Raman spectra of the Pr-form of phytochrome. Photochem Photobiol (1988) 0.88
Chipping away at complex behavior: transcriptome/phenotype correlations in the mouse brain. Physiol Behav (2001) 0.88
Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci U S A (1990) 0.87
Comparison of lipid/gramicidin dispersions and cocrystals by Raman scattering. Biochemistry (1987) 0.86
Raman spectroscopic elucidation of DNA backbone conformations for poly(dG-dT).poly(dA-dC) and poly(dA-dT).poly(dA-dT) in CsF solution. Biopolymers (1985) 0.85
Yolk proteins in Drosophila: identification and site of synthesis. J Exp Zool (1974) 0.83
Analysis of substrate specificity of the PaeR7 endonuclease: effect of base methylation on the kinetics of cleavage. Nucleic Acids Res (1990) 0.82
Multiplex metallica. Nat Biotechnol (2001) 0.82
Introduction and expression of the bacterial PaeR7 restriction endonuclease gene in mouse cells containing the PaeR7 methylase. Nucleic Acids Res (1988) 0.78
Lipid-tail group dependent structure of the fd gene 8 protein. Prog Clin Biol Res (1981) 0.78
Resonance Raman spectra of bacteriorhodopsin mutants with substitutions at Asp-85, Asp-96, and Arg-82. Photochem Photobiol (1991) 0.77
Ultraviolet resonance Raman spectroscopy as a probe of protein structure in the fd virus. Biotechniques (1988) 0.77
Restriction endonucleases and their recognition sequences. Biochem Soc Trans (1980) 0.76
Lipid-dependent Structural Changes of an Amphomorphic Membrane Protein. Biophys J (1982) 0.75
Analysis of drug pharmacology towards predicting drug behavior by expression profiling using high-density oligonucleotide arrays. Ann N Y Acad Sci (2000) 0.75
Information content of the adenovirus-2 genome. Cold Spring Harb Symp Quant Biol (1983) 0.75
Ultraviolet resonance Raman spectroscopy of bacteriorhodopsin. Photochem Photobiol (1990) 0.75
Specific immunoglobulin cDNA clones produced from hybridoma cell lines and murine spleen fragment cultures by 3SR amplification. PCR Methods Appl (1994) 0.75