Decoding randomly ordered DNA arrays.

PubWeight™: 3.49‹?› | Rank: Top 1%

🔗 View Article (PMC 479114)

Published in Genome Res on April 12, 2004

Authors

Kevin L Gunderson1, Semyon Kruglyak, Michael S Graige, Francisco Garcia, Bahram G Kermani, Chanfeng Zhao, Diping Che, Todd Dickinson, Eliza Wickham, Jim Bierle, Dennis Doucet, Monika Milewski, Robert Yang, Chris Siegmund, Juergen Haas, Lixin Zhou, Arnold Oliphant, Jian-Bing Fan, Steven Barnard, Mark S Chee

Author Affiliations

1: Illumina, Inc., San Diego, California 92121, USA.

Articles citing this

High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05

A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nat Genet (2009) 7.65

Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet (2008) 7.13

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41

A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32

Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66

Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14. BMC Genet (2005) 3.04

Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol (2004) 3.04

Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am J Respir Crit Care Med (2008) 2.64

Variation in the gene encoding the serotonin 2A receptor is associated with outcome of antidepressant treatment. Am J Hum Genet (2006) 2.55

A trap-and-release integrated microfluidic system for dynamic microarray applications. Proc Natl Acad Sci U S A (2007) 2.52

Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res (2004) 2.22

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics (2008) 2.11

Overlapping pools for high-throughput targeted resequencing. Genome Res (2009) 2.11

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 Res (2008) 2.11

Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev (2009) 1.70

Linkage disequilibrium in related breeding lines of chickens. Genetics (2007) 1.66

Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet (2012) 1.52

Substrate cleavage analysis of furin and related proprotein convertases. A comparative study. J Biol Chem (2008) 1.40

Comprehensive linkage and association analyses identify haplotype, near to the TNFSF15 gene, significantly associated with spondyloarthritis. PLoS Genet (2009) 1.36

Synergism between particle-based multiplexing and microfluidics technologies may bring diagnostics closer to the patient. Anal Bioanal Chem (2008) 1.35

Nanodisk codes. Nano Lett (2007) 1.24

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics (2008) 1.14

ICAM1 and VCAM1 polymorphisms, coronary artery calcium, and circulating levels of soluble ICAM-1: the multi-ethnic study of atherosclerosis (MESA). Atherosclerosis (2008) 1.12

Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative. J Mol Diagn (2006) 1.06

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells. BMC Bioinformatics (2008) 1.05

Magnetic assembly of high-density DNA arrays for genomic analyses. Anal Chem (2008) 1.02

Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res (2010) 1.02

Integrating global gene expression analysis and genetics. Adv Genet (2008) 1.01

Markers of B-vitamin deficiency and frailty in older women. J Nutr Health Aging (2008) 0.98

A single molecule array for digital targeted molecular analyses. Nucleic Acids Res (2008) 0.95

Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J Zhejiang Univ Sci B (2012) 0.95

Transcobalamin 2 variant associated with poststroke homocysteine modifies recurrent stroke risk. Neurology (2011) 0.94

Integrative predictive model of coronary artery calcification in atherosclerosis. Circulation (2009) 0.94

Adipocyte gene expression is altered in formerly obese mice and as a function of diet composition. J Nutr (2008) 0.93

Optimization of microfluidic microsphere-trap arrays. Biomicrofluidics (2013) 0.92

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics (2010) 0.92

In praise of arrays. Pediatr Nephrol (2008) 0.91

Multiplexed protein detection using antibody-conjugated microbead arrays in a microfabricated electrophoretic device. Lab Chip (2010) 0.89

Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. Theor Appl Genet (2014) 0.88

Pleiotropic effects and compensation mechanisms determine tissue specificity in mitochondrial myopathy and sideroblastic anemia (MLASA). Mol Genet Metab (2007) 0.87

Genetic variation in cholinergic muscarinic-2 receptor gene modulates M2 receptor binding in vivo and accounts for reduced binding in bipolar disorder. Mol Psychiatry (2010) 0.87

Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles. Anal Chem (2009) 0.87

Overview of electrochemical DNA biosensors: new approaches to detect the expression of life. Sensors (Basel) (2009) 0.86

Significant linkage at chromosome 19q for otitis media with effusion and/or recurrent otitis media (COME/ROM). BMC Med Genet (2011) 0.86

Associations of candidate genes to age-related macular degeneration among racial/ethnic groups in the multi-ethnic study of atherosclerosis. Am J Ophthalmol (2013) 0.85

Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB. Int J Neuropsychopharmacol (2010) 0.85

Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol (2013) 0.85

Association of PDE11A global haplotype with major depression and antidepressant drug response. Neuropsychiatr Dis Treat (2009) 0.83

Multiplexed VeraCode bead-based serological immunoassay for colorectal cancer. J Immunol Methods (2013) 0.81

The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Lipids (2009) 0.81

A common variant in SLC8A1 is associated with the duration of the electrocardiographic QT interval. Am J Hum Genet (2012) 0.80

Development of a microscopic platform for real-time monitoring of biomolecular interactions. Genome Res (2005) 0.80

Intra-familial tests of association between familial idiopathic scoliosis and linked regions on 9q31.3-q34.3 and 16p12.3-q22.2. Hum Hered (2012) 0.79

Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes. Microarrays (Basel) (2013) 0.78

Photocleavage-based affinity purification and printing of cell-free expressed proteins: application to proteome microarrays. Anal Biochem (2008) 0.78

BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies. Cancer Inform (2010) 0.77

Platform dependence of inference on gene-wise and gene-set involvement in human lung development. BMC Bioinformatics (2009) 0.77

Image decoding of photonic crystal beads array in the microfluidic chip for multiplex assays. Sci Rep (2014) 0.77

Expression profiling of drug response--from genes to pathways. Dialogues Clin Neurosci (2006) 0.77

Associations between NOS1AP single nucleotide polymorphisms (SNPs) and QT interval duration in four racial/ethnic groups in the Multi-Ethnic Study of Atherosclerosis (MESA). Ann Noninvasive Electrocardiol (2013) 0.77

Transcobalamin-II variants, decreased vitamin B12 availability and increased risk of frailty. J Nutr Health Aging (2010) 0.77

Retracted Microarray in parasitic infections. Trop Parasitol (2012) 0.75

Particle-Based Microarrays of Oligonucleotides and Oligopeptides. Microarrays (Basel) (2014) 0.75

Highly parallel oligonucleotide purification and functionalization using reversible chemistry. Nucleic Acids Res (2011) 0.75

Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics (2016) 0.75

Identifying differentially expressed genes in human acute leukemia and mouse brain microarray datasets utilizing QTModel. Funct Integr Genomics (2008) 0.75

Articles cited by this

Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol (1975) 503.08

Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48

Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol (1996) 72.84

Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 71.36

Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature (1953) 47.27

Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science (1992) 24.32

Detection of specific RNAs or specific fragments of DNA by fractionation in gels and transfer to diazobenzyloxymethyl paper. Methods Enzymol (1979) 18.24

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 18.23

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol (2000) 15.79

Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science (2001) 15.54

Light-directed, spatially addressable parallel chemical synthesis. Science (1991) 15.09

Accessing genetic information with high-density DNA arrays. Science (1996) 13.89

Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet (2003) 11.84

Genomics, gene expression and DNA arrays. Nature (2000) 11.48

Large-scale genotyping of complex DNA. Nat Biotechnol (2003) 10.00

Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A (1994) 9.59

Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol (2003) 9.10

Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol (2003) 7.02

Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat Biotechnol (2001) 6.30

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics (1992) 6.02

Single-cell gene expression profiling. Science (2002) 5.07

Luminescent quantum dots for multiplexed biological detection and imaging. Curr Opin Biotechnol (2002) 4.93

Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res (2002) 4.69

A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19

Advanced multiplexed analysis with the FlowMetrix system. Clin Chem (1997) 4.03

Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol (2002) 3.94

A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res (2000) 2.94

Options available--from start to finish--for obtaining data from DNA microarrays II. Nat Genet (2002) 2.62

Submicrometer metallic barcodes. Science (2001) 2.62

Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mol Biol (1999) 2.47

Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol (1998) 1.83

Automatic registration of microarray images. II. Hexagonal grid. Bioinformatics (2003) 1.70

Encoding microcarriers: present and future technologies. Nat Rev Drug Discov (2002) 1.48

Sequence verification as quality-control step for production of cDNA microarrays. Biotechniques (2001) 1.45

Mutation detection by ligation to complete n-mer DNA arrays. Genome Res (1998) 1.41

Randomly ordered addressable high-density optical sensor arrays. Anal Chem (1998) 1.34

Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucleic Acids Res (2003) 1.25

Analysis of DNA microarrays by non-destructive fluorescent staining using SYBR green II. Biotechniques (2000) 1.20

Multiplex gene expression analysis for high-throughput drug discovery: screening and analysis of compounds affecting genes overexpressed in cancer cells. Mol Cancer Ther (2002) 1.14

Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. Genomics (1996) 1.10

Automatic registration of microarray images. I. Rectangular grid. Bioinformatics (2003) 0.89

Quality control in manufacturing oligo arrays: a combinatorial design approach. J Comput Biol (2002) 0.86

Nondestructive quality control for microarray production. Biotechniques (2002) 0.85

Multiplex metallica. Nat Biotechnol (2001) 0.82

Fidelity probes for DNA arrays. Proc Int Conf Intell Syst Mol Biol (1999) 0.80

Articles by these authors

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res (2006) 10.45

High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35

High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05

A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet (2005) 7.64

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res (2011) 6.90

Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics (2009) 6.08

BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques (2002) 5.98

A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32

Highly parallel genomic assays. Nat Rev Genet (2006) 4.24

A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19

Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol (2002) 3.94

Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet (2008) 3.92

High-throughput SNP genotyping on universal bead arrays. Mutat Res (2005) 3.78

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74

Interim guidance for the use of human papillomavirus DNA testing as an adjunct to cervical cytology for screening. Obstet Gynecol (2004) 3.67

DNA methylation signatures within the human brain. Am J Hum Genet (2007) 3.50

Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet (2007) 3.29

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet (2012) 3.08

Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interference. Mol Biol Cell (2005) 3.04

Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14. BMC Genet (2005) 3.04

Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol (2004) 3.04

Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am J Obstet Gynecol (2012) 2.92

Human embryonic stem cells have a unique epigenetic signature. Genome Res (2006) 2.89

American Cancer Society Guideline for human papillomavirus (HPV) vaccine use to prevent cervical cancer and its precursors. CA Cancer J Clin (2007) 2.81

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79

Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenat Diagn (2012) 2.79

A highly informative SNP linkage panel for human genetic studies. Nat Methods (2004) 2.74

microRNA-29a induces aberrant self-renewal capacity in hematopoietic progenitors, biased myeloid development, and acute myeloid leukemia. J Exp Med (2010) 2.68

Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma. Gastroenterology (2011) 2.66

Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells (2008) 2.52

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res (2010) 2.50

Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes. Gastroenterology (2013) 2.42

Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. Am J Obstet Gynecol (2012) 2.39

Gene-expression signature of vascular invasion in hepatocellular carcinoma. J Hepatol (2011) 2.39

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics (2013) 2.25

Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res (2004) 2.22

Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One (2009) 2.21

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Nat Protoc (2012) 2.21

Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A (2007) 2.17

Whole-genome genotyping. Methods Enzymol (2006) 2.16

GoldenGate assay for DNA methylation profiling. Methods Mol Biol (2009) 2.15

The impact of accepting living kidney donors with mild hypertension or proteinuria on transplantation rates. Am J Kidney Dis (2006) 2.14

Assessment of template based protein structure predictions in CASP9. Proteins (2011) 2.14

Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov (2013) 2.11

Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res (2006) 2.11

Compressing genomic sequence fragments using SlimGene. J Comput Biol (2011) 2.10

L-selectin is a possible biomarker for individual PML risk in natalizumab-treated MS patients. Neurology (2013) 2.02

New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood (2008) 1.97

Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma. Prenat Diagn (2013) 1.87

Dynamic cellular automata: an alternative approach to cellular simulation. In Silico Biol (2005) 1.85

Analysis of gene expression in stage I serous tumors identifies critical pathways altered in ovarian cancer. Gynecol Oncol (2009) 1.82

Expression signatures that correlated with Gleason score and relapse in prostate cancer. Genomics (2007) 1.78

Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods (2008) 1.69

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (2009) 1.68

Interferon beta-induced restoration of regulatory T-cell function in multiple sclerosis is prompted by an increase in newly generated naive regulatory T cells. Arch Neurol (2008) 1.62

Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol (2011) 1.60

Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res (2009) 1.58

Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell (2008) 1.57

Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing. Genome Res (2009) 1.55

Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res (2008) 1.54

Reactivation of the p53 pathway as a treatment modality for KSHV-induced lymphomas. J Clin Invest (2007) 1.49

A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One (2009) 1.48

Whole-genome haplotyping by dilution, amplification, and sequencing. Proc Natl Acad Sci U S A (2013) 1.44

APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Res (2013) 1.43

Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics (2006) 1.39

Genome-wide DNA methylation profiling. Wiley Interdiscip Rev Syst Biol Med (2010) 1.37

Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages. PLoS Genet (2012) 1.37

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36