Published in Genome Biol on January 28, 2005
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Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
The long-term stability of the human gut microbiota. Science (2013) 5.15
High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol (2007) 3.53
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Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PLoS One (2010) 2.32
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Mutant-specific gene programs in the zebrafish. Blood (2005) 2.15
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Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent. BMC Genomics (2007) 1.96
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Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics (2005) 1.70
The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics (2007) 1.67
Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes. Genome Med (2010) 1.64
Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol (2006) 1.62
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Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling. Neuron (2011) 1.34
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Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays. BMC Genomics (2008) 1.25
Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus. Infect Immun (2006) 1.24
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Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity. Algorithms Mol Biol (2009) 1.24
High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Appl Environ Microbiol (2009) 1.24
Towards the uniform distribution of null P values on Affymetrix microarrays. Genome Biol (2007) 1.23
Efficiency analysis of competing tests for finding differentially expressed genes in lung adenocarcinoma. Cancer Inform (2008) 1.21
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Bayesian optimal discovery procedure for simultaneous significance testing. BMC Bioinformatics (2009) 1.10
Disruption of the Fbxw8 gene results in pre- and postnatal growth retardation in mice. Mol Cell Biol (2007) 1.10
Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis (2010) 1.08
Estimation and correction of non-specific binding in a large-scale spike-in experiment. Genome Biol (2007) 1.07
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Background correction using dinucleotide affinities improves the performance of GCRMA. BMC Bioinformatics (2008) 1.06
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Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development (2012) 1.05
A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray. BMC Genomics (2006) 1.05
Improving comparability between microarray probe signals by thermodynamic intensity correction. Nucleic Acids Res (2007) 1.05
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Gene expression patterns in visual cortex during the critical period: synaptic stabilization and reversal by visual deprivation. Proc Natl Acad Sci U S A (2008) 1.05
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer (2009) 1.03
A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates. BMC Bioinformatics (2006) 1.03
Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation. BMC Genomics (2006) 1.02
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics (2009) 1.01
Biological assessment of robust noise models in microarray data analysis. Bioinformatics (2011) 1.00
A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs. Mol Cell Biol (2012) 1.00
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Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling. Genome Biol (2007) 0.98
Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Res (2011) 0.98
Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays. PLoS One (2008) 0.97
A close examination of double filtering with fold change and T test in microarray analysis. BMC Bioinformatics (2009) 0.96
The cell adhesion gene PVRL3 is associated with congenital ocular defects. Hum Genet (2011) 0.96
Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. FEMS Microbiol Ecol (2010) 0.96
Use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinformatics (2008) 0.95
A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data. BMC Genomics (2009) 0.95
A systems level, functional genomics analysis of chronic epilepsy. PLoS One (2011) 0.94
Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression. BMC Bioinformatics (2006) 0.93
A comparison of probe-level and probeset models for small-sample gene expression data. BMC Bioinformatics (2010) 0.92
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network. Proc Natl Acad Sci U S A (2012) 0.92
HIV infection and antiretroviral therapy have divergent effects on mitochondria in adipose tissue. J Infect Dis (2012) 0.92
Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma). BMC Genomics (2008) 0.92
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
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A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol (2003) 9.98
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl (2001) 8.50
Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol (2001) 7.01
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics (2003) 3.33
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Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics (2004) 2.04
A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol (2003) 2.03
Statistical methods for ranking differentially expressed genes. Genome Biol (2003) 2.02
RNA-guided human genome engineering via Cas9. Science (2013) 48.29
Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol (2011) 12.86
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol (2013) 11.35
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
Advanced sequencing technologies: methods and goals. Nat Rev Genet (2004) 9.31
Modular epistasis in yeast metabolism. Nat Genet (2004) 8.64
Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res (2013) 7.77
Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96
A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91
Cas9 as a versatile tool for engineering biology. Nat Methods (2013) 6.87
The promise and perils of Wnt signaling through beta-catenin. Science (2002) 6.11
Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods (2006) 5.96
From genetic privacy to open consent. Nat Rev Genet (2008) 5.95
Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods (2013) 5.93
The brain activity map project and the challenge of functional connectomics. Neuron (2012) 5.52
Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22
Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19
A logic-gated nanorobot for targeted transport of molecular payloads. Science (2012) 4.96
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Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25
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Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol (2013) 3.84
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Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74
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Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68
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The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61
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Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (2011) 3.49
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Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol (2002) 3.28
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Signaling role of hemocytes in Drosophila JAK/STAT-dependent response to septic injury. Dev Cell (2003) 3.05
Requirement of prorenin receptor and vacuolar H+-ATPase-mediated acidification for Wnt signaling. Science (2010) 3.04
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The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99
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High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol (2010) 2.68
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Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature (2007) 2.27
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Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol (2009) 1.99
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