Published in Nat Biotechnol on January 16, 2005
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol (2006) 4.30
Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res (2012) 2.54
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. Genome Biol (2009) 1.52
Searching for differentially expressed gene combinations. Genome Biol (2005) 1.48
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. Eur J Hum Genet (2011) 1.40
False positive reduction in protein-protein interaction predictions using gene ontology annotations. BMC Bioinformatics (2007) 1.25
Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics (2008) 1.25
Multi-gene expression predictors of single drug responses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resistance. PLoS One (2012) 1.23
Assessing human germ-cell mutagenesis in the Postgenome Era: a celebration of the legacy of William Lawson (Bill) Russell. Environ Mol Mutagen (2007) 1.20
Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics (2011) 1.19
Strategy for encoding and comparison of gene expression signatures. Genome Biol (2007) 1.18
Improving cancer classification accuracy using gene pairs. PLoS One (2010) 1.17
An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. BMC Genomics (2008) 1.14
Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res (2006) 1.14
Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol (2011) 1.12
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data. Bioinformatics (2008) 1.04
Integrative missing value estimation for microarray data. BMC Bioinformatics (2006) 0.97
An integrative network approach to map the transcriptome to the phenome. J Comput Biol (2009) 0.95
New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior. Proc Natl Acad Sci U S A (2012) 0.95
Microarray data mining using landmark gene-guided clustering. BMC Bioinformatics (2008) 0.93
Storing, linking, and mining microarray databases using SRS. BMC Bioinformatics (2005) 0.87
Class-specific correlations of gene expressions: identification and their effects on clustering analyses. Am J Hum Genet (2008) 0.87
Systematic noise degrades gene co-expression signals but can be corrected. BMC Bioinformatics (2015) 0.86
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database (Oxford) (2009) 0.85
Motif-guided sparse decomposition of gene expression data for regulatory module identification. BMC Bioinformatics (2011) 0.85
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics (2011) 0.83
Deciphering modular and dynamic behaviors of transcriptional networks. Genomic Med (2007) 0.83
Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome. Age (Dordr) (2009) 0.81
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. J Comput Biol (2012) 0.79
WeGET: predicting new genes for molecular systems by weighted co-expression. Nucleic Acids Res (2015) 0.78
A formal concept analysis approach to consensus clustering of multi-experiment expression data. BMC Bioinformatics (2014) 0.78
A pathway analysis tool for analyzing microarray data of species with low physiological information. Adv Bioinformatics (2008) 0.78
Retrospective analysis of survival improvement by molecular biomarker-based personalized chemotherapy for recurrent ovarian cancer. PLoS One (2014) 0.77
Functional Annotation: extracting functional and regulatory order from microarrays. Mol Syst Biol (2005) 0.76
A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells. Adv Appl Bioinform Chem (2008) 0.75
Interval Graph Limits. Ann Comb (2013) 0.75
Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space. Comput Math Methods Med (2016) 0.75
Disrupted cooperation between transcription factors across diverse cancer types. BMC Genomics (2016) 0.75
Three-way interaction model to trace the mechanisms involved in Alzheimer's disease transgenic mice. PLoS One (2017) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics (2008) 24.32
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell (2004) 9.41
GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space. Appl Bioinformatics (2004) 7.84
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics (2004) 6.78
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics (2005) 5.68
Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med (2008) 5.62
Atherosclerosis across 4000 years of human history: the Horus study of four ancient populations. Lancet (2013) 5.61
Synaptic targeting by Alzheimer's-related amyloid beta oligomers. J Neurosci (2004) 5.10
Alzheimer's disease-affected brain: presence of oligomeric A beta ligands (ADDLs) suggests a molecular basis for reversible memory loss. Proc Natl Acad Sci U S A (2003) 4.80
Genomic analysis of mouse retinal development. PLoS Biol (2004) 4.66
Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009) 4.32
Evolutionary medicine: from dwarf model systems to healthy centenarians? Science (2003) 4.31
Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci U S A (2002) 3.93
Phenotypic landscape of a bacterial cell. Cell (2010) 3.50
Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array. Physiol Genomics (2003) 3.39
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol (2006) 3.39
High red blood cell distribution width is closely associated with nonalcoholic fatty liver disease. Eur J Gastroenterol Hepatol (2014) 3.35
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res (2003) 3.31
Infection, inflammation, height, and longevity. Proc Natl Acad Sci U S A (2005) 3.17
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
A gene regulatory network in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 2.94
Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86
Self-assembly of Abeta(1-42) into globular neurotoxins. Biochemistry (2003) 2.85
Cytokines and cognition--the case for a head-to-toe inflammatory paradigm. J Am Geriatr Soc (2002) 2.79
Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (2008) 2.54
Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proc Natl Acad Sci U S A (2005) 2.51
Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science (2012) 2.50
Temporal dissection of tumorigenesis in primary cancers. Cancer Discov (2011) 2.40
The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci U S A (2007) 2.30
Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics (2005) 2.28
Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PLoS One (2010) 2.26
Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci U S A (2002) 2.20
Progesterone receptors: form and function in brain. Front Neuroendocrinol (2008) 2.15
The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol (2004) 2.10
Improving PacBio long read accuracy by short read alignment. PLoS One (2012) 2.06
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci U S A (2011) 2.05
Absence of glial fibrillary acidic protein and vimentin prevents hypertrophy of astrocytic processes and improves post-traumatic regeneration. J Neurosci (2004) 2.03
Mrc1 is required for normal progression of replication forks throughout chromatin in S. cerevisiae. Mol Cell (2005) 1.99
Caloric restriction attenuates Abeta-deposition in Alzheimer transgenic models. Neurobiol Aging (2004) 1.97
Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A (2010) 1.96
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A (2010) 1.84
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics (2006) 1.83
Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol (2007) 1.81
Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev (2009) 1.78
Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. Dev Cell (2012) 1.75
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc Natl Acad Sci U S A (2002) 1.74
NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. J Bacteriol (2010) 1.71
Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell (2012) 1.70
Systemic inflammation, infection, ApoE alleles, and Alzheimer disease: a position paper. Curr Alzheimer Res (2007) 1.68
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics (2011) 1.68
Peroxynitrite mediates neurotoxicity of amyloid beta-peptide1-42- and lipopolysaccharide-activated microglia. J Neurosci (2002) 1.66
Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62
Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell (2012) 1.61
Outcomes of early- and late-identified children at 3 years of age: findings from a prospective population-based study. Ear Hear (2013) 1.61
Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics (2007) 1.61
A graph-based approach to systematically reconstruct human transcriptional regulatory modules. Bioinformatics (2007) 1.59
Clustering analysis of SAGE data using a Poisson approach. Genome Biol (2004) 1.58
Differential patterns of age-related mortality increase in middle age and old age. J Gerontol A Biol Sci Med Sci (2003) 1.57
Short-term calorie and protein restriction provide partial protection from chemotoxicity but do not delay glioma progression. Exp Gerontol (2013) 1.57
What accounts for the wide variation in life span of genetically identical organisms reared in a constant environment? Mech Ageing Dev (2005) 1.57
goCluster integrates statistical analysis and functional interpretation of microarray expression data. Bioinformatics (2005) 1.50
Ageing: the old worm turns more slowly. Nature (2002) 1.49
Statistical Modeling of RNA-Seq Data. Stat Sci (2011) 1.49
Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A (2013) 1.48
The rise and fall of excess male infant mortality. Proc Natl Acad Sci U S A (2008) 1.47
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res (2012) 1.46
Chemical genetic modifier screens: small molecule trichostatin suppressors as probes of intracellular histone and tubulin acetylation. Chem Biol (2003) 1.46
Expression of heat shock proteins and heat shock protein messenger ribonucleic acid in human prostate carcinoma in vitro and in tumors in vivo. Cell Stress Chaperones (2005) 1.41
Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J Comput Biol (2004) 1.40
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc Natl Acad Sci U S A (2010) 1.39
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res (2012) 1.36
Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A (2010) 1.33
Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility. Mol Biol Cell (2004) 1.33
Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage. Proc Natl Acad Sci U S A (2007) 1.32
Gene profiling of skeletal muscle in an amyotrophic lateral sclerosis mouse model. Physiol Genomics (2007) 1.31
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database (Oxford) (2010) 1.31
Blood lipids, infection, and inflammatory markers in the Tsimane of Bolivia. Am J Hum Biol (2010) 1.30
Glutamatergic neurons in rodent models respond to nanoscale particulate urban air pollutants in vivo and in vitro. Environ Health Perspect (2011) 1.29
Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci U S A (2002) 1.28
H2A.Z functions to regulate progression through the cell cycle. Mol Cell Biol (2006) 1.27
A small-molecule inhibitor of Mps1 blocks the spindle-checkpoint response to a lack of tension on mitotic chromosomes. Curr Biol (2005) 1.26
SiO2 nanoparticles induce cytotoxicity and protein expression alteration in HaCaT cells. Part Fibre Toxicol (2010) 1.24