Published in Bioinformatics on August 05, 2010
Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell (2014) 2.60
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection. Nat Med (2013) 2.06
Intestinal inflammation modulates expression of the iron-regulating hormone hepcidin depending on erythropoietic activity and the commensal microbiota. J Immunol (2014) 2.05
KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (2012) 1.99
Identification of Hipk2 as an essential regulator of white fat development. Proc Natl Acad Sci U S A (2014) 1.75
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog (2013) 1.72
Self-renewing resident arterial macrophages arise from embryonic CX3CR1(+) precursors and circulating monocytes immediately after birth. Nat Immunol (2015) 1.67
Glioma cancer stem cells secrete Gremlin1 to promote their maintenance within the tumor hierarchy. Genes Dev (2014) 1.57
Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells. Proc Natl Acad Sci U S A (2012) 1.54
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res (2012) 1.54
Transcriptome responses to combinations of stresses in Arabidopsis. Plant Physiol (2013) 1.53
Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism. Proc Natl Acad Sci U S A (2014) 1.40
PIK3CA(H1047R) induces multipotency and multi-lineage mammary tumours. Nature (2015) 1.32
A chromatin-modifying function of JNK during stem cell differentiation. Nat Genet (2011) 1.31
Translational profiling of cardiomyocytes identifies an early Jak1/Stat3 injury response required for zebrafish heart regeneration. Proc Natl Acad Sci U S A (2013) 1.27
HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells. PLoS One (2013) 1.25
The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J (2014) 1.19
The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol (2015) 1.16
Activation of the NOTCH pathway in head and neck cancer. Cancer Res (2013) 1.15
The G protein α subunit Gαs is a tumor suppressor in Sonic hedgehog-driven medulloblastoma. Nat Med (2014) 1.11
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DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol (2015) 1.07
ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor. PLoS One (2013) 1.06
Pesticide methoxychlor promotes the epigenetic transgenerational inheritance of adult-onset disease through the female germline. PLoS One (2014) 1.05
MiR-155 has a protective role in the development of non-alcoholic hepatosteatosis in mice. PLoS One (2013) 1.04
The DEAH-box RNA helicase RHAU binds an intramolecular RNA G-quadruplex in TERC and associates with telomerase holoenzyme. Nucleic Acids Res (2011) 1.04
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Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation. PLoS Genet (2014) 1.01
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. Elife (2014) 1.01
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Differential response to abiraterone acetate and di-n-butyl phthalate in an androgen-sensitive human fetal testis xenograft bioassay. Toxicol Sci (2013) 1.00
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Graft union formation in grapevine induces transcriptional changes related to cell wall modification, wounding, hormone signalling, and secondary metabolism. J Exp Bot (2013) 0.97
A therapeutically targetable mechanism of BCR-ABL-independent imatinib resistance in chronic myeloid leukemia. Sci Transl Med (2014) 0.97
Long-term in vitro culture of grape berries and its application to assess the effects of sugar supply on anthocyanin accumulation. J Exp Bot (2014) 0.96
Rituximab efficiently depletes increased CD20-expressing T cells in multiple sclerosis patients. J Immunol (2014) 0.95
A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat. Mol Pain (2014) 0.95
The basic leucine zipper transcription factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 is an important transcriptional regulator of abscisic acid-dependent grape berry ripening processes. Plant Physiol (2013) 0.94
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Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.92
HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain. Pain (2013) 0.91
Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PLoS Genet (2014) 0.91
Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine. BMC Plant Biol (2013) 0.91
TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation. J Immunol (2014) 0.91
Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue. Cell Metab (2014) 0.90
Gestational age-dependent changes in gene expression of metabolic enzymes and transporters in pregnant mice. Drug Metab Dispos (2012) 0.90
Suppression of IFN-induced transcription underlies IFN defects generated by activated Ras/MEK in human cancer cells. PLoS One (2012) 0.89
Drosophila melanogaster linker histone dH1 is required for transposon silencing and to preserve genome integrity. Nucleic Acids Res (2012) 0.89
Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells. Leukemia (2015) 0.89
Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nat Med (2015) 0.89
A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients. Sci Rep (2015) 0.88
A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. DNA Res (2016) 0.87
Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues. BMC Genomics (2013) 0.86
Post-transcriptional regulatory elements and spatiotemporal specification of neocortical stem cells and projection neurons. Neuroscience (2013) 0.86
Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes. Retrovirology (2014) 0.86
A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits. PLoS One (2016) 0.85
Confounding in ex vivo models of Diamond-Blackfan anemia. Blood (2017) 0.85
Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury. Sci Rep (2015) 0.85
GROUP B STREPTOCOCCUS CIRCUMVENTS NEUTROPHILS AND NEUTROPHIL EXTRACELLULAR TRAPS DURING AMNIOTIC CAVITY INVASION AND PRETERM LABOR. Sci Immunol (2016) 0.85
Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease. PLoS Genet (2016) 0.85
Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice. Oncotarget (2015) 0.84
Therapeutically Targetable ALK Mutations in Leukemia. Cancer Res (2015) 0.84
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation. BMC Genomics (2014) 0.84
Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Res (2014) 0.83
Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. BMC Genomics (2013) 0.83
Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis. PLoS One (2013) 0.83
Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling. J Nat Prod (2015) 0.83
Memory T cells specific for murine cytomegalovirus re-emerge after multiple challenges and recapitulate immunity in various adoptive transfer scenarios. J Immunol (2015) 0.83
Mapping gene regulatory circuitry of Pax6 during neurogenesis. Cell Discov (2016) 0.82
Two histone deacetylases, FfHda1 and FfHda2, are important for Fusarium fujikuroi secondary metabolism and virulence. Appl Environ Microbiol (2013) 0.82
The nature and extent of mutational pleiotropy in gene expression of male Drosophila serrata. Genetics (2014) 0.82
Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress. Front Plant Sci (2013) 0.82
Transcriptome sequencing reveals a profile that corresponds to genomic variants in Waldenström macroglobulinemia. Blood (2016) 0.82
Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection. Sci Rep (2012) 0.82
Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma. PLoS One (2015) 0.81
Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. BMC Genomics (2012) 0.81
The genomic distribution of sex-biased genes in drosophila serrata: X chromosome demasculinization, feminization, and hyperexpression in both sexes. Genome Biol Evol (2013) 0.81
Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells. J Biol Chem (2015) 0.81
Structure-function studies of the bHLH phosphorylation domain of TWIST1 in prostate cancer cells. Neoplasia (2015) 0.81
Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus. J Clin Invest (2015) 0.81
Equalizer reduces SNP bias in Affymetrix microarrays. BMC Bioinformatics (2015) 0.81
Growth Cone Localization of the mRNA Encoding the Chromatin Regulator HMGN5 Modulates Neurite Outgrowth. Mol Cell Biol (2015) 0.80
GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge. PLoS One (2015) 0.80
A new approach for the study of lung smooth muscle phenotypes and its application in a murine model of allergic airway inflammation. PLoS One (2013) 0.80
Blocking sense-strand activity improves potency, safety and specificity of anti-hepatitis B virus short hairpin RNA. EMBO Mol Med (2016) 0.80
Attenuated monocyte apoptosis, a new mechanism for osteoporosis suggested by a transcriptome-wide expression study of monocytes. PLoS One (2015) 0.79
ISL1 regulates peroxisome proliferator-activated receptor γ activation and early adipogenesis via bone morphogenetic protein 4-dependent and -independent mechanisms. Mol Cell Biol (2014) 0.79
Pleiotropic mutations are subject to strong stabilizing selection. Genetics (2014) 0.79
The Effect of Statins on Blood Gene Expression in COPD. PLoS One (2015) 0.79
Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis. Nat Commun (2016) 0.79
Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues. Integr Biol (Camb) (2016) 0.79
T-cell acute leukaemia exhibits dynamic interactions with bone marrow microenvironments. Nature (2016) 0.78
TCR signal strength controls thymic differentiation of discrete proinflammatory γδ T cell subsets. Nat Immunol (2016) 0.78
TBR1 regulates autism risk genes in the developing neocortex. Genome Res (2016) 0.78
A molecular classification of human mesenchymal stromal cells. PeerJ (2016) 0.78
Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma. Mod Pathol (2015) 0.78
Uterine overdistention induces preterm labor mediated by inflammation: observations in pregnant women and nonhuman primates. Am J Obstet Gynecol (2015) 0.78
Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Genomics (2012) 0.78
Galahad: a web server for drug effect analysis from gene expression. Nucleic Acids Res (2015) 0.78
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Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
The International HapMap Project. Nature (2003) 73.65
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62
Comparison of Affymetrix GeneChip expression measures. Bioinformatics (2006) 7.49
Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (2006) 5.20
Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res (2002) 2.71
Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol (2006) 2.39
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (2009) 1.83
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat (2008) 1.75
Quantifying uncertainty in genotype calls. Bioinformatics (2009) 1.74
Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Stat Appl Genet Mol Biol (2003) 1.45
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Intra-individual change over time in DNA methylation with familial clustering. JAMA (2008) 6.17
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
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Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
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Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet (2009) 5.52
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (2006) 5.20
Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature (2004) 5.05
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A gene expression bar code for microarray data. Nat Methods (2007) 4.20
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol (2014) 3.89
Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med (2010) 3.81
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Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol (2012) 3.62
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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol (2012) 3.13
Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics (2010) 2.70
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res (2011) 2.42
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Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (2010) 2.11
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Global synthetic-lethality analysis and yeast functional profiling. Trends Genet (2005) 1.82
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Significance analysis and statistical dissection of variably methylated regions. Biostatistics (2011) 1.74
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Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol (2008) 1.61
Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure. Physiol Genomics (2005) 1.54
Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation (2004) 1.47
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Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC Bioinformatics (2011) 1.45
Using the R Package crlmm for Genotyping and Copy Number Estimation. J Stat Softw (2011) 1.41
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In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology. BMC Genomics (2005) 1.39
Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics (2011) 1.36
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DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. Int J Epidemiol (2012) 1.30
Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol (2008) 1.23
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol (2014) 1.22
Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res (2005) 1.21
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Measuring cell-type specific differential methylation in human brain tissue. Genome Biol (2013) 1.19
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The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Res (2013) 1.09
Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics (2012) 1.07
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Intensity normalization improves color calling in SOLiD sequencing. Nat Methods (2010) 1.03
Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. BMC Genomics (2011) 1.00
Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes (2010) 0.98
Gene expression in giant cell myocarditis: Altered expression of immune response genes. Int J Cardiol (2005) 0.98
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics (2012) 0.97
The psychophysiology of the maternal-fetal relationship. Psychophysiology (2004) 0.95
Prenatal development of intrafetal and maternal-fetal synchrony. Behav Neurosci (2006) 0.95
Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics (2003) 0.95
Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control (2015) 0.94
Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics (2003) 0.90
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics (2013) 0.89
Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics (2011) 0.88
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics (2012) 0.87
Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions. BMC Genomics (2008) 0.85
Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res (2005) 0.84
Stacking the deck: double-tiled DNA microarrays. Nat Methods (2006) 0.81
Leydig cell gene expression: effects of age and caloric restriction. Exp Gerontol (2004) 0.80
Fast wavelet based functional models for transcriptome analysis with tiling arrays. Stat Appl Genet Mol Biol (2012) 0.77
The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC Bioinformatics (2012) 0.75