Published in Nat Biotechnol on February 17, 2008
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) 10.63
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Circular RNAs are a large class of animal RNAs with regulatory potency. Nature (2013) 8.54
Transcriptional amplification in tumor cells with elevated c-Myc. Cell (2012) 8.24
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A (2008) 5.94
Peroxisomes are signaling platforms for antiviral innate immunity. Cell (2010) 5.24
Cancer regression and neurological toxicity following anti-MAGE-A3 TCR gene therapy. J Immunother (2013) 4.80
MicroRNA profiling: approaches and considerations. Nat Rev Genet (2012) 4.39
ClearCode34: A prognostic risk predictor for localized clear cell renal cell carcinoma. Eur Urol (2014) 4.00
Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81
CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell (2014) 3.68
Revisiting global gene expression analysis. Cell (2012) 3.63
Patients With Proneural Glioblastoma May Derive Overall Survival Benefit From the Addition of Bevacizumab to First-Line Radiotherapy and Temozolomide: Retrospective Analysis of the AVAglio Trial. J Clin Oncol (2015) 3.24
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol (2010) 3.09
HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature (2012) 3.08
Dynamic regulatory network controlling TH17 cell differentiation. Nature (2013) 3.07
The microglial sensome revealed by direct RNA sequencing. Nat Neurosci (2013) 2.73
Single cell analysis: the new frontier in 'omics'. Trends Biotechnol (2010) 2.71
Modulating inflammatory monocytes with a unique microRNA gene signature ameliorates murine ALS. J Clin Invest (2012) 2.67
High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples. J Clin Invest (2009) 2.66
Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science (2014) 2.63
Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A (2012) 2.59
Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples. Acta Neuropathol (2011) 2.53
The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Neuron (2012) 2.53
The Host Shapes the Gut Microbiota via Fecal MicroRNA. Cell Host Microbe (2016) 2.48
Practical implications of gene-expression-based assays for breast oncologists. Nat Rev Clin Oncol (2011) 2.38
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature (2014) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res (2011) 2.34
TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus. Nature (2010) 2.31
Predicting degree of benefit from adjuvant trastuzumab in NSABP trial B-31. J Natl Cancer Inst (2013) 2.28
A scalable system for production of functional pancreatic progenitors from human embryonic stem cells. PLoS One (2012) 2.24
mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol (2011) 2.20
Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol (2011) 2.15
Plasma microRNAs as novel biomarkers for endometriosis and endometriosis-associated ovarian cancer. Clin Cancer Res (2013) 2.15
The clinical implications of medulloblastoma subgroups. Nat Rev Neurol (2012) 2.12
A genomic approach to human autoimmune diseases. Annu Rev Immunol (2010) 2.10
Membrane-bound IL-21 promotes sustained ex vivo proliferation of human natural killer cells. PLoS One (2012) 2.09
Developing a clinically feasible personalized medicine approach to pediatric septic shock. Am J Respir Crit Care Med (2015) 2.09
Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis. Genome Biol (2009) 2.04
PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. BMC Med Genomics (2012) 2.01
Development of a genomic metric that can be rapidly used to predict clinical outcome in severely injured trauma patients. Crit Care Med (2013) 1.94
System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ (2014) 1.93
Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst (2014) 1.93
Response to MET inhibitors in patients with stage IV lung adenocarcinomas harboring MET mutations causing exon 14 skipping. Cancer Discov (2015) 1.91
Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog (2010) 1.90
Assessing the human immune system through blood transcriptomics. BMC Biol (2010) 1.86
NK cell-derived interferon-γ orchestrates cellular dynamics and the differentiation of monocytes into dendritic cells at the site of infection. Immunity (2012) 1.84
Multiplexed measurements of gene signatures in different analytes using the Nanostring nCounter Assay System. BMC Res Notes (2009) 1.80
TGF-β inhibition enhances chemotherapy action against triple-negative breast cancer. J Clin Invest (2013) 1.76
Prognostic Significance of Diffuse Large B-Cell Lymphoma Cell of Origin Determined by Digital Gene Expression in Formalin-Fixed Paraffin-Embedded Tissue Biopsies. J Clin Oncol (2015) 1.73
Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature (2015) 1.72
Determining cell-of-origin subtypes of diffuse large B-cell lymphoma using gene expression in formalin-fixed paraffin-embedded tissue. Blood (2014) 1.71
Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature (2015) 1.65
Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C. Gut (2013) 1.63
Relationships of PBMC microRNA expression, plasma viral load, and CD4+ T-cell count in HIV-1-infected elite suppressors and viremic patients. Retrovirology (2012) 1.62
Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides. Mucosal Immunol (2012) 1.62
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. Gene Expr Patterns (2010) 1.61
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. Dev Biol (2009) 1.59
Mycobacterium tuberculosis triggers host type I IFN signaling to regulate IL-1β production in human macrophages. J Immunol (2011) 1.58
Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance. Nat Med (2012) 1.55
The phosphoproteome of toll-like receptor-activated macrophages. Mol Syst Biol (2010) 1.55
Reprogramming CD19-specific T cells with IL-21 signaling can improve adoptive immunotherapy of B-lineage malignancies. Cancer Res (2011) 1.53
Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell (2013) 1.51
Portrait of Candida albicans adherence regulators. PLoS Pathog (2012) 1.51
Prion infections and anti-PrP antibodies trigger converging neurotoxic pathways. PLoS Pathog (2015) 1.49
Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens. BMC Cancer (2014) 1.48
Gene-expression-based prognostic assays for breast cancer. Nat Rev Clin Oncol (2010) 1.47
Capturing native long-range contiguity by in situ library construction and optical sequencing. Proc Natl Acad Sci U S A (2012) 1.47
Association between α-synuclein blood transcripts and early, neuroimaging-supported Parkinson's disease. Brain (2015) 1.46
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. Bioinformatics (2012) 1.45
Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol (2012) 1.44
Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer. PLoS One (2013) 1.43
Digital mRNA profiling. Nat Biotechnol (2008) 1.43
Distinct perturbation of the translatome by the antidiabetic drug metformin. Proc Natl Acad Sci U S A (2012) 1.43
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol (2009) 1.42
A molecular wound response program associated with regeneration initiation in planarians. Genes Dev (2012) 1.41
Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. Nat Neurosci (2013) 1.39
Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Lett (2009) 1.39
Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome. Cancer Res (2016) 1.39
miR-29ab1 deficiency identifies a negative feedback loop controlling Th1 bias that is dysregulated in multiple sclerosis. J Immunol (2012) 1.35
Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell (2011) 1.35
DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. Nature (2009) 1.34
Racial differences in human platelet PAR4 reactivity reflect expression of PCTP and miR-376c. Nat Med (2013) 1.34
Methodological challenges in utilizing miRNAs as circulating biomarkers. J Cell Mol Med (2014) 1.34
PAX-FOXO1 fusion status drives unfavorable outcome for children with rhabdomyosarcoma: a children's oncology group report. Pediatr Blood Cancer (2013) 1.32
Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem (2010) 1.32
Using the heat-shock response to discover anticancer compounds that target protein homeostasis. ACS Chem Biol (2011) 1.31
Divergent targets of Candida albicans biofilm regulator Bcr1 in vitro and in vivo. Eukaryot Cell (2012) 1.30
Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem (2012) 1.30
Gene expression-based model using formalin-fixed paraffin-embedded biopsies predicts overall survival in advanced-stage classical Hodgkin lymphoma. J Clin Oncol (2012) 1.28
Micro-RNA dysregulation in multiple sclerosis favours pro-inflammatory T-cell-mediated autoimmunity. Brain (2011) 1.27
Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol (2013) 1.25
Gene expression profiling in sepsis: timing, tissue, and translational considerations. Trends Mol Med (2014) 1.25
Clinical review: sepsis and septic shock--the potential of gene arrays. Crit Care (2012) 1.25
A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol (2005) 27.17
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
A genomic regulatory network for development. Science (2002) 9.67
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods (2005) 6.23
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A (2002) 5.98
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
Gene regulatory networks for development. Proc Natl Acad Sci U S A (2005) 4.45
Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood. Nat Biotechnol (2008) 4.40
Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc Natl Acad Sci U S A (2002) 4.26
PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet (2007) 4.09
Persistence of HIV-1 receptor-positive cells after HSV-2 reactivation is a potential mechanism for increased HIV-1 acquisition. Nat Med (2009) 4.03
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68
Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res (2004) 3.46
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35
Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci U S A (2008) 3.27
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics (2005) 3.21
A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93
A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A (2006) 2.89
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87
Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A (2009) 2.76
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics. Proc Natl Acad Sci U S A (2003) 2.70
The evolution of hierarchical gene regulatory networks. Nat Rev Genet (2009) 2.62
Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development (2007) 2.60
Extracellular microRNA: a new source of biomarkers. Mutat Res (2011) 2.55
Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics (2002) 2.54
Modeling transcriptional regulatory networks. Bioessays (2002) 2.50
Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. J Virol (2003) 2.46
Immune surveillance by CD8αα+ skin-resident T cells in human herpes virus infection. Nature (2013) 2.38
Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A (2007) 2.38
Clustering gene-expression data with repeated measurements. Genome Biol (2003) 2.37
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res (2011) 2.34
Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol (2002) 2.30
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. Proc Natl Acad Sci U S A (2003) 2.30
Comparison of PAM50 risk of recurrence score with oncotype DX and IHC4 for predicting risk of distant recurrence after endocrine therapy. J Clin Oncol (2013) 2.28
Hepatic resection associated with good survival for selected patients with intermediate and advanced-stage hepatocellular carcinoma. Ann Surg (2014) 2.27
On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics (2006) 2.27
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol (2002) 2.26
Small bilaterian fossils from 40 to 55 million years before the cambrian. Science (2004) 2.25
Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A (2003) 2.24
Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A (2005) 2.24
The last common bilaterian ancestor. Development (2002) 2.19
Hematopoietic stem cells contribute to the regeneration of renal tubules after renal ischemia-reperfusion injury in mice. J Am Soc Nephrol (2003) 2.12
Predictive computation of genomic logic processing functions in embryonic development. Proc Natl Acad Sci U S A (2012) 2.11
Computational representation of developmental genetic regulatory networks. Dev Biol (2005) 2.11
A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev Biol (2002) 2.09
A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science (2007) 2.04
The DNA sequence and analysis of human chromosome 14. Nature (2003) 2.02
A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc Natl Acad Sci U S A (2007) 2.00
cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol (2006) 1.96
A combined genomewide linkage scan of 1,233 families for prostate cancer-susceptibility genes conducted by the international consortium for prostate cancer genetics. Am J Hum Genet (2005) 1.96
Donuts, scratches and blanks: robust model-based segmentation of microarray images. Bioinformatics (2005) 1.90
Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res (2004) 1.90
Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J Bacteriol (2006) 1.89
Genetic effects on age-dependent onset and islet cell autoantibody markers in type 1 diabetes. Diabetes (2002) 1.89
New computational approaches for analysis of cis-regulatory networks. Dev Biol (2002) 1.85
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol (2012) 1.82
A gene regulatory network controlling the embryonic specification of endoderm. Nature (2011) 1.81
Evolution of gene regulatory networks controlling body plan development. Cell (2011) 1.80
The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis. BMC Genomics (2011) 1.79
Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med (2011) 1.78
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. Dev Biol (2006) 1.77
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim Biophys Acta (2008) 1.77
A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A (2005) 1.77
Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc Natl Acad Sci U S A (2011) 1.76
Sea urchin Forkhead gene family: phylogeny and embryonic expression. Dev Biol (2006) 1.76
Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res (2004) 1.74
Multifunctionality of PAI-1 in fibrogenesis: evidence from obstructive nephropathy in PAI-1-overexpressing mice. Kidney Int (2005) 1.74
Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development. Dev Biol (2008) 1.73
Activation of pmar1 controls specification of micromeres in the sea urchin embryo. Dev Biol (2003) 1.72
Boosting signal-to-noise in complex biology: prior knowledge is power. Cell (2011) 1.71
Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics. Hum Genet (2006) 1.70
Differential gene expression profiling of adult murine hematopoietic stem cells. Blood (2002) 1.69
A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med (2013) 1.69
Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One (2009) 1.68
Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A (2004) 1.66
Identification of high and low responders to lipopolysaccharide in normal subjects: an unbiased approach to identify modulators of innate immunity. J Immunol (2005) 1.66
CTC1 deletion results in defective telomere replication, leading to catastrophic telomere loss and stem cell exhaustion. EMBO J (2012) 1.65
cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev Biol (2005) 1.63
Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A (2007) 1.62
Gene regulatory network controlling embryonic specification in the sea urchin. Curr Opin Genet Dev (2004) 1.62
The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Dev Biol (2006) 1.62