Published in Proc Natl Acad Sci U S A on September 02, 2005
Inflammation and the Host Response to Injury (Trauma) | NCT00257231
MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res (2009) 23.27
Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet (2007) 12.08
A genomic storm in critically injured humans. J Exp Med (2011) 6.67
Harmonics of circadian gene transcription in mammals. PLoS Genet (2009) 4.97
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature (2013) 4.74
High-content flow cytometry and temporal data analysis for defining a cellular signature of graft-versus-host disease. Biol Blood Marrow Transplant (2007) 4.14
Dynamic regulatory network controlling TH17 cell differentiation. Nature (2013) 3.07
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol (2008) 3.02
Monitoring immune dysfunctions in the septic patient: a new skin for the old ceremony. Mol Med (2008) 2.93
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics (2008) 2.27
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection. PLoS Genet (2011) 2.10
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
Supervised normalization of microarrays. Bioinformatics (2010) 2.00
Modeling host responses in ferrets during A/California/07/2009 influenza infection. Virology (2010) 1.93
Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PLoS Pathog (2012) 1.84
Mouse ES cell-derived cardiac precursor cells are multipotent and facilitate identification of novel cardiac genes. J Clin Invest (2008) 1.80
Impulse control: temporal dynamics in gene transcription. Cell (2011) 1.79
The effects of genetic variation on gene expression dynamics during development. Nature (2013) 1.75
Extracting binary signals from microarray time-course data. Nucleic Acids Res (2007) 1.67
Discovering biological progression underlying microarray samples. PLoS Comput Biol (2011) 1.65
Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet (2010) 1.59
Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu Rev Biomed Eng (2007) 1.55
Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes. PLoS Comput Biol (2007) 1.55
Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res (2012) 1.47
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinformatics (2009) 1.43
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. J Comput Biol (2010) 1.41
Transcriptional programs controlling perinatal lung maturation. PLoS One (2012) 1.41
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLoS Comput Biol (2015) 1.39
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
BATS: a Bayesian user-friendly software for analyzing time series microarray experiments. BMC Bioinformatics (2008) 1.32
A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell (2013) 1.31
The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol (2009) 1.29
MicroRNA networks in mouse lung organogenesis. PLoS One (2010) 1.28
Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models. Mol Psychiatry (2010) 1.28
Gene silencing in severe systemic inflammation. Am J Respir Crit Care Med (2007) 1.27
Gene expression profiling in sepsis: timing, tissue, and translational considerations. Trends Mol Med (2014) 1.25
Significance analysis of microarray transcript levels in time series experiments. BMC Bioinformatics (2007) 1.22
Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation. Funct Integr Genomics (2008) 1.21
Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster. Genome Res (2007) 1.21
Individual matrix metalloproteinases control distinct transcriptional responses in airway epithelial cells infected with Pseudomonas aeruginosa. Infect Immun (2007) 1.20
Expression microarray analysis implicates apoptosis and interferon-responsive mechanisms in susceptibility to experimental cerebral malaria. Am J Pathol (2007) 1.20
Beyond good and evil in the oral cavity: insights into host-microbe relationships derived from transcriptional profiling of gingival cells. J Dent Res (2008) 1.18
Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics (2010) 1.17
Rapid acid treatment of Escherichia coli: transcriptomic response and recovery. BMC Microbiol (2008) 1.17
Modeling endotoxin-induced systemic inflammation using an indirect response approach. Math Biosci (2008) 1.13
Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2). BMC Genomics (2008) 1.12
Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment. J Transl Med (2008) 1.11
A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences. PLoS One (2010) 1.09
Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One (2010) 1.08
A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression. BMC Bioinformatics (2011) 1.08
Predicting Viral Infection From High-Dimensional Biomarker Trajectories. J Am Stat Assoc (2011) 1.07
Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol (2008) 1.06
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. BMC Bioinformatics (2008) 1.06
A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol (2009) 1.05
Genome-wide patterns of Arabidopsis gene expression in nature. PLoS Genet (2012) 1.05
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells. BMC Bioinformatics (2008) 1.05
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays. BMC Bioinformatics (2012) 1.05
Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol (2010) 1.04
In silico simulation of corticosteroids effect on an NFkB- dependent physicochemical model of systemic inflammation. PLoS One (2009) 1.04
Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer. BMC Med Genomics (2008) 1.04
Down-regulation of the Notch pathway mediated by a gamma-secretase inhibitor induces anti-tumour effects in mouse models of T-cell leukaemia. Br J Pharmacol (2009) 1.04
A computational approach to the functional clustering of periodic gene-expression profiles. Genetics (2008) 1.04
Significance analysis of microarray for relative quantitation of LC/MS data in proteomics. BMC Bioinformatics (2008) 1.04
Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes. PLoS Genet (2013) 1.03
Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol (2015) 1.03
Analysis of DNA microarray expression data. Best Pract Res Clin Haematol (2009) 1.03
Activin modulates the transcriptional response of LbetaT2 cells to gonadotropin-releasing hormone and alters cellular proliferation. Mol Endocrinol (2006) 1.02
A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res (2008) 1.02
High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. J Am Stat Assoc (2012) 1.01
A permutation-based multiple testing method for time-course microarray experiments. BMC Bioinformatics (2009) 1.00
Differential expression and network inferences through functional data modeling. Biometrics (2008) 1.00
The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol (2012) 1.00
Time series expression analyses using RNA-seq: a statistical approach. Biomed Res Int (2013) 0.98
Identification and interpretation of longitudinal gene expression changes in trauma. PLoS One (2010) 0.98
Comparison of the cytokine and chemokine dynamics of the early inflammatory response in models of burn injury and infection. Cytokine (2011) 0.97
Functional assessment of time course microarray data. BMC Bioinformatics (2009) 0.97
Estimating replicate time shifts using Gaussian process regression. Bioinformatics (2010) 0.97
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature. Sci Rep (2013) 0.97
A statistical framework for biomarker discovery in metabolomic time course data. Bioinformatics (2011) 0.96
Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. Aging Cell (2013) 0.96
Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction. BMC Genomics (2007) 0.96
Alternative transcript initiation and splicing as a response to DNA damage. PLoS One (2011) 0.95
Microarray-based expression profiling and informatics. Curr Opin Biotechnol (2007) 0.94
Dynamic metabolomic data analysis: a tutorial review. Metabolomics (2009) 0.94
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics (2014) 0.94
Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates. BMC Immunol (2010) 0.94
Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays. Microb Cell Fact (2007) 0.94
Microarray analyses of pituitary adenylate cyclase activating polypeptide (PACAP)-regulated gene targets in sympathetic neurons. Peptides (2007) 0.93
Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures. FEMS Yeast Res (2011) 0.93
Increased ratio of anti-apoptotic to pro-apoptotic Bcl2 gene-family members in lithium-responders one month after treatment initiation. Biol Mood Anxiety Disord (2012) 0.93
Conditional clustering of temporal expression profiles. BMC Bioinformatics (2008) 0.92
An intuitive graphical visualization technique for the interrogation of transcriptome data. Nucleic Acids Res (2011) 0.92
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Comput Biol (2013) 0.92
Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles. PLoS One (2010) 0.91
Modulators of prostate cancer cell proliferation and viability identified by short-hairpin RNA library screening. PLoS One (2012) 0.90
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol (2014) 0.90
Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain. Microb Cell Fact (2012) 0.90
Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery. EBioMedicine (2016) 0.90
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
Gene-expression profiles in hereditary breast cancer. N Engl J Med (2001) 29.80
Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A (2000) 18.42
From patterns to pathways: gene expression data analysis comes of age. Nat Genet (2002) 10.35
Statistical tests for differential expression in cDNA microarray experiments. Genome Biol (2003) 7.65
TACI and BCMA are receptors for a TNF homologue implicated in B-cell autoimmune disease. Nature (2000) 6.54
Nonparametric mixed effects models for unequally sampled noisy curves. Biometrics (2001) 6.45
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics (2003) 4.15
Hypomagnesemia with secondary hypocalcemia is caused by mutations in TRPM6, a new member of the TRPM gene family. Nat Genet (2002) 3.90
A transcriptional profile of aging in the human kidney. PLoS Biol (2004) 3.69
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A (2003) 2.10
An inactivating point mutation in the inhibitory wedge of CD45 causes lymphoproliferation and autoimmunity. Cell (2000) 2.00
Connecting proliferation and apoptosis in development and disease. Nat Rev Mol Cell Biol (2004) 1.97
C1q deficiency and autoimmunity: the effects of genetic background on disease expression. J Immunol (2002) 1.88
Lack of chemokine receptor CCR1 enhances Th1 responses and glomerular injury during nephrotoxic nephritis. J Clin Invest (1999) 1.84
Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Mol Biol Cell (2003) 1.79
Lupus-like kidney disease in mice deficient in the Src family tyrosine kinases Lyn and Fyn. Curr Biol (2001) 1.58
Assessing homeostasis through circadian patterns. Biometrics (2001) 1.11
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Isolation of rare circulating tumour cells in cancer patients by microchip technology. Nature (2007) 19.33
Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A (2013) 16.74
Detection of mutations in EGFR in circulating lung-cancer cells. N Engl J Med (2008) 13.54
A network-based analysis of systemic inflammation in humans. Nature (2005) 12.60
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Gene expression during the life cycle of Drosophila melanogaster. Science (2002) 11.36
Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol (2010) 10.05
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81
Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol (2003) 7.02
A genomic storm in critically injured humans. J Exp Med (2011) 6.67
The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A (2004) 6.34
Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res (2005) 6.32
An estimate of the science-wise false discovery rate and application to the top medical literature. Biostatistics (2013) 5.31
Dissecting the architecture of a quantitative trait locus in yeast. Nature (2002) 5.24
Microbes on the human vaginal epithelium. Proc Natl Acad Sci U S A (2005) 5.15
Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A (2004) 5.10
Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics (2005) 5.08
Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature (2011) 5.01
Systematic screen for human disease genes in yeast. Nat Genet (2002) 4.97
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet (2007) 4.59
Continuous inertial focusing, ordering, and separation of particles in microchannels. Proc Natl Acad Sci U S A (2007) 4.44
Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci U S A (2007) 3.93
Isolation and characterization of circulating tumor cells from patients with localized and metastatic prostate cancer. Sci Transl Med (2010) 3.90
Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PLoS One (2012) 3.74
A transcriptional profile of aging in the human kidney. PLoS Biol (2004) 3.69
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol (2012) 3.62
A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev Cell (2004) 3.56
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A (2007) 3.52
Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci U S A (2005) 3.49
Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genet (2006) 3.34
Multiplex protein assays based on real-time magnetic nanotag sensing. Proc Natl Acad Sci U S A (2008) 3.34
Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication. Proc Natl Acad Sci U S A (2004) 3.30
High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A (2007) 3.25
Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics (2004) 3.22
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device. Proc Natl Acad Sci U S A (2009) 3.19
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics (2011) 3.12
Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet (2005) 3.09
On the design and analysis of gene expression studies in human populations. Nat Genet (2007) 3.07
Support of the metabolic response to burn injury. Lancet (2004) 3.06
A microfluidic device for practical label-free CD4(+) T cell counting of HIV-infected subjects. Lab Chip (2006) 2.89
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res (2006) 2.81
Effect of flow and surface conditions on human lymphocyte isolation using microfluidic chambers. Langmuir (2004) 2.76
High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A (2010) 2.74
Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci U S A (2002) 2.72
American Burn Association consensus conference to define sepsis and infection in burns. J Burn Care Res (2007) 2.71
Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature (2009) 2.70
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res (2007) 2.70
Metabolic specialization associated with phenotypic switching in Candidaalbicans. Proc Natl Acad Sci U S A (2002) 2.69
The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics (2006) 2.57
Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics (2005) 2.50
Mesenchymal stem cells: Mechanisms of immunomodulation and homing. Cell Transplant (2010) 2.50
Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res (2005) 2.46
The Drosophila melanogaster toll pathway participates in resistance to infection by the gram-negative human pathogen Pseudomonas aeruginosa. Infect Immun (2003) 2.41
Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans. Nat Genet (2007) 2.36
Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet (2005) 2.32
Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol (2004) 2.31
High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics (2006) 2.25
An integrated platform of genomic assays reveals small-molecule bioactivities. Nat Chem Biol (2008) 2.21
The changing pattern and implications of multiple organ failure after blunt injury with hemorrhagic shock. Crit Care Med (2012) 2.17
Equilibrium separation and filtration of particles using differential inertial focusing. Anal Chem (2008) 2.13
Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 2.09
A microchip approach for practical label-free CD4+ T-cell counting of HIV-infected subjects in resource-poor settings. J Acquir Immune Defic Syndr (2007) 2.08
Benchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures. Ann Surg (2012) 2.07
High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci U S A (2012) 2.03
Long-term posttraumatic stress symptoms vary inversely with early opiate dosing in children recovering from serious burns: effects durable at 4 years. J Trauma Acute Care Surg (2014) 2.03
Regulatory networks affected by iron availability in Candida albicans. Mol Microbiol (2004) 2.02
Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression. Proc Natl Acad Sci U S A (2005) 2.02
Clinical microfluidics for neutrophil genomics and proteomics. Nat Med (2010) 2.02