Published in BMC Bioinformatics on May 26, 2010
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst Biol (2011) 1.19
Time series expression analyses using RNA-seq: a statistical approach. Biomed Res Int (2013) 0.98
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: transcriptional dynamics and regulatory structures. BMC Bioinformatics (2010) 0.79
Deconvolution of the confounding variations for reverse transcription quantitative real-time polymerase chain reaction by separate analysis of biological replicate data. Anal Biochem (2012) 0.76
Understanding Physiology in the Continuum: Integration of Information from Multiple -Omics Levels. Front Pharmacol (2017) 0.75
Effect of fasting on the metabolic response of liver to experimental burn injury. PLoS One (2013) 0.75
TTCA: an R package for the identification of differentially expressed genes in time course microarray data. BMC Bioinformatics (2017) 0.75
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Functional discovery via a compendium of expression profiles. Cell (2000) 31.39
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A (2005) 8.65
Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A (2000) 7.67
Fundamentals of experimental design for cDNA microarrays. Nat Genet (2002) 7.49
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
A model for measurement error for gene expression arrays. J Comput Biol (2001) 5.58
A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics (2002) 5.44
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics (2002) 4.73
Comparison of four basic models of indirect pharmacodynamic responses. J Pharmacokinet Biopharm (1993) 3.96
Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics (2009) 3.41
Bayesian mixture model based clustering of replicated microarray data. Bioinformatics (2004) 3.08
Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics (2002) 2.56
The effect of replication on gene expression microarray experiments. Bioinformatics (2003) 2.49
Clustering gene-expression data with repeated measurements. Genome Biol (2003) 2.37
How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol (2002) 2.10
A mixture model with random-effects components for clustering correlated gene-expression profiles. Bioinformatics (2006) 1.85
Using ANOVA to analyze microarray data. Biotechniques (2004) 1.77
Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J Pharmacol Exp Ther (2003) 1.71
Using ANOVA for gene selection from microarray studies of the nervous system. Methods (2003) 1.69
Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats. J Pharmacol Exp Ther (2002) 1.36
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach. Bioinformatics (2006) 1.19
Circadian variations in rat liver gene expression: relationships to drug actions. J Pharmacol Exp Ther (2008) 1.05
An approach for clustering gene expression data with error information. BMC Bioinformatics (2006) 1.05
A microarray analysis of the temporal response of liver to methylprednisolone: a comparative analysis of two dosing regimens. Endocrinology (2007) 1.03
Replication, variation and normalisation in microarray experiments. Appl Bioinformatics (2005) 1.02
Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development. Pac Symp Biocomput (2003) 0.98
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient. BMC Bioinformatics (2008) 0.97
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics (2007) 0.96
Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. OMICS (2009) 0.91
Adding confidence to gene expression clustering. Genetics (2005) 0.90
Identification of global transcriptional dynamics. PLoS One (2009) 0.84
Microarray data analysis: a hierarchical T-test to handle heteroscedasticity. Appl Bioinformatics (2004) 0.82
Power estimation of the t test for detecting differential gene expression. Funct Integr Genomics (2007) 0.77
Mass distributed clustering: a new algorithm for repeated measurements in gene expression data. Genome Inform (2005) 0.76
Diversity of mechanism-based pharmacodynamic models. Drug Metab Dispos (2003) 1.93
Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J Pharmacol Exp Ther (2003) 1.71
Cytoskeleton-based forecasting of stem cell lineage fates. Proc Natl Acad Sci U S A (2009) 1.68
Pharmacokinetic and pharmacodynamic modeling of recombinant human erythropoietin after single and multiple doses in healthy volunteers. J Clin Pharmacol (2004) 1.45
Attenuation of colistin bactericidal activity by high inoculum of Pseudomonas aeruginosa characterized by a new mechanism-based population pharmacodynamic model. Antimicrob Agents Chemother (2010) 1.44
Pharmacokinetic/pharmacodynamic modelling in diabetes mellitus. Clin Pharmacokinet (2008) 1.44
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res (2004) 1.40
Fifth-generation model for corticosteroid pharmacodynamics: application to steady-state receptor down-regulation and enzyme induction patterns during seven-day continuous infusion of methylprednisolone in rats. J Pharmacokinet Pharmacodyn (2002) 1.40
Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats. J Pharmacol Exp Ther (2002) 1.36
Physiologically based pharmacokinetic modeling of FTY720 (2-amino-2[2-(-4-octylphenyl)ethyl]propane-1,3-diol hydrochloride) in rats after oral and intravenous doses. Drug Metab Dispos (2006) 1.33
Receptor-mediated pharmacokinetics and pharmacodynamics of interferon-beta1a in monkeys. J Pharmacol Exp Ther (2003) 1.31
Sepsis: Something old, something new, and a systems view. J Crit Care (2011) 1.29
Development and qualification of a pharmacodynamic model for the pronounced inoculum effect of ceftazidime against Pseudomonas aeruginosa. Antimicrob Agents Chemother (2008) 1.26
Pharmacodynamic models for agents that alter production of natural cells with various distributions of lifespans. J Pharmacokinet Pharmacodyn (2006) 1.20
Gene expression analysis of hepatic roles in cause and development of diabetes in Goto-Kakizaki rats. J Endocrinol (2008) 1.18
Modeling the influence of circadian rhythms on the acute inflammatory response. J Theor Biol (2010) 1.18
Scaling pharmacodynamics from in vitro and preclinical animal studies to humans. Drug Metab Pharmacokinet (2009) 1.17
Gene arrays and temporal patterns of drug response: corticosteroid effects on rat liver. Funct Integr Genomics (2003) 1.16
Modeling corticosteroid effects in a rat model of rheumatoid arthritis I: mechanistic disease progression model for the time course of collagen-induced arthritis in Lewis rats. J Pharmacol Exp Ther (2008) 1.16
Dose equivalency evaluation of major corticosteroids: pharmacokinetics and cell trafficking and cortisol dynamics. J Clin Pharmacol (2003) 1.16
Pharmacokinetic and pharmacodynamic modeling of recombinant human erythropoietin after multiple subcutaneous doses in healthy subjects. Eur J Pharm Sci (2005) 1.16
Corticosteroid-regulated genes in rat kidney: mining time series array data. Am J Physiol Endocrinol Metab (2005) 1.14
Identification of a gene regulatory network necessary for the initiation of oligodendrocyte differentiation. PLoS One (2011) 1.11
Pharmacogenomic responses of rat liver to methylprednisolone: an approach to mining a rich microarray time series. AAPS J (2005) 1.11
Modeling circadian rhythms of glucocorticoid receptor and glutamine synthetase expression in rat skeletal muscle. Pharm Res (2006) 1.10
Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens. Physiol Genomics (2007) 1.10
Circadian rhythms in gene expression: Relationship to physiology, disease, drug disposition and drug action. Adv Drug Deliv Rev (2010) 1.10
Semi-mechanistic pharmacokinetic/pharmacodynamic modelling of the antimalarial effect of artemisinin. Br J Clin Pharmacol (2005) 1.09
Pharmacodynamic interaction of recombinant human interleukin-10 and prednisolone using in vitro whole blood lymphocyte proliferation. J Pharm Sci (2002) 1.09
Interspecies comparisons of pharmacokinetics and pharmacodynamics of recombinant human erythropoietin. Drug Metab Dispos (2007) 1.09
Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One (2010) 1.08
Target-mediated pharmacokinetic and pharmacodynamic model of recombinant human erythropoietin (rHuEPO). J Pharmacokinet Pharmacodyn (2007) 1.08
Pharmacokinetic and pharmacodynamic modeling of recombinant human erythropoietin after intravenous and subcutaneous administration in rats. J Pharmacol Exp Ther (2006) 1.06
In vivo multi-tissue corticosteroid microarray time series available online at Public Expression Profile Resource (PEPR). Pharmacogenomics (2003) 1.06
Circadian variations in rat liver gene expression: relationships to drug actions. J Pharmacol Exp Ther (2008) 1.05
The genomic response of skeletal muscle to methylprednisolone using microarrays: tailoring data mining to the structure of the pharmacogenomic time series. Pharmacogenomics (2004) 1.05
Utility of cleavable isotope-coded affinity-tagged reagents for quantification of low-copy proteins induced by methylprednisolone using liquid chromatography/tandem mass spectrometry. Anal Chem (2006) 1.05
Mechanistic population pharmacokinetics of total and unbound paclitaxel for a new nanodroplet formulation versus Taxol in cancer patients. Cancer Chemother Pharmacol (2008) 1.05
Pharmacokinetic and pharmacodynamic modeling of recombinant human erythropoietin after intravenous and subcutaneous dose administration in cynomolgus monkeys. J Pharmacol Exp Ther (2003) 1.04
In silico simulation of corticosteroids effect on an NFkB- dependent physicochemical model of systemic inflammation. PLoS One (2009) 1.04
Methods of utilizing baseline values for indirect response models. J Pharmacokinet Pharmacodyn (2009) 1.03
Receptor-mediated pharmacokinetic/pharmacodynamic model of interferon-beta 1a in humans. Pharm Res (2002) 1.03
A microarray analysis of the temporal response of liver to methylprednisolone: a comparative analysis of two dosing regimens. Endocrinology (2007) 1.03
Receptor/gene-mediated pharmacodynamic effects of methylprednisolone on phosphoenolpyruvate carboxykinase regulation in rat liver. J Pharmacol Exp Ther (2004) 1.02
Pharmacokinetic and pharmacodynamic modeling of exendin-4 in type 2 diabetic Goto-Kakizaki rats. J Pharmacol Exp Ther (2010) 1.02
Area/moment and compartmental modeling of pharmacokinetics during pregnancy: applications to maternal/fetal exposures to corticosteroids in sheep and rats. Pharm Res (2004) 1.01
Target-mediated pharmacokinetic and pharmacodynamic model of exendin-4 in rats, monkeys, and humans. Drug Metab Dispos (2012) 1.00
Temporal profiling of the transcriptional basis for the development of corticosteroid-induced insulin resistance in rat muscle. J Endocrinol (2005) 1.00
Modeling the metabolic effects of terbutaline in beta2-adrenergic receptor diplotypes. Clin Pharmacol Ther (2004) 1.00
Adipose tissue deficiency and chronic inflammation in diabetic Goto-Kakizaki rats. PLoS One (2011) 0.99
Stabilization and HPLC analysis of betamethasone sodium phosphate in plasma. J Pharm Sci (2004) 0.99
Comparison of dexamethasone pharmacokinetics in female rats after intravenous and intramuscular administration. Biopharm Drug Dispos (2005) 0.99
Modeling of corticosteroid effects on hepatic low-density lipoprotein receptors and plasma lipid dynamics in rats. Pharm Res (2007) 0.98
Integrated QSPR--pharmacodynamic model of genomic effects of several corticosteroids. J Pharm Sci (2003) 0.98
Second-generation minimal physiologically-based pharmacokinetic model for monoclonal antibodies. J Pharmacokinet Pharmacodyn (2013) 0.98
Relationships between circadian rhythms and modulation of gene expression by glucocorticoids in skeletal muscle. Am J Physiol Regul Integr Comp Physiol (2008) 0.98
Modeling corticosteroid effects in a rat model of rheumatoid arthritis II: mechanistic pharmacodynamic model for dexamethasone effects in Lewis rats with collagen-induced arthritis. J Pharmacol Exp Ther (2008) 0.98
Control of hepatic differentiation via cellular aggregation in an alginate microenvironment. Biotechnol Bioeng (2007) 0.97
Applications of minimal physiologically-based pharmacokinetic models. J Pharmacokinet Pharmacodyn (2012) 0.97
Comparison of the cytokine and chemokine dynamics of the early inflammatory response in models of burn injury and infection. Cytokine (2011) 0.97
Pharmacokinetics and antibody responses to the CD3 antibody otelixizumab used in the treatment of type 1 diabetes. J Clin Pharmacol (2010) 0.96
Modeling diabetes disease progression and salsalate intervention in Goto-Kakizaki rats. J Pharmacol Exp Ther (2011) 0.96
Assessment of drug interactions relevant to pharmacodynamic indirect response models. J Pharmacokinet Pharmacodyn (2004) 0.96
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics (2007) 0.96
Pharmacokinetic/pharmacodynamic model for prednisolone inhibition of whole blood lymphocyte proliferation. Br J Clin Pharmacol (2002) 0.96
Betamethasone pharmacokinetics after two prodrug formulations in sheep: implications for antenatal corticosteroid use. Drug Metab Dispos (2005) 0.95
Modeling autonomic regulation of cardiac function and heart rate variability in human endotoxemia. Physiol Genomics (2011) 0.95
Synergism between arsenic trioxide and heat shock protein 90 inhibitors on signal transducer and activator of transcription protein 3 activity--pharmacodynamic drug-drug interaction modeling. Clin Cancer Res (2007) 0.94
Pharmacodynamics and pharmacogenomics of diverse receptor-mediated effects of methylprednisolone in rats using microarray analysis. J Pharmacokinet Pharmacodyn (2002) 0.94