Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data.

PubWeight™: 2.32‹?› | Rank: Top 2%

🔗 View Article (PMID 14960459)

Published in Bioinformatics on February 12, 2004

Authors

Y Luan1, H Li

Author Affiliations

1: Rowe Program in Human Genetics, School of Medicine, University of California, Davis, CA 95616, USA.

Articles citing this

A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20

Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14

Circadian control of global gene expression patterns. Annu Rev Genet (2010) 1.85

Circadian clocks are resounding in peripheral tissues. PLoS Comput Biol (2006) 1.66

Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLoS Comput Biol (2015) 1.39

The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast (2006) 1.32

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics (2007) 1.24

Detecting periodic genes from irregularly sampled gene expressions: a comparison study. EURASIP J Bioinform Syst Biol (2008) 1.16

A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol (2009) 1.05

Bayesian detection of periodic mRNA time profiles without use of training examples. BMC Bioinformatics (2006) 1.05

A computational approach to the functional clustering of periodic gene-expression profiles. Genetics (2008) 1.04

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

Pho91 Is a vacuolar phosphate transporter that regulates phosphate and polyphosphate metabolism in Saccharomyces cerevisiae. Mol Biol Cell (2007) 1.00

Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics (2008) 0.98

Evolutionary and transcriptional analysis of karyopherin beta superfamily proteins. Mol Cell Proteomics (2008) 0.98

Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling. Heredity (Edinb) (2011) 0.97

Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments. Funct Integr Genomics (2005) 0.96

Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. BMC Bioinformatics (2009) 0.95

Spectral estimation in unevenly sampled space of periodically expressed microarray time series data. BMC Bioinformatics (2007) 0.95

Functional clustering of periodic transcriptional profiles through ARMA(p,q). PLoS One (2010) 0.94

Bayesian detection of non-sinusoidal periodic patterns in circadian expression data. Bioinformatics (2009) 0.87

A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments. BMC Bioinformatics (2007) 0.85

Principal-oscillation-pattern analysis of gene expression. PLoS One (2012) 0.84

Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects. BMC Bioinformatics (2012) 0.83

Robust discovery of periodically expressed genes using the laplace periodogram. BMC Bioinformatics (2009) 0.81

Predicting cell cycle regulated genes by causal interactions. PLoS One (2009) 0.81

Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration. BMC Bioinformatics (2008) 0.81

Bayesian functional data clustering for temporal microarray data. Int J Plant Genomics (2008) 0.80

Exploiting the full power of temporal gene expression profiling through a new statistical test: application to the analysis of muscular dystrophy data. BMC Bioinformatics (2006) 0.80

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC Syst Biol (2009) 0.79

Analysis of Correlated Gene Expression Data on Ordered Categories. J Indian Soc Agric Stat (2010) 0.79

SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. BMC Bioinformatics (2015) 0.78

Cancer survival analysis using semi-supervised learning method based on Cox and AFT models with L1/2 regularization. BMC Med Genomics (2016) 0.78

Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge. EURASIP J Bioinform Syst Biol (2009) 0.76

Time-course analysis of cyanobacterium transcriptome: detecting oscillatory genes. PLoS One (2011) 0.75

Robust test method for time-course microarray experiments. BMC Bioinformatics (2010) 0.75

H-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data. BMC Bioinformatics (2007) 0.75

Articles by these authors

Mutations of the VHL tumour suppressor gene in renal carcinoma. Nat Genet (1994) 10.14

Modular chemistry: secondary building units as a basis for the design of highly porous and robust metal-organic carboxylate frameworks. Acc Chem Res (2001) 9.19

Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92

Notch signalling controls pancreatic cell differentiation. Nature (1999) 7.18

Crystal structure of a T-cell receptor beta-chain complexed with a superantigen. Nature (1996) 7.11

Refined structure of alpha beta-tubulin at 3.5 A resolution. J Mol Biol (2001) 7.08

Mechanical unfolding intermediates in titin modules. Nature (1999) 6.12

Highly purified CD44+ prostate cancer cells from xenograft human tumors are enriched in tumorigenic and metastatic progenitor cells. Oncogene (2006) 5.86

A major role for VCAM-1, but not ICAM-1, in early atherosclerosis. J Clin Invest (2001) 4.98

An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl Environ Microbiol (2001) 4.59

A mouse model for spinal muscular atrophy. Nat Genet (2000) 4.37

Neutralizing antibody responses in acute human immunodeficiency virus type 1 subtype C infection. J Virol (2007) 4.13

Mechanisms underlying endothelial dysfunction in diabetes mellitus. Circ Res (2001) 3.89

PDGF-C is a new protease-activated ligand for the PDGF alpha-receptor. Nat Cell Biol (2000) 3.81

Patterns of vascular cell adhesion molecule-1 and intercellular adhesion molecule-1 expression in rabbit and mouse atherosclerotic lesions and at sites predisposed to lesion formation. Circ Res (1999) 3.69

Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia. J Med Genet (2004) 3.45

Oral ganciclovir for patients with cytomegalovirus retinitis treated with a ganciclovir implant. Roche Ganciclovir Study Group. N Engl J Med (1999) 3.38

Proton-pump inhibitors and risk of fractures: an update meta-analysis. Osteoporos Int (2016) 3.30

Crystal structure of constitutive endothelial nitric oxide synthase: a paradigm for pterin function involving a novel metal center. Cell (1998) 3.20

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci U S A (2000) 3.18

Structure of translation factor eIF4E bound to m7GDP and interaction with 4E-binding protein. Nat Struct Biol (1997) 3.14

Hormone-dependent, CARM1-directed, arginine-specific methylation of histone H3 on a steroid-regulated promoter. Curr Biol (2001) 3.09

Metastasis stage, adjuvant treatment, and residual tumor are prognostic factors for medulloblastoma in children: conclusions from the Children's Cancer Group 921 randomized phase III study. J Clin Oncol (1999) 3.08

Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog Biophys Mol Biol (2000) 3.00

TMPRSS2-ERG fusion, a common genomic alteration in prostate cancer activates C-MYC and abrogates prostate epithelial differentiation. Oncogene (2008) 2.94

Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J Clin Microbiol (2000) 2.87

Validation of near-infrared spectroscopy in humans. J Appl Physiol (1985) (1994) 2.77

tRNA splicing. J Biol Chem (1998) 2.77

Current neurosurgical management and the impact of the extent of resection in the treatment of malignant gliomas of childhood: a report of the Children's Cancer Group trial no. CCG-945. J Neurosurg (1998) 2.75

Feasibility of a high-speed gamma-camera design using the high-yield-pileup-event-recovery method. J Nucl Med (2001) 2.69

Targeted disruption of the murine VCAM1 gene: essential role of VCAM-1 in chorioallantoic fusion and placentation. Genes Dev (1995) 2.61

Solution structure of BID, an intracellular amplifier of apoptotic signaling. Cell (1999) 2.58

Dilated cardiomyopathy and atrioventricular conduction blocks induced by heart-specific inactivation of mitochondrial DNA gene expression. Nat Genet (1999) 2.57

Treatment of spinal muscular atrophy by sodium butyrate. Proc Natl Acad Sci U S A (2001) 2.56

Fps1p controls the accumulation and release of the compatible solute glycerol in yeast osmoregulation. Mol Microbiol (1999) 2.52

LIM homeodomain factors Lhx3 and Lhx4 assign subtype identities for motor neurons. Cell (1998) 2.50

Nephrin mediates actin reorganization via phosphoinositide 3-kinase in podocytes. Kidney Int (2007) 2.44

Functional consequences of elimination of i(to,f) and i(to,s): early afterdepolarizations, atrioventricular block, and ventricular arrhythmias in mice lacking Kv1.4 and expressing a dominant-negative Kv4 alpha subunit. Circ Res (2000) 2.39

Clinical and genetic characteristics of type 2 diabetes with and without GAD antibodies. Diabetes (1999) 2.36

Changing sexual attitudes and behaviour in China: implications for the spread of HIV and other sexually transmitted diseases. AIDS Care (1999) 2.35

An Arabidopsis mutant defective in the plastid general protein import apparatus. Science (1998) 2.35

Structure of a cytochrome P450-redox partner electron-transfer complex. Proc Natl Acad Sci U S A (1999) 2.30

Targeting of lung cancer mutational hotspots by polycyclic aromatic hydrocarbons. J Natl Cancer Inst (2000) 2.27

Novel gene mutations in patients with left ventricular noncompaction or Barth syndrome. Circulation (2001) 2.24

An absence of cutaneous neurofibromas associated with a 3-bp inframe deletion in exon 17 of the NF1 gene (c.2970-2972 delAAT): evidence of a clinically significant NF1 genotype-phenotype correlation. Am J Hum Genet (2006) 2.23

Survival and prognostic factors following radiation therapy and chemotherapy for ependymomas in children: a report of the Children's Cancer Group. J Neurosurg (1998) 2.22

Attitudes to HIV and HIV testing in high prevalence areas of China: informing the introduction of voluntary counselling and testing programmes. Sex Transm Infect (2005) 2.14

Targeted disruption of the apolipoprotein C-III gene in mice results in hypotriglyceridemia and protection from postprandial hypertriglyceridemia. J Biol Chem (1994) 2.09

Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility. Development (1995) 2.03

Comparison of protein A gene sequencing with pulsed-field gel electrophoresis and epidemiologic data for molecular typing of methicillin-resistant Staphylococcus aureus. J Clin Microbiol (2000) 2.03

Occurrence of a new metallo-beta-lactamase IMP-4 carried on a conjugative plasmid in Citrobacter youngae from the People's Republic of China. FEMS Microbiol Lett (2001) 2.01

Apoptosis primarily accounts for the growth-inhibitory properties of sulindac metabolites and involves a mechanism that is independent of cyclooxygenase inhibition, cell cycle arrest, and p53 induction. Cancer Res (1997) 2.00

Vaginal bilateral cervical lips suture in combination with intrauterine Foley catheter to arrest postpartum hemorrhage. Clin Exp Obstet Gynecol (2015) 2.00

Exisulind induction of apoptosis involves guanosine 3',5'-cyclic monophosphate phosphodiesterase inhibition, protein kinase G activation, and attenuated beta-catenin. Cancer Res (2000) 2.00

Amplification of target-specific, ligation-dependent circular probe. Gene (1998) 1.96

Sulindac sulfone inhibits azoxymethane-induced colon carcinogenesis in rats without reducing prostaglandin levels. Cancer Res (1997) 1.96

Anti-RhoA and anti-RhoC siRNAs inhibit the proliferation and invasiveness of MDA-MB-231 breast cancer cells in vitro and in vivo. Mol Ther (2005) 1.95

The DExH box protein Suv3p is a component of a yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity. Cell (1996) 1.94

Molecular characterization of the beta-N-acetylglucosaminidase of Escherichia coli and its role in cell wall recycling. J Bacteriol (2000) 1.93

Sterol methyltransferase 1 controls the level of cholesterol in plants. Plant Cell (2000) 1.89

The complete sequence of hepatitis E virus genotype 4 reveals an alternative strategy for translation of open reading frames 2 and 3. J Gen Virol (2000) 1.89

Gamma delta T-cell receptor repertoire in acute multiple sclerosis lesions. Proc Natl Acad Sci U S A (1992) 1.88

Computing the Cox model for case cohort designs. Lifetime Data Anal (1999) 1.85

Analysis of the p53 gene and its expression in human glioblastoma cells. Cancer Res (1994) 1.84

Fine-structure genetic mapping of human chromosomes using the polymerase chain reaction on single sperm: experimental design considerations. Am J Hum Genet (1989) 1.83

Evidence that HetR protein is an unusual serine-type protease. Proc Natl Acad Sci U S A (1998) 1.83

Functional epigenetics identifies a protocadherin PCDH10 as a candidate tumor suppressor for nasopharyngeal, esophageal and multiple other carcinomas with frequent methylation. Oncogene (2006) 1.82

Predictors of subclinical nodal involvement in clinical stages I and II non-small cell lung cancer: implications in the inoperable and three-dimensional dose-escalation settings. Int J Radiat Oncol Biol Phys (1999) 1.82

Multistep control of pituitary organogenesis. Science (1997) 1.82

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ (2012) 1.81

Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii. Proc Natl Acad Sci U S A (2001) 1.81

The major 8p22 tumor suppressor DLC1 is frequently silenced by methylation in both endemic and sporadic nasopharyngeal, esophageal, and cervical carcinomas, and inhibits tumor cell colony formation. Oncogene (2006) 1.80

A new twist in trypanosome RNA metabolism: cis-splicing of pre-mRNA. RNA (2000) 1.79

Chronic and recovered cases of sheep-associated malignant catarrhal fever in cattle. Vet Rec (1997) 1.78

Robust increase of cutaneous sensitivity, cytokine production and sympathetic sprouting in rats with localized inflammatory irritation of the spinal ganglia. Neuroscience (2006) 1.78

Molecular design of aquaporin-1 water channel as revealed by electron crystallography. Nat Struct Biol (1997) 1.77

Evidence for a dystrophin missense mutation as a cause of X-linked dilated cardiomyopathy. Circulation (1997) 1.76

Assembly of metal-organic frameworks from large organic and inorganic secondary building units: new examples and simplifying principles for complex structures. J Am Chem Soc (2001) 1.74

Risk factors for oesophageal cancer in northeast China. Int J Cancer (1994) 1.73

Penile implant success in patients with corporal fibrosis using multiple incisions and minimal scar tissue excision. Urology (1999) 1.71

Attenuation of the slow component of delayed rectification, action potential prolongation, and triggered activity in mice expressing a dominant-negative Kv2 alpha subunit. Circ Res (1999) 1.71

Gamma interferon as a crucial host defense against Rickettsia conorii in vivo. Infect Immun (1987) 1.70

Analysis of plasma and urinary tea polyphenols in human subjects. Cancer Epidemiol Biomarkers Prev (1995) 1.70

Absorption, distribution, elimination of tea polyphenols in rats. Drug Metab Dispos (1997) 1.69

Peripheral benzodiazepine receptor in cholesterol transport and steroidogenesis. Steroids (1997) 1.69

Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma. Allergy (2008) 1.69

Long-term effects of a randomised trial of a 6-year lifestyle intervention in impaired glucose tolerance on diabetes-related microvascular complications: the China Da Qing Diabetes Prevention Outcome Study. Diabetologia (2010) 1.68

Hypothalamic obesity caused by cranial insult in children: altered glucose and insulin dynamics and reversal by a somatostatin agonist. J Pediatr (1999) 1.63

SMRTe, a silencing mediator for retinoid and thyroid hormone receptors-extended isoform that is more related to the nuclear receptor corepressor. Proc Natl Acad Sci U S A (1999) 1.63

Patterns of parapatric speciation. Evolution (2000) 1.63

Peripheral-type benzodiazepine receptor (PBR) in human breast cancer: correlation of breast cancer cell aggressive phenotype with PBR expression, nuclear localization, and PBR-mediated cell proliferation and nuclear transport of cholesterol. Cancer Res (1999) 1.63

Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus. J Biol Chem (2000) 1.63

Understanding the role of the essential Asp251 in cytochrome p450cam using site-directed mutagenesis, crystallography, and kinetic solvent isotope effect. Biochemistry (1998) 1.62

Expression and clinical significance of the stem cell marker CD133 in hepatocellular carcinoma. Int J Clin Pract (2008) 1.62

Safety enhanced photodynamic therapy with half dose verteporfin for chronic central serous chorioretinopathy: a short term pilot study. Br J Ophthalmol (2006) 1.61

A randomized trial of acupuncture as an adjunctive therapy in osteoarthritis of the knee. Rheumatology (Oxford) (1999) 1.60

Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions. Phys Rev Lett (2011) 1.60

A divergent genotype of hepatitis E virus in Chinese patients with acute hepatitis. J Gen Virol (1999) 1.59

Matrix metalloproteinase inhibition attenuates left ventricular remodeling and dysfunction in a rat model of progressive heart failure. Circulation (2001) 1.59