Published in BMC Bioinformatics on December 13, 2009
Systems biology and cancer: promises and perils. Prog Biophys Mol Biol (2011) 0.85
Functional clustering of time series gene expression data by Granger causality. BMC Syst Biol (2012) 0.75
[''R"--project for statistical computing]. Ugeskr Laeger (2008) 41.69
Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98
Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med (2008) 10.12
An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics (2004) 7.85
Human housekeeping genes are compact. Trends Genet (2003) 7.65
Harmonics of circadian gene transcription in mammals. PLoS Genet (2009) 4.97
Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biol (2004) 2.95
Probe-level measurement error improves accuracy in detecting differential gene expression. Bioinformatics (2006) 1.83
Applying dynamic Bayesian networks to perturbed gene expression data. BMC Bioinformatics (2006) 1.77
Causality and pathway search in microarray time series experiment. Bioinformatics (2006) 1.74
Fundamentals of cDNA microarray data analysis. Trends Genet (2003) 1.72
Modeling gene expression measurement error: a quasi-likelihood approach. BMC Bioinformatics (2003) 1.72
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics (2009) 1.71
Circadian rhythms in a nutshell. Physiol Genomics (2000) 1.70
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol (2007) 1.69
Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc Natl Acad Sci U S A (2004) 1.58
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics (2005) 1.56
Intervention in context-sensitive probabilistic Boolean networks. Bioinformatics (2004) 1.48
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics (2007) 1.43
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J Comput Biol (2000) 1.38
Relevance network between chemosensitivity and transcriptome in human hepatoma cells. Mol Cancer Ther (2003) 1.12
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol (2009) 1.06
Bayesian normalization and identification for differential gene expression data. J Comput Biol (2005) 0.91
Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. J Bioinform Comput Biol (2009) 0.88
A proposed metric for assessing the measurement quality of individual microarrays. BMC Bioinformatics (2006) 0.87
Modeling nonlinear gene regulatory networks from time series gene expression data. J Bioinform Comput Biol (2008) 0.86
Transcript quantification based on chemical labeling of RNA associated with fluorescent detection. Anal Biochem (2001) 0.80
Methods for estimating and mitigating errors in spotted, dual-color DNA microarrays. OMICS (2007) 0.80
Quality control and reproducibility in DNA microarray experiments. Genome Inform (2009) 0.78
International network of cancer genome projects. Nature (2010) 20.35
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res (2011) 6.02
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet (2012) 4.84
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. N Engl J Med (2015) 3.42
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac Symp Biocomput (2002) 2.30
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet (2013) 2.14
Somatic SETBP1 mutations in myeloid malignancies. Nat Genet (2013) 2.12
Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet (2010) 2.08
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform (2003) 2.08
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics (2003) 1.95
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood (2013) 1.79
Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet (2013) 1.71
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol (2007) 1.69
The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One (2013) 1.69
ACTN1 mutations cause congenital macrothrombocytopenia. Am J Hum Genet (2013) 1.49
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems (2004) 1.47
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinform Comput Biol (2003) 1.44
A neural network method for identification of RNA-interacting residues in protein. Genome Inform (2004) 1.42
Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Lett (2004) 1.40
Inferring the global structure of chromosomes from structural variations. BMC Genomics (2015) 1.37
Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol (2003) 1.37
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics (2008) 1.33
The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet (2013) 1.31
Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Res (2013) 1.29
Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics (2003) 1.26
A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Trans Comput Biol Bioinform (2012) 1.25
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res (2013) 1.24
Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol (2007) 1.20
Meditation training increases brain efficiency in an attention task. Neuroimage (2011) 1.17
BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood (2013) 1.16
Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol (2004) 1.16
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics (2011) 1.15
Art for reward's sake: visual art recruits the ventral striatum. Neuroimage (2010) 1.12
Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest (2014) 1.09
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res (2011) 1.08
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol (2009) 1.06
Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Inform (2006) 1.04
Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol (2004) 1.01
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst Biol (2009) 1.00
Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities. Genome Inform (2004) 1.00
Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor-associated macrophages. Cancer Res (2013) 0.99
An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics (2007) 0.99
Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J Biosci (2007) 0.99
Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients. J Hum Genet (2003) 0.98
Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics (2011) 0.98
Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy. Am J Hum Genet (2002) 0.98
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics (2005) 0.96
Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension. Mol Biosyst (2011) 0.95
Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS One (2012) 0.95
Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab (2009) 0.94
MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics (2011) 0.94
A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform (2004) 0.94
Cell Illustrator 4.0: a computational platform for systems biology. In Silico Biol (2010) 0.94
Depression in Parkinson's disease: convergence from voxel-based morphometry and functional magnetic resonance imaging in the limbic thalamus. Neuroimage (2009) 0.94
Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform (2006) 0.93
A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Inform (2010) 0.92
Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl Bioinformatics (2003) 0.91
Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy. J Hum Genet (2002) 0.91
Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Int J Oncol (2012) 0.91
Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform (2005) 0.91
Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac Symp Biocomput (2009) 0.91
rTMS treatment for depression in Parkinson's disease increases BOLD responses in the left prefrontal cortex. Int J Neuropsychopharmacol (2007) 0.90
The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer. Ann Surg Oncol (2012) 0.90
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics (2010) 0.89
A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays. Genome Inform (2006) 0.89
Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS One (2010) 0.89
Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philos Trans R Soc Lond B Biol Sci (2007) 0.89
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics (2007) 0.88
Abnormal visual activation in Parkinson's disease patients. Mov Disord (2010) 0.88
Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. J Bioinform Comput Biol (2009) 0.88
Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia. Br J Haematol (2014) 0.88
Cell cycle gene networks are associated with melanoma prognosis. PLoS One (2012) 0.88
DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics (2010) 0.88
GEDI: a user-friendly toolbox for analysis of large-scale gene expression data. BMC Bioinformatics (2007) 0.88
Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics (2008) 0.88
A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS One (2011) 0.88
Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.88
Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pac Symp Biocomput (2006) 0.88
Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis (2009) 0.88
Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform (2006) 0.88
N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Res (2011) 0.88
Clonal leukemic evolution in myelodysplastic syndromes with TET2 and IDH1/2 mutations. Haematologica (2013) 0.87
Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones. J Exp Zool A Comp Exp Biol (2006) 0.87
A pilot study of hippocampal volume and N-acetylaspartate (NAA) as response biomarkers in riluzole-treated patients with GAD. Eur Neuropsychopharmacol (2012) 0.87
Identifying drug active pathways from gene networks estimated by gene expression data. Genome Inform (2005) 0.86
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Proc IEEE Comput Soc Bioinform Conf (2002) 0.86
Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. Nat Commun (2013) 0.86
A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. BMC Genomics (2012) 0.86
Modeling nonlinear gene regulatory networks from time series gene expression data. J Bioinform Comput Biol (2008) 0.86
Brain activity patterns during phonological verbal fluency performance with varying levels of difficulty: a functional magnetic resonance imaging study in Portuguese-speaking healthy individuals. J Clin Exp Neuropsychol (2011) 0.85
Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Inform (2007) 0.85
Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Inform (2007) 0.85