Published in Genome Biol on October 25, 2004
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An Arabidopsis gene network based on the graphical Gaussian model. Genome Res (2007) 2.45
Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol (2006) 2.36
Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet (2009) 2.34
Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics (2006) 1.79
CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol (2008) 1.60
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Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol (2011) 1.52
Carotenoid biosynthesis in Arabidopsis: a colorful pathway. Arabidopsis Book (2012) 1.40
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst Biol (2007) 1.34
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Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism. BMC Plant Biol (2008) 1.22
Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models. Proc Natl Acad Sci U S A (2009) 1.17
Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC Syst Biol (2009) 1.15
Elucidation of the transcription network governing mammalian sex determination by exploiting strain-specific susceptibility to sex reversal. Genes Dev (2009) 1.10
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Gene expression analysis, proteomics, and network discovery. Plant Physiol (2009) 1.09
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. BMC Bioinformatics (2011) 1.04
A Survey of Statistical Models for Reverse Engineering Gene Regulatory Networks. IEEE Signal Process Mag (2009) 0.97
Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks. BMC Bioinformatics (2010) 0.97
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Assessment method for a power analysis to identify differentially expressed pathways. PLoS One (2012) 0.93
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Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Res (2012) 0.92
Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol Biosyst (2009) 0.91
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Front Cell Dev Biol (2014) 0.90
Statistical analysis of big data on pharmacogenomics. Adv Drug Deliv Rev (2013) 0.89
On the degrees of freedom of reduced-rank estimators in multivariate regression. Biometrika (2015) 0.89
Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct (2012) 0.88
Network-based identification of biomarkers coexpressed with multiple pathways. Cancer Inform (2014) 0.88
Gene network landscape of the ciliate Tetrahymena thermophila. PLoS One (2011) 0.88
Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet (2013) 0.88
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Calibrated Precision Matrix Estimation for High-Dimensional Elliptical Distributions. IEEE Trans Inf Theory (2014) 0.85
An efficient method for identifying statistical interactors in gene association networks. Biostatistics (2009) 0.84
Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps. BMC Microbiol (2008) 0.84
Continuous cotemporal probabilistic modeling of systems biology networks from sparse data. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.83
B-cell lymphoma gene regulatory networks: biological consistency among inference methods. Front Genet (2013) 0.83
Using biologically interrelated experiments to identify pathway genes in Arabidopsis. Bioinformatics (2012) 0.82
The impact of measurement errors in the identification of regulatory networks. BMC Bioinformatics (2009) 0.81
Gene Network Reconstruction by Integration of Prior Biological Knowledge. G3 (Bethesda) (2015) 0.80
Systems biology and brain activity in neuronal pathways by smart device and advanced signal processing. Front Genet (2014) 0.80
Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock. PLoS One (2012) 0.79
Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. BMC Bioinformatics (2016) 0.78
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation. BMC Bioinformatics (2007) 0.77
The five-gene-network data analysis with local causal discovery algorithm using causal Bayesian networks. Ann N Y Acad Sci (2009) 0.77
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks. BMC Bioinformatics (2007) 0.76
Untangling statistical and biological models to understand network inference: the need for a genomics network ontology. Front Genet (2014) 0.76
Metabolic module mining based on Independent Component Analysis in Arabidopsis thaliana. Mol Cells (2012) 0.76
Algorithms for modeling global and context-specific functional relationship networks. Brief Bioinform (2015) 0.76
Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation. Biometrics (2014) 0.75
Bayesian probabilistic network modeling from multiple independent replicates. BMC Bioinformatics (2012) 0.75
The cluster graphical lasso for improved estimation of Gaussian graphical models. Comput Stat Data Anal (2015) 0.75
Mode Estimation for High Dimensional Discrete Tree Graphical Models. Adv Neural Inf Process Syst (2014) 0.75
Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC Plant Biol (2017) 0.75
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Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11
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Long-term region-wide declines in Caribbean corals. Science (2003) 13.74
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics (2002) 5.88
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J (2004) 4.30
Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics. Plant Physiol (2002) 4.18
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol (2003) 4.06
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput (2001) 3.97
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics (2003) 3.78
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Auxin-mediated cell cycle activation during early lateral root initiation. Plant Cell (2002) 3.36
The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol (2004) 3.16
Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2003) 3.01
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Cross-talk between the cytosolic mevalonate and the plastidial methylerythritol phosphate pathways in tobacco bright yellow-2 cells. J Biol Chem (2003) 2.16
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Metabolic cross talk between cytosolic and plastidial pathways of isoprenoid biosynthesis: unidirectional transport of intermediates across the chloroplast envelope membrane. Arch Biochem Biophys (2003) 1.88
Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism. Plant Mol Biol (2003) 1.47
Distinct light-mediated pathways regulate the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development. Plant Cell (2003) 1.46
Contribution of the mevalonate and methylerythritol phosphate pathways to the biosynthesis of gibberellins in Arabidopsis. J Biol Chem (2002) 1.46
Mevalonic acid partially restores chloroplast and etioplast development in Arabidopsis lacking the non-mevalonate pathway. Planta (2002) 1.31
Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data. Genome Inform Ser Workshop Genome Inform (2000) 0.91
MGraph: graphical models for microarray data analysis. Bioinformatics (2003) 0.86
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol (2004) 19.29
Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics (2007) 9.87
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics (2008) 8.36
A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics (2006) 5.36
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science (2008) 4.38
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol (2004) 3.16
Calmodulins and calcineurin B-like proteins: calcium sensors for specific signal response coupling in plants. Plant Cell (2002) 3.15
Genome-wide gene expression in an Arabidopsis cell suspension. Plant Mol Biol (2003) 3.12
The importance of size: successful recanalization by intravenous thrombolysis in acute anterior stroke depends on thrombus length. Stroke (2011) 3.03
Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2003) 3.01
The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev (2003) 2.99
Survival ensembles. Biostatistics (2005) 2.88
Supervised clustering of genes. Genome Biol (2002) 2.86
The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots. Cell (2005) 2.77
Gene-expression analysis and network discovery using Genevestigator. Trends Plant Sci (2005) 2.69
Predicting causal effects in large-scale systems from observational data. Nat Methods (2010) 2.68
Boosting for tumor classification with gene expression data. Bioinformatics (2003) 2.64
Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. EMBO J (2003) 2.56
Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol (2005) 2.46
MissForest--non-parametric missing value imputation for mixed-type data. Bioinformatics (2011) 2.46
Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol (2009) 2.38
A role for codon order in translation dynamics. Cell (2010) 2.30
Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res (2006) 2.26
Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana. Plant Cell (2005) 2.23
BicAT: a biclustering analysis toolbox. Bioinformatics (2006) 2.21
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics (2005) 2.15
RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics (2011) 2.14
Genome-wide analysis of gene expression profiles associated with cell cycle transitions in growing organs of Arabidopsis. Plant Physiol (2005) 2.06
HypE: an algorithm for fast hypervolume-based many-objective optimization. Evol Comput (2010) 2.01
Cell cycle-regulated gene expression in Arabidopsis. J Biol Chem (2002) 2.00
Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature (2004) 1.91
Transcriptional programs of early reproductive stages in Arabidopsis. Plant Physiol (2004) 1.86
Genome-wide identification of potential plant E2F target genes. Plant Physiol (2005) 1.85
Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics (2006) 1.79
Arabidopsis transcript profiling on Affymetrix GeneChip arrays. Plant Mol Biol (2003) 1.79
Combining convergence and diversity in evolutionary multiobjective optimization. Evol Comput (2002) 1.77
Gene expression signatures identify rhabdomyosarcoma subtypes and detect a novel t(2;2)(q35;p23) translocation fusing PAX3 to NCOA1. Cancer Res (2004) 1.67
Arabidopsis MSI1 is required for epigenetic maintenance of reproductive development. Development (2003) 1.65
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol (2010) 1.59
ATP-binding cassette transporter A1 locus is not a major determinant of HDL-C levels in a population at high risk for coronary heart disease. Atherosclerosis (2003) 1.58
Low-order conditional independence graphs for inferring genetic networks. Stat Appl Genet Mol Biol (2006) 1.53
H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet (2010) 1.51
NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal Chem (2005) 1.49
Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiol (2010) 1.46
Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway. Genes Dev (2006) 1.41
Network analysis of the MVA and MEP pathways for isoprenoid synthesis. Annu Rev Plant Biol (2013) 1.41
The BioCassava plus program: biofortification of cassava for sub-Saharan Africa. Annu Rev Plant Biol (2011) 1.40
Arabidopsis RETINOBLASTOMA-RELATED is required for stem cell maintenance, cell differentiation, and lateral organ production. Plant Cell (2010) 1.39
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol (2012) 1.38
Causal stability ranking. Bioinformatics (2012) 1.38
CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. PLoS Genet (2009) 1.36
Exploiting the combination of natural and genetically engineered resistance to cassava mosaic and cassava brown streak viruses impacting cassava production in Africa. PLoS One (2012) 1.33
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
Rice endosperm iron biofortification by targeted and synergistic action of nicotianamine synthase and ferritin. Plant Biotechnol J (2009) 1.33
MSI1-like proteins: an escort service for chromatin assembly and remodeling complexes. Trends Cell Biol (2005) 1.30
MIAME/Plant - adding value to plant microarrray experiments. Plant Methods (2006) 1.29
Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana. J Biol Chem (2006) 1.29
Proteome dynamics during plastid differentiation in rice. Plant Physiol (2006) 1.28
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27
pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integr Biol (Camb) (2011) 1.26
iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration. Plant J (2011) 1.23
Inactivation of the phloem-specific Dof zinc finger gene DAG1 affects response to light and integrity of the testa of Arabidopsis seeds. Plant Physiol (2002) 1.22