Published in BMC Genomics on December 05, 2008
PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res (2009) 3.12
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol (2010) 1.82
Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol (2011) 1.21
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics (2010) 1.20
Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. Planta (2014) 0.85
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genomics (2014) 0.83
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. BMC Plant Biol (2011) 0.83
Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PLoS One (2015) 0.83
Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events. Plant Physiol (2016) 0.79
Oncoviruses and Pathogenic MicroRNAs in Humans. Open Virol J (2009) 0.78
Genetical genomics of Populus leaf shape variation. BMC Plant Biol (2015) 0.76
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (2005) 24.04
Hierarchical organization of modularity in metabolic networks. Science (2002) 22.47
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (2006) 21.03
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
Analysis of variance for gene expression microarray data. J Comput Biol (2000) 16.28
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res (2001) 11.93
Genetical genomics: the added value from segregation. Trends Genet (2001) 8.23
Revealing modular organization in the yeast transcriptional network. Nat Genet (2002) 6.73
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
How to infer gene networks from expression profiles. Mol Syst Biol (2007) 5.79
Leptin-specific patterns of gene expression in white adipose tissue. Genes Dev (2000) 4.57
Two independent and polarized processes of cell elongation regulate leaf blade expansion in Arabidopsis thaliana (L.) Heynh. Development (1996) 4.36
Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature (2001) 4.17
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Reverse engineering cellular networks. Nat Protoc (2006) 3.67
Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development (1999) 3.51
Defining transcription modules using large-scale gene expression data. Bioinformatics (2004) 3.33
Understanding network concepts in modules. BMC Syst Biol (2007) 3.28
The epidermis both drives and restricts plant shoot growth. Nature (2007) 3.18
Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics (2006) 3.10
PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics (2007) 3.01
The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta. Nat Genet (2006) 2.95
A transcriptional roadmap to wood formation. Proc Natl Acad Sci U S A (2001) 2.85
Structure and function of photosystems I and II. Annu Rev Plant Biol (2006) 2.70
FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev (1999) 2.58
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
Local expression of expansin induces the entire process of leaf development and modifies leaf shape. Proc Natl Acad Sci U S A (2001) 2.31
Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities. Development (2004) 2.24
The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J (2003) 2.23
Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development (2003) 2.17
A Populus EST resource for plant functional genomics. Proc Natl Acad Sci U S A (2004) 2.04
Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum Mol Genet (2005) 1.96
Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics (2004) 1.92
Quantitative trait locus analysis of growth-related traits in a new Arabidopsis recombinant inbred population. Plant Physiol (2004) 1.90
The YABBY gene family and abaxial cell fate. Curr Opin Plant Biol (2000) 1.77
Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics (2006) 1.76
The genetics and genomics of the drought response in Populus. Plant J (2006) 1.72
A transcriptional timetable of autumn senescence. Genome Biol (2004) 1.70
Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics (2005) 1.64
Genetic analysis of natural variations in the architecture of Arabidopsis thaliana vegetative leaves. Genetics (2002) 1.60
Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Plant J (2007) 1.58
New normalization methods for cDNA microarray data. Bioinformatics (2003) 1.56
DPTF: a database of poplar transcription factors. Bioinformatics (2007) 1.56
A comparative study of the genetic bases of natural variation in tomato leaf, sepal, and petal morphology. Theor Appl Genet (2004) 1.44
In silico gene function prediction using ontology-based pattern identification. Bioinformatics (2004) 1.44
CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation. Plant J (2003) 1.38
Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture. Evol Dev (2005) 1.36
The control of leaf development. New Phytol (2005) 1.31
The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. New Phytol (2009) 1.31
LONGIFOLIA1 and LONGIFOLIA2, two homologous genes, regulate longitudinal cell elongation in Arabidopsis. Development (2006) 1.29
The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium. Plant Mol Biol (2006) 1.19
Conservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development. Proc Natl Acad Sci U S A (2003) 1.16
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol (2007) 1.16
A genomic approach to investigate developmental cell death in woody tissues of Populus trees. Genome Biol (2005) 1.16
UPSC-BASE--Populus transcriptomics online. Plant J (2006) 1.13
Molecular genetics of growth and development in Populus (Salicaceae). v. mapping quantitative trait loci affecting leaf variation. Am J Bot (1997) 1.13
Arabidopsis D-type cyclin CYCD4;1 is a novel cyclin partner of B2-type cyclin-dependent kinase. Plant Physiol (2003) 1.11
Elucidating genomic regions determining enhanced leaf growth and delayed senescence in elevated CO2. Plant Cell Environ (2006) 1.11
Orthogonal projections to latent structures as a strategy for microarray data normalization. BMC Bioinformatics (2007) 1.09
Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development. New Phytol (2007) 1.03
Gene network analysis in plant development by genomic technologies. Int J Dev Biol (2005) 1.00
ERECTA is required for protection against heat-stress in the AS1/ AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. Planta (2004) 1.00
Variable gene expression in eukaryotes: a network perspective. J Exp Biol (2007) 0.99
The transcriptome of Populus in elevated CO2. New Phytol (2005) 0.95
Plant development: YABBYs claw to the fore. Curr Biol (1999) 0.87
Global expression profiling in leaves of free-growing aspen. BMC Plant Biol (2008) 0.86
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Prenatal exposure to PBDEs and neurodevelopment. Environ Health Perspect (2010) 5.02
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science (2006) 4.26
Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Anal Chem (2005) 4.14
Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models. Anal Chem (2007) 4.04
Polybrominated diphenyl ether (PBDE) flame retardants and thyroid hormone during pregnancy. Environ Health Perspect (2010) 2.79
Rapid regulation of light harvesting and plant fitness in the field. Science (2002) 2.74
PBDE concentrations in women's serum and fecundability. Environ Health Perspect (2010) 2.57
In utero and childhood polybrominated diphenyl ether (PBDE) exposures and neurodevelopment in the CHAMACOS study. Environ Health Perspect (2012) 2.56
LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biol (2008) 2.44
An overview of commercially used brominated flame retardants, their applications, their use patterns in different countries/regions and possible modes of release. Environ Int (2003) 2.39
High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Anal Chem (2005) 2.38
Serum PBDEs in a North Carolina toddler cohort: associations with handwipes, house dust, and socioeconomic variables. Environ Health Perspect (2012) 2.29
Low dose organochlorine pesticides and polychlorinated biphenyls predict obesity, dyslipidemia, and insulin resistance among people free of diabetes. PLoS One (2011) 2.28
Low dose of some persistent organic pollutants predicts type 2 diabetes: a nested case-control study. Environ Health Perspect (2010) 2.15
Extraction and GC/MS analysis of the human blood plasma metabolome. Anal Chem (2005) 2.13
A Populus EST resource for plant functional genomics. Proc Natl Acad Sci U S A (2004) 2.04
Chemometrics in metabolomics--a review in human disease diagnosis. Anal Chim Acta (2009) 1.96
Gene expression in autumn leaves. Plant Physiol (2003) 1.91
Association of prenatal exposure to polybrominated diphenyl ethers and infant birth weight. Am J Epidemiol (2011) 1.90
Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm). Anal Bioanal Chem (2004) 1.88
Partition of environmental chemicals between maternal and fetal blood and tissues. Environ Sci Technol (2010) 1.77
Absence of the Lhcb1 and Lhcb2 proteins of the light-harvesting complex of photosystem II - effects on photosynthesis, grana stacking and fitness. Plant J (2003) 1.76
The genetics and genomics of the drought response in Populus. Plant J (2006) 1.72
EST data suggest that poplar is an ancient polyploid. New Phytol (2005) 1.70
A transcriptional timetable of autumn senescence. Genome Biol (2004) 1.70
Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol (2005) 1.66
A cellular timetable of autumn senescence. Plant Physiol (2005) 1.66
Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes. Ecol Lett (2013) 1.66
A comparison of PBDE serum concentrations in Mexican and Mexican-American children living in California. Environ Health Perspect (2011) 1.62
Birth delivery mode modifies the associations between prenatal polychlorinated biphenyl (PCB) and polybrominated diphenyl ether (PBDE) and neonatal thyroid hormone levels. Environ Health Perspect (2008) 1.62
Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae). Genetics (2008) 1.61
Serum polybrominated diphenyl ether (PBDE) levels are higher in children (2-5 years of age) than in infants and adults. Environ Health Perspect (2009) 1.60
Exposure to PBDEs in the office environment: evaluating the relationships between dust, handwipes, and serum. Environ Health Perspect (2011) 1.59
Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Plant J (2007) 1.58
PROTON GRADIENT REGULATION5 is essential for proper acclimation of Arabidopsis photosystem I to naturally and artificially fluctuating light conditions. Plant Cell (2012) 1.56
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. Nucleic Acids Res (2011) 1.56
Lack of the light-harvesting complex CP24 affects the structure and function of the grana membranes of higher plant chloroplasts. Plant Cell (2006) 1.54
Apparent half-lives of hepta- to decabrominated diphenyl ethers in human serum as determined in occupationally exposed workers. Environ Health Perspect (2006) 1.54
Impact of dust from multiple microenvironments and diet on PentaBDE body burden. Environ Sci Technol (2011) 1.52
New high-resolution mass spectrometric approach for the measurement of polychlorinated biphenyls and organochlorine pesticides in human serum. J Chromatogr B Analyt Technol Biomed Life Sci (2003) 1.44
Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant J (2007) 1.41
Measurement of urinary monohydroxy polycyclic aromatic hydrocarbons using automated liquid-liquid extraction and gas chromatography/isotope dilution high-resolution mass spectrometry. Anal Chem (2006) 1.39
Variability of urinary concentrations of polycyclic aromatic hydrocarbon metabolite in general population and comparison of spot, first-morning, and 24-h void sampling. J Expo Sci Environ Epidemiol (2009) 1.37
Genomics and forest biology: Populus emerges as the perennial favorite. Plant Cell (2002) 1.34
Structure, function and regulation of plant photosystem I. Biochim Biophys Acta (2007) 1.34
The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. New Phytol (2009) 1.31
Genome-wide profiling of populus small RNAs. BMC Genomics (2009) 1.28
Evaluation of exposure reduction to indoor air pollution in stove intervention projects in Peru by urinary biomonitoring of polycyclic aromatic hydrocarbon metabolites. Environ Int (2011) 1.26
Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice. J Proteome Res (2006) 1.25
Determinants of prenatal exposure to polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in an urban population. Environ Health Perspect (2007) 1.25
Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.): a comparison of neutral markers, candidate genes and phenotypic traits. Evolution (2007) 1.23
The structure of photosystem II in Arabidopsis: localization of the CP26 and CP29 antenna complexes. Biochemistry (2003) 1.23
Protease gene families in Populus and Arabidopsis. BMC Plant Biol (2006) 1.22
Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data--a potential tool for multi-parametric diagnosis. J Proteome Res (2006) 1.21
Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments. Plant Physiol (2006) 1.19
Clinal variation in phyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen (Populus tremula). Genetics (2005) 1.19
Gestational exposure to endocrine-disrupting chemicals and reciprocal social, repetitive, and stereotypic behaviors in 4- and 5-year-old children: the HOME study. Environ Health Perspect (2014) 1.18
The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia. Environ Microbiol (2012) 1.17
Prenatal exposure to polycyclic aromatic hydrocarbons, benzo[a]pyrene-DNA adducts, and genomic DNA methylation in cord blood. Environ Health Perspect (2012) 1.17
AtFtsH6 is involved in the degradation of the light-harvesting complex II during high-light acclimation and senescence. Proc Natl Acad Sci U S A (2005) 1.16
Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants. Plant Physiol (2006) 1.16
A genomic approach to investigate developmental cell death in woody tissues of Populus trees. Genome Biol (2005) 1.16
Prenatal polybrominated diphenyl ether exposures and neurodevelopment in U.S. children through 5 years of age: the HOME study. Environ Health Perspect (2014) 1.16
Exposure to polybrominated diphenyl ethers and tetrabromobisphenol A among computer technicians. Chemosphere (2002) 1.15
Exposures among pregnant women near the World Trade Center site on 11 September 2001. Environ Health Perspect (2005) 1.13
UPSC-BASE--Populus transcriptomics online. Plant J (2006) 1.13
Serum levels of polybrominated diphenyl ethers (PBDEs) in foam recyclers and carpet installers working in the United States. Environ Sci Technol (2008) 1.11
Excretion profiles and half-lives of ten urinary polycyclic aromatic hydrocarbon metabolites after dietary exposure. Chem Res Toxicol (2012) 1.11
Individual variation in lipidomic profiles of healthy subjects in response to omega-3 Fatty acids. PLoS One (2013) 1.10
Lactational exposure to polybrominated diphenyl ethers and its relation to social and emotional development among toddlers. Environ Health Perspect (2012) 1.10
Diagnostic properties of metabolic perturbations in rheumatoid arthritis. Arthritis Res Ther (2011) 1.09
Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets. Analyst (2005) 1.09
Orthogonal projections to latent structures as a strategy for microarray data normalization. BMC Bioinformatics (2007) 1.09
Assessment of non-occupational exposure to polycyclic aromatic hydrocarbons through personal air sampling and urinary biomonitoring. J Environ Monit (2010) 1.08
The photosystem II light-harvesting protein Lhcb3 affects the macrostructure of photosystem II and the rate of state transitions in Arabidopsis. Plant Cell (2009) 1.08
A unique program for cell death in xylem fibers of Populus stem. Plant J (2008) 1.07
Polybrominated diphenyl ether levels in the blood of pregnant women living in an agricultural community in California. Environ Health Perspect (2007) 1.07
Determinants of serum polybrominated diphenyl ether (PBDE) levels among pregnant women in the CHAMACOS cohort. Environ Sci Technol (2011) 1.05
Genetic variation in functional traits influences arthropod community composition in aspen (Populus tremula L.). PLoS One (2012) 1.05
Comprehensive solid-phase extraction method for persistent organic pollutants. Validation and application to the analysis of persistent chlorinated pesticides. Anal Chem (2003) 1.04
Is each light-harvesting complex protein important for plant fitness? Plant Physiol (2004) 1.04
Improper excess light energy dissipation in Arabidopsis results in a metabolic reprogramming. BMC Plant Biol (2009) 1.03