Published in Genome Inform on January 01, 2005
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res (2008) 13.51
Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics (2008) 7.12
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet (2009) 2.15
Stage- and gender-specific proteomic analysis of Brugia malayi excretory-secretory products. PLoS Negl Trop Dis (2008) 2.06
De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics (2011) 1.62
Proteomic analysis of the secretome of Leishmania donovani. Genome Biol (2008) 1.54
Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PLoS One (2015) 1.54
Exploring early micronutrient deficiencies in rainbow Trout (Oncorhynchus mykiss) by next-generation sequencing technology--from black box to functional genomics. PLoS One (2013) 1.46
Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc Natl Acad Sci U S A (2008) 1.38
A majority of cotton genes are expressed in single-celled fiber. Planta (2007) 1.38
Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. Evodevo (2011) 1.38
An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research. BMC Genomics (2011) 1.37
Regulatory mechanisms underlying oil palm fruit mesocarp maturation, ripening, and functional specialization in lipid and carotenoid metabolism. Plant Physiol (2011) 1.35
The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet (2008) 1.28
Genes related to ion-transport and energy production are upregulated in response to CO2-driven pH decrease in corals: new insights from transcriptome analysis. PLoS One (2013) 1.15
Developmental transcriptome of Aplysia californica. J Exp Zool B Mol Dev Evol (2010) 1.14
Insecticide resistance mechanisms in the green peach aphid Myzus persicae (Hemiptera: Aphididae) I: A transcriptomic survey. PLoS One (2012) 1.13
Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. PLoS Genet (2010) 1.12
A lover and a fighter: the genome sequence of an entomopathogenic nematode Heterorhabditis bacteriophora. PLoS One (2013) 1.11
Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genetics (2008) 1.06
An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals. BMC Evol Biol (2009) 1.05
Genome-wide analysis of cold adaptation in indigenous Siberian populations. PLoS One (2014) 1.02
Proteomic analysis of excretory-secretory products of Heligmosomoides polygyrus assessed with next-generation sequencing transcriptomic information. PLoS Negl Trop Dis (2011) 1.01
TransFind--predicting transcriptional regulators for gene sets. Nucleic Acids Res (2010) 1.01
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. Genome Res (2010) 1.00
Comparative transcriptome analysis and marker development of two closely related Primrose species (Primula poissonii and Primula wilsonii). BMC Genomics (2013) 0.99
Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress. BMC Plant Biol (2011) 0.99
In silico prediction of two classes of honeybee genes with CpG deficiency or CpG enrichment and sorting according to gene ontology classes. J Mol Evol (2009) 0.99
Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol (2014) 0.99
Adaptations to endosymbiosis in a cnidarian-dinoflagellate association: differential gene expression and specific gene duplications. PLoS Genet (2011) 0.98
Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One (2013) 0.98
Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis. Int J Biol Sci (2012) 0.97
A compendium of canine normal tissue gene expression. PLoS One (2011) 0.97
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics (2007) 0.96
Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS One (2011) 0.95
Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics (2006) 0.94
iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening. BMC Plant Biol (2013) 0.94
Global gene expression profiling of ischemic preconditioning in the rat retina. Mol Vis (2007) 0.94
Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. BMC Genomics (2010) 0.93
Discovery and characterization of nutritionally regulated genes associated with muscle growth in Atlantic salmon. Physiol Genomics (2010) 0.91
Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries. BMC Genomics (2007) 0.89
New resources for functional analysis of omics data for the genus Aspergillus. BMC Genomics (2011) 0.89
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. BMC Genomics (2010) 0.88
The evolution of evolvability in microRNA target sites in vertebrates. Genome Res (2013) 0.88
Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Front Genet (2015) 0.88
The global phosphoproteome of Chlamydomonas reinhardtii reveals complex organellar phosphorylation in the flagella and thylakoid membrane. Mol Cell Proteomics (2014) 0.88
Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome. BMC Genomics (2011) 0.87
Interactions of a pesticide/heavy metal mixture in marine bivalves: a transcriptomic assessment. BMC Genomics (2011) 0.85
Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One (2011) 0.85
Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol (2015) 0.85
Patterns and architecture of genomic islands in marine bacteria. BMC Genomics (2012) 0.85
De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes. BMC Genomics (2014) 0.85
Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development. BMC Genomics (2013) 0.85
Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves. DNA Res (2014) 0.84
Fine mapping of Rcr1 and analyses of its effect on transcriptome patterns during infection by Plasmodiophora brassicae. BMC Genomics (2014) 0.84
Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS One (2009) 0.84
Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 grown under carbon-sufficient, nitrogen-limited enological conditions. Appl Environ Microbiol (2012) 0.84
Towards a system level understanding of non-model organisms sampled from the environment: a network biology approach. PLoS Comput Biol (2011) 0.83
Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis. Plant Physiol (2015) 0.83
Identification of key drought stress-related genes in the hyacinth bean. PLoS One (2013) 0.82
A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator. Sci Rep (2015) 0.82
Thermal stress triggers broad Pocillopora damicornis transcriptomic remodeling, while Vibrio coralliilyticus infection induces a more targeted immuno-suppression response. PLoS One (2014) 0.81
Transcriptional responses to temperature and low oxygen stress in Atlantic salmon studied with next-generation sequencing technology. BMC Genomics (2013) 0.81
Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics (2013) 0.81
Analysis of a botryllid enriched-full-length cDNA library: insight into the evolution of spliced leader trans-splicing in tunicates. Dev Genes Evol (2011) 0.81
Gene transcription, metabolite and lipid profiling in eco-indicator daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame-retardants. Environ Sci Technol (2015) 0.80
Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biol (2010) 0.80
RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout. PLoS One (2014) 0.80
The molecular biology of the olive fly comes of age. BMC Genet (2014) 0.79
Weighted set enrichment of gene expression data. BMC Syst Biol (2013) 0.78
Target Gene and Function Prediction of Differentially Expressed MicroRNAs in Lactating Mammary Glands of Dairy Goats. Int J Genomics (2013) 0.78
Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks. PLoS Comput Biol (2015) 0.78
Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences. Int J Genomics (2013) 0.78
Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics (2013) 0.78
Genome-wide transcription analysis of histidine-related cataract in Atlantic salmon (Salmo salar L). Mol Vis (2009) 0.78
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation. Mol Biol Evol (2016) 0.77
Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure. Genome Biol Evol (2015) 0.77
Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system. BMC Genomics (2015) 0.77
Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics (2016) 0.76
RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc. PLoS One (2015) 0.76
Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. Front Plant Sci (2015) 0.76
BioMiner: Paving the Way for Personalized Medicine. Cancer Inform (2015) 0.76
A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC Genomics (2016) 0.76
The Trichoderma atroviride putative transcription factor Blu7 controls light responsiveness and tolerance. BMC Genomics (2016) 0.75
Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes. Int J Mol Sci (2015) 0.75
Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species. Front Plant Sci (2017) 0.75
Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics (2015) 0.75
Transcriptomic Profiling Analysis of Arabidopsis thaliana Treated with Exogenous Myo-Inositol. PLoS One (2016) 0.75
Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity. Genet Mol Biol (2013) 0.75
RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms. Front Microbiol (2017) 0.75
Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev (2006) 3.78
Spontaneous synchronization of coupled circadian oscillators. Biophys J (2005) 2.55
Distinct types of tumor-initiating cells form human colon cancer tumors and metastases. Cell Stem Cell (2011) 2.47
UniHI: an entry gate to the human protein interactome. Nucleic Acids Res (2006) 2.45
Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol (2006) 2.30
Molecular insights into human daily behavior. Proc Natl Acad Sci U S A (2008) 2.03
Coupling governs entrainment range of circadian clocks. Mol Syst Biol (2010) 1.85
Effects of sequestration on signal transduction cascades. FEBS J (2006) 1.84
Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol (2005) 1.82
Comparison of human protein-protein interaction maps. Bioinformatics (2007) 1.79
3D multi-cell simulation of tumor growth and angiogenesis. PLoS One (2009) 1.72
Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput Biol (2007) 1.71
Regulation of clock-controlled genes in mammals. PLoS One (2009) 1.65
Beta-TrCP1-mediated degradation of PERIOD2 is essential for circadian dynamics. J Biol Rhythms (2007) 1.64
How robust are switches in intracellular signaling cascades? J Theor Biol (2003) 1.47
Functioning and robustness of a bacterial circadian clock. Mol Syst Biol (2007) 1.46
Modeling feedback loops of the Mammalian circadian oscillator. Biophys J (2004) 1.45
Comparison of biomechanical modeling of register transitions and voice instabilities with excised larynx experiments. J Acoust Soc Am (2007) 1.43
Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol (2008) 1.41
Eradication of glioblastoma, and breast and colon carcinoma xenografts by Hsp70 depletion. Cancer Res (2002) 1.40
Natural killer cells are scarce in colorectal carcinoma tissue despite high levels of chemokines and cytokines. Clin Cancer Res (2011) 1.40
Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations. Philos Trans A Math Phys Eng Sci (2006) 1.36
Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res (2005) 1.26
Small RNAs establish delays and temporal thresholds in gene expression. Biophys J (2008) 1.24
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinformatics (2004) 1.22
Tissue inhibitor of metalloproteinases-1 promotes liver metastasis by induction of hepatocyte growth factor signaling. Cancer Res (2007) 1.21
Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics (2008) 1.20
Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res (2003) 1.18
Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput Biol (2011) 1.18
Invasion front-specific expression and prognostic significance of microRNA in colorectal liver metastases. Cancer Sci (2011) 1.18
Nonlinear analysis of irregular animal vocalizations. J Acoust Soc Am (2002) 1.17
Quantification of circadian rhythms in single cells. PLoS Comput Biol (2009) 1.14
Measuring similarities between transcription factor binding sites. BMC Bioinformatics (2005) 1.13
Competing docking interactions can bring about bistability in the MAPK cascade. Biophys J (2007) 1.13
Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. PLoS Genet (2010) 1.12
Overexpression of ZEB2 at the invasion front of colorectal cancer is an independent prognostic marker and regulates tumor invasion in vitro. Clin Cancer Res (2011) 1.12
Transcriptional activation of the beta-catenin gene at the invasion front of colorectal liver metastases. J Pathol (2009) 1.10
Global parameter search reveals design principles of the mammalian circadian clock. BMC Syst Biol (2008) 1.08
Quantitative analysis of ultrasensitive responses. FEBS J (2005) 1.08
Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences. J Immunol Methods (2002) 1.05
Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb. Physica A (2007) 1.05
Periodicities of 10-11bp as indicators of the supercoiled state of genomic DNA. J Mol Biol (2004) 1.05
How to achieve fast entrainment? The timescale to synchronization. PLoS One (2009) 1.04
Entrainment in a model of the mammalian circadian oscillator. J Biol Rhythms (2005) 1.03
Extracting information from cDNA arrays. Chaos (2001) 1.02
Front instabilities and invasiveness of simulated avascular tumors. Bull Math Biol (2009) 1.02
Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment. Math Biosci Eng (2008) 1.02
HuSiDa--the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. Nucleic Acids Res (2005) 1.02
YB-1 relocates to the nucleus in adenovirus-infected cells and facilitates viral replication by inducing E2 gene expression through the E2 late promoter. J Biol Chem (2002) 1.01
Nonlinear phenomena in contemporary vocal music. J Voice (2004) 0.98
DNA motifs and sequence periodicities. In Silico Biol (2006) 0.98
Systematic functional assessment of human protein-protein interaction maps. Genome Inform (2006) 0.97
Cytoskeletal remodeling in lymphocyte activation. Curr Opin Immunol (2003) 0.97
Biomechanical modeling of register transitions and the role of vocal tract resonators. J Acoust Soc Am (2010) 0.96
Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction. PLoS Comput Biol (2005) 0.95
From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development. Comput Sci Eng (2007) 0.95
Repeats and correlations in human DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.94
Bifurcations and chaos in register transitions of excised larynx experiments. Chaos (2008) 0.93
Down-regulation of CXCL1 inhibits tumor growth in colorectal liver metastasis. Cytokine (2011) 0.93
Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick. Curr Top Dev Biol (2008) 0.93
The interplay of cis-regulatory elements rules circadian rhythms in mouse liver. PLoS One (2012) 0.93
Why do cells cycle with a 24 hour period? Genome Inform (2006) 0.92
Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res (2009) 0.92
Biomechanics and control of vocalization in a non-songbird. J R Soc Interface (2008) 0.91
Mechanism for 12 hr rhythm generation by the circadian clock. Cell Rep (2013) 0.91
Computer simulations of cell sorting due to differential adhesion. PLoS One (2011) 0.91
Human chronotypes from a theoretical perspective. PLoS One (2013) 0.90
Promoter analysis of Mammalian clock controlled genes. Genome Inform (2007) 0.90
Visualization of system dynamics using phasegrams. J R Soc Interface (2013) 0.90
High reproducibility of large-gel two-dimensional electrophoresis. Electrophoresis (2004) 0.89
Annexin A2 as a differential diagnostic marker of hepatocellular tumors. Pathol Res Pract (2010) 0.89
Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. Mol Syst Biol (2012) 0.88
Tumor growth rate determines the timing of optimal chronomodulated treatment schedules. PLoS Comput Biol (2010) 0.88
Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study. PLoS Comput Biol (2012) 0.87
Effects of a hypercaloric diet on β-cell responsivity in lean healthy men. Clin Endocrinol (Oxf) (2013) 0.85
Adenovirus-mediated overexpression of tissue inhibitor of metalloproteinases-1 in the liver: efficient protection against T-cell lymphoma and colon carcinoma metastasis. J Gene Med (2004) 0.85
Circadian desynchronization. Interface Focus (2010) 0.84
Kinetic modelling of NSAID action on COX-1: focus on in vitro/in vivo aspects and drug combinations. Eur J Pharm Sci (2008) 0.84
Prediction of cis-regulatory elements of coregulated genes. Genome Inform (2004) 0.83
Prediction of regulatory transcription factors in T helper cell differentiation and maintenance. Genome Inform (2010) 0.83
Paracrine signalling in colorectal liver metastases involving tumor cell-derived PDGF-C and hepatic stellate cell-derived PAK-2. Clin Exp Metastasis (2012) 0.83
Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases. Int J Cancer (2006) 0.83
Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset. BMC Bioinformatics (2011) 0.83
3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming. Nucleic Acids Res (2011) 0.83
Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity. Nucleic Acids Res (2007) 0.83
Comparison of different surgical techniques in distal pancreatectomy: an experimental study in a porcine model. Surg Innov (2011) 0.83
Hepatic metastases of colorectal cancer are rather homogeneous but differ from primary lesions in terms of immune cell infiltration. Oncoimmunology (2013) 0.82
HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics (2004) 0.82
Computer simulation of cellular patterning within the Drosophila pupal eye. PLoS Comput Biol (2010) 0.82
Sequential metastases of colorectal cancer: Immunophenotypes and spatial distributions of infiltrating immune cells in relation to time and treatments. Oncoimmunology (2012) 0.81
Regulation of mammalian cell cycle progression in the regenerating liver. J Theor Biol (2011) 0.80
Stable IL-2 decision making by endogenous c-Fos amounts in peripheral memory T-helper cells. J Biol Chem (2012) 0.80
IL-2 Expression in Activated Human Memory FOXP3(+) Cells Critically Depends on the Cellular Levels of FOXP3 as Well as of Four Transcription Factors of T Cell Activation. Front Immunol (2012) 0.80