Published in Toxicol Sci on August 13, 2012
The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Front Mol Biosci (2014) 1.04
Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol (2015) 0.94
Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing. Sci Rep (2014) 0.85
High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity. Nucleic Acids Res (2015) 0.83
Transcriptomic Changes in Zebrafish Embryos and Larvae Following Benzo[a]pyrene Exposure. Toxicol Sci (2015) 0.80
RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue. BMC Genomics (2014) 0.79
Analysis of the transcriptome in molecular epidemiology studies. Environ Mol Mutagen (2013) 0.79
Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. Arch Toxicol (2016) 0.79
RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal. Mol Biosyst (2013) 0.79
New insights into BaP-induced toxicity: role of major metabolites in transcriptomics and contribution to hepatocarcinogenesis. Arch Toxicol (2015) 0.77
Identification of Novel Reference Genes Suitable for qRT-PCR Normalization with Respect to the Zebrafish Developmental Stage. PLoS One (2016) 0.76
ZEBRAFISH AS AN IN VIVO MODEL FOR SUSTAINABLE CHEMICAL DESIGN. Green Chem (2016) 0.75
The Regulation of para-Nitrophenol Degradation in Pseudomonas putida DLL-E4. PLoS One (2016) 0.75
Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data. Cell Cycle (2017) 0.75
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
International network of cancer genome projects. Nature (2010) 20.35
A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
The DNA sequence of the human X chromosome. Nature (2005) 6.97
The genome of a songbird. Nature (2010) 5.90
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Dissecting the genomic complexity underlying medulloblastoma. Nature (2012) 4.77
Toward interoperable bioscience data. Nat Genet (2012) 4.72
Mutations in DNAH5 cause primary ciliary dyskinesia and randomization of left-right asymmetry. Nat Genet (2002) 4.64
Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database. PLoS Genet (2012) 4.27
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res (2010) 3.36
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
The senescence-related mitochondrial/oxidative stress pathway is repressed in human induced pluripotent stem cells. Stem Cells (2010) 3.17
Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell (2013) 3.08
Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res (2003) 3.02
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Res (2004) 2.99
The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res (2012) 2.94
Construction and analysis of a human-chimpanzee comparative clone map. Science (2002) 2.83
ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79
ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res (2008) 2.77
A gene expression map of human chromosome 21 orthologues in the mouse. Nature (2002) 2.76
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol (2007) 2.70
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res (2010) 2.61
A dictionary to identify small molecules and drugs in free text. Bioinformatics (2009) 2.54
Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature (2004) 2.54
A bile acid-like steroid modulates Caenorhabditis elegans lifespan through nuclear receptor signaling. Proc Natl Acad Sci U S A (2007) 2.50
T cells become licensed in the lung to enter the central nervous system. Nature (2012) 2.45
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet (2013) 2.42
Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. Mol Biol Cell (2007) 2.30
Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome. Genome Res (2004) 2.29
Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics (2011) 2.24
A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics (2004) 2.21
On the origin of the chordate central nervous system: expression of onecut in the sea urchin embryo. Evol Dev (2004) 2.19
Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells (2006) 2.18
MicroRNA profiling of clear cell renal cell cancer identifies a robust signature to define renal malignancy. J Cell Mol Med (2009) 2.12
Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis. PLoS One (2010) 2.10
Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics (2008) 2.09
A prospective evaluation of pain associated with stone passage, stents, and stent removal using a visual analog scale. Urology (2013) 2.05
Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One (2009) 2.04
Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev (2008) 1.96
GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics (2012) 1.91
Fibroblast growth factor 2 modulates transforming growth factor beta signaling in mouse embryonic fibroblasts and human ESCs (hESCs) to support hESC self-renewal. Stem Cells (2006) 1.88
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (2010) 1.86
TLR2 has a detrimental role in mouse transient focal cerebral ischemia. Biochem Biophys Res Commun (2007) 1.84
An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun (2006) 1.82
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining. J Cheminform (2010) 1.82
A centrosome-independent role for gamma-TuRC proteins in the spindle assembly checkpoint. Science (2006) 1.76
High throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Mol Cell Proteomics (2005) 1.75
Genetic analysis of the mouse brain proteome. Nat Genet (2002) 1.73
Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase. J Theor Biol (2005) 1.71
Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells (2005) 1.68
No evidence for a shift in pyruvate kinase PKM1 to PKM2 expression during tumorigenesis. Oncotarget (2011) 1.68
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res (2003) 1.65
Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics (2011) 1.63
Kidney fusion anomalies revisited: clinical and radiological analysis of 209 cases of crossed fused ectopia and horseshoe kidney. BJU Int (2008) 1.61
A catabolic block does not sufficiently explain how 2-deoxy-D-glucose inhibits cell growth. Proc Natl Acad Sci U S A (2008) 1.54
Detection of angiotensin II in supernatants of stimulated mononuclear leukocytes by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass analysis. Hypertension (2005) 1.52
Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010. Arch Toxicol (2011) 1.46
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics (2011) 1.46
Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes. Genome Res (2003) 1.45
Miniaturization in functional genomics and proteomics. Nat Rev Genet (2005) 1.44
Human induced pluripotent stem cells harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining human embryonic stem cell-like metabolic reprogramming. Stem Cells (2011) 1.42
Pyruvate kinase triggers a metabolic feedback loop that controls redox metabolism in respiring cells. Cell Metab (2011) 1.40
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics (2013) 1.38
The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. J Biol Chem (2011) 1.36
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res (2013) 1.35
Probing the SELEX process with next-generation sequencing. PLoS One (2011) 1.34
A nonredundant human protein chip for antibody screening and serum profiling. Mol Cell Proteomics (2003) 1.31
The pentose phosphate pathway is a metabolic redox sensor and regulates transcription during the antioxidant response. Antioxid Redox Signal (2011) 1.31
A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One (2010) 1.31
Identification of benzothiazoles as potential polyglutamine aggregation inhibitors of Huntington's disease by using an automated filter retardation assay. Proc Natl Acad Sci U S A (2002) 1.30
High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome. Plant Mol Biol (2005) 1.30
Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal Biochem (2002) 1.29
Genome-wide array analysis of normal and malformed human hearts. Circulation (2003) 1.28
Proteomic and functional analysis of the mitotic Drosophila centrosome. EMBO J (2010) 1.27
Hedgehog-EGFR cooperation response genes determine the oncogenic phenotype of basal cell carcinoma and tumour-initiating pancreatic cancer cells. EMBO Mol Med (2012) 1.27
An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26
Reverse engineering of gene regulatory networks: a comparative study. EURASIP J Bioinform Syst Biol (2009) 1.22
Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal. BMC Dev Biol (2007) 1.21
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways. Hum Mol Genet (2005) 1.21
Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation. Cancer Discov (2012) 1.21