Published in Genome Res on May 01, 2005
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics (2006) 5.50
Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res (2008) 3.29
Different levels of alternative splicing among eukaryotes. Nucleic Acids Res (2006) 3.07
DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One (2011) 2.80
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A (2013) 2.75
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics (2006) 2.41
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics (2008) 2.27
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res (2007) 2.12
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells (2008) 2.02
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res (2006) 1.90
Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Dev Biol (2007) 1.61
An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. Gene Expr Patterns (2007) 1.44
Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet (2008) 1.37
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res (2008) 1.36
A statistical method for the detection of alternative splicing using RNA-seq. PLoS One (2010) 1.26
A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays. Genetics (2005) 1.25
A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis. PLoS One (2009) 1.23
Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes. BMC Genomics (2006) 1.20
Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA (2012) 1.12
Effects of aging and calorie restriction on the global gene expression profiles of mouse testis and ovary. BMC Biol (2008) 1.00
Mammalian mRNA splice-isoform selection is tightly controlled. Genetics (2006) 0.92
Repression of global protein synthesis by Eif1a-like genes that are expressed specifically in the two-cell embryos and the transient Zscan4-positive state of embryonic stem cells. DNA Res (2013) 0.87
Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics (2008) 0.86
Width of gene expression profile drives alternative splicing. PLoS One (2008) 0.85
Expression profiling of the mouse early embryo: reflections and perspectives. Dev Dyn (2006) 0.84
Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics (2011) 0.84
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. BMC Bioinformatics (2015) 0.80
Cloning and characterization of a novel alternatively spliced transcript of the human CHD7 putative helicase. BMC Res Notes (2010) 0.79
The LuWD40-1 gene encoding WD repeat protein regulates growth and pollen viability in flax (Linum Usitatissimum L.). PLoS One (2013) 0.79
Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome. PLoS One (2015) 0.78
Gene expression profiling of mouse embryos with microarrays. Methods Enzymol (2010) 0.77
A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinformatics (2007) 0.77
Salt suppresses IFNγ inducible chemokines through the IFNγ-JAK1-STAT1 signaling pathway in proximal tubular cells. Sci Rep (2017) 0.75
Gene array analysis of neural crest cells identifies transcription factors necessary for direct conversion of embryonic fibroblasts into neural crest cells. Biol Open (2016) 0.75
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res (2001) 45.29
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
dbEST--database for "expressed sequence tags". Nat Genet (1993) 41.10
A catalogue of splice junction sequences. Nucleic Acids Res (1982) 39.41
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
GenBank: update. Nucleic Acids Res (2004) 12.28
Ensembl 2004. Nucleic Acids Res (2004) 11.88
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res (2004) 9.85
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res (2001) 8.44
Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res (2001) 7.27
Frequent alternative splicing of human genes. Genome Res (1999) 6.68
Computational identification of promoters and first exons in the human genome. Nat Genet (2001) 5.88
Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res (2001) 5.38
Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res (2000) 4.29
ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res (2004) 3.85
Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res (2001) 3.44
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res (2003) 3.21
Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet (2003) 3.11
Selecting for functional alternative splices in ESTs. Genome Res (2002) 2.90
STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res (2001) 2.85
Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet (2003) 2.30
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics (2002) 2.22
Detection and evaluation of intron retention events in the human transcriptome. RNA (2004) 2.18
Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. J Biomed Sci (2004) 2.11
Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet (2003) 1.80
Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol (2003) 1.75
Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics (2004) 1.74
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res (2004) 1.70
Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol (2004) 1.67
Computational discovery of internal micro-exons. Genome Res (2003) 1.52
Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment. Oncogene (2004) 1.39
Database and analyses of known alternatively spliced genes in plants. Genomics (2003) 1.13
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol (2007) 6.69
Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell (2004) 4.97
A web-based tool for principal component and significance analysis of microarray data. Bioinformatics (2005) 3.42
Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res (2008) 3.29
AGEMAP: a gene expression database for aging in mice. PLoS Genet (2007) 3.22
Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science (2005) 2.72
Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells. Science (2011) 2.69
Klf4 cooperates with Oct3/4 and Sox2 to activate the Lefty1 core promoter in embryonic stem cells. Mol Cell Biol (2006) 2.59
Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PLoS One (2006) 2.46
Zscan4 regulates telomere elongation and genomic stability in ES cells. Nature (2010) 2.46
Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript. PLoS Biol (2010) 2.38
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell (2009) 2.32
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics (2008) 2.27
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Genome Biol (2005) 2.18
Age-associated alteration of gene expression patterns in mouse oocytes. Hum Mol Genet (2004) 2.11
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells (2008) 2.02
Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res (2009) 1.94
Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res (2002) 1.77
Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol (2003) 1.75
Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells. Dev Biol (2007) 1.63
Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Dev Biol (2007) 1.61
In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Res (2003) 1.58
A conserved Oct4/POUV-dependent network links adhesion and migration to progenitor maintenance. Curr Biol (2013) 1.54
Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells. Stem Cells (2005) 1.53
Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc Natl Acad Sci U S A (2004) 1.52
Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci (2013) 1.46
An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. Gene Expr Patterns (2007) 1.44
Identification of target genes and a unique cis element regulated by IRF-8 in developing macrophages. Blood (2005) 1.44
Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells. BMC Dev Biol (2008) 1.43
High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization. Gene Expr Patterns (2005) 1.43
Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Rep (2013) 1.43
Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. Genome Biol (2007) 1.41
Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet (2008) 1.37
Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells. DNA Res (2008) 1.35
Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells. Sci Rep (2012) 1.29
Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. Genome Res (2002) 1.25
Gene expression changes at metamorphosis induced by thyroid hormone in Xenopus laevis tadpoles. Dev Biol (2006) 1.20
Dax1 binds to Oct3/4 and inhibits its transcriptional activity in embryonic stem cells. Mol Cell Biol (2009) 1.20
A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development. J Pathol (2014) 1.17
The NIA cDNA project in mouse stem cells and early embryos. C R Biol (2004) 1.16
Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci U S A (2007) 1.15
Forkhead transcription factor FoxA1 regulates sweat secretion through Bestrophin 2 anion channel and Na-K-Cl cotransporter 1. Proc Natl Acad Sci U S A (2012) 1.13
Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci Rep (2011) 1.11
Plac8 and Plac9, novel placental-enriched genes identified through microarray analysis. Gene (2003) 1.11
Zscan4 restores the developmental potency of embryonic stem cells. Nat Commun (2013) 1.10
Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep (2013) 1.08
CisView: a browser and database of cis-regulatory modules predicted in the mouse genome. DNA Res (2006) 1.06
Mouse ovary developmental RNA and protein markers from gene expression profiling. Dev Biol (2005) 1.05
Microarray analysis of somitogenesis reveals novel targets of different WNT signaling pathways in the somitic mesoderm. Dev Biol (2003) 1.04
Requirement for Shh and Fox family genes at different stages in sweat gland development. Hum Mol Genet (2009) 1.03
Identification of Zfp-57 as a downstream molecule of STAT3 and Oct-3/4 in embryonic stem cells. Biochem Biophys Res Commun (2005) 1.02
Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. PLoS One (2012) 1.01
Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair. PLoS One (2010) 1.01
A role for borg5 during trophectoderm differentiation. Stem Cells (2010) 0.99
Human ES cell profiling broadens the reach of bivalent domains. Cell Stem Cell (2007) 0.97
Expression profiling of placentomegaly associated with nuclear transplantation of mouse ES cells. Dev Biol (2003) 0.96
EDA targets revealed by skin gene expression profiles of wild-type, Tabby and Tabby EDA-A1 transgenic mice. Hum Mol Genet (2002) 0.94
Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency. Cell Rep (2012) 0.94
Esg1, expressed exclusively in preimplantation embryos, germline, and embryonic stem cells, is a putative RNA-binding protein with broad RNA targets. Dev Growth Differ (2006) 0.93
A global view of gene expression in the preimplantation mouse embryo: morula versus blastocyst. Eur J Obstet Gynecol Reprod Biol (2004) 0.91
Use of Chuk as an internal standard suitable for quantitative RT-PCR in mouse preimplantation embryos. Reprod Biomed Online (2006) 0.90
Silencing or amplification of endocannabinoid signaling in blastocysts via CB1 compromises trophoblast cell migration. J Biol Chem (2012) 0.88
Repression of global protein synthesis by Eif1a-like genes that are expressed specifically in the two-cell embryos and the transient Zscan4-positive state of embryonic stem cells. DNA Res (2013) 0.87
Trim43a, Trim43b, and Trim43c: Novel mouse genes expressed specifically in mouse preimplantation embryos. Gene Expr Patterns (2009) 0.86
Comparative analysis of oocyte transcript profiles reveals a high degree of conservation among species. Reproduction (2008) 0.86
Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics (2008) 0.86
Molecular mechanisms of pancreatic stone formation in chronic pancreatitis. Front Physiol (2012) 0.85
Developmental arrest and mouse antral not-surrounded nucleolus oocytes. Biol Reprod (2013) 0.85
Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics (2011) 0.84
Inflammation increases cells expressing ZSCAN4 and progenitor cell markers in the adult pancreas. Am J Physiol Gastrointest Liver Physiol (2013) 0.84
Chromatin properties of regulatory DNA probed by manipulation of transcription factors. J Comput Biol (2014) 0.80
Maintenance of undifferentiated mouse embryonic stem cells in suspension by the serum- and feeder-free defined culture condition. Dev Dyn (2008) 0.78
Changes in global gene expression during in vitro decidualization of rat endometrial stromal cells. J Cell Physiol (2010) 0.78
Gene expression profiling of mouse embryos with microarrays. Methods Enzymol (2010) 0.77
Stochastic modeling for the expression of a gene regulated by competing transcription factors. PLoS One (2012) 0.76
Genomic approaches to early embryogenesis and stem cell biology. Semin Reprod Med (2006) 0.76
Identification, molecular characterization, and tissue expression of OVCOV1. Mamm Genome (2002) 0.76
SHAVE: shrinkage estimator measured for multiple visits increases power in GWAS of quantitative traits. Eur J Hum Genet (2012) 0.76
Gene content of the 750-kb critical region for mouse embryonic ectoderm lethal tcl-w5. Mamm Genome (2004) 0.75
Efficacy of 2-methoxyethoxy-modified antisense oligonucleotides for the study of mouse preimplantation development. Reprod Biomed Online (2003) 0.75