Published in BMC Bioinformatics on May 15, 2007
Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC Plant Biol (2010) 1.36
Human neural crest cells display molecular and phenotypic hallmarks of stem cells. Hum Mol Genet (2008) 1.23
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics (2008) 1.18
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res (2009) 1.07
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics (2008) 0.88
5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics (2013) 0.85
Expressed sequence tag analysis of adult human optic nerve for NEIBank: identification of cell type and tissue markers. BMC Neurosci (2009) 0.78
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. BMC Genomics (2015) 0.75
A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling. BMC Bioinformatics (2009) 0.75
Increased frequency of single base substitutions in a population of transcripts expressed in cancer cells. BMC Cancer (2012) 0.75
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Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40
NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res (2005) 17.61
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Ensembl 2005. Nucleic Acids Res (2005) 15.13
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science (2001) 12.35
The Ensembl automatic gene annotation system. Genome Res (2004) 12.24
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
SAGEmap: a public gene expression resource. Genome Res (2000) 10.41
Using the transcriptome to annotate the genome. Nat Biotechnol (2002) 9.04
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol (2004) 7.61
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol (2004) 6.67
Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res (2004) 5.14
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet (2005) 4.56
An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A (2002) 4.45
The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res (2003) 4.21
In search of antisense. Trends Biochem Sci (2004) 3.93
Embryonic stem cells: prospects for developmental biology and cell therapy. Physiol Rev (2005) 3.27
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res (2005) 2.80
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A (2005) 2.35
ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog Nucleic Acid Res Mol Biol (2005) 1.78
Correction of sequence-based artifacts in serial analysis of gene expression. Bioinformatics (2004) 1.64
A quantitative evaluation of SAGE. Genome Res (2000) 1.57
A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics (2006) 1.55
Assessment of SAGE in transcript identification. Genome Res (2003) 1.52
Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods (2001) 1.46
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res (2006) 1.40
Letter from the editor: Adenosine-to-inosine RNA editing in Alu repeats in the human genome. EMBO Rep (2005) 1.20
The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucleic Acids Res (2004) 1.19
Evidence that functional transcription units cover at least half of the human genome. Trends Genet (2004) 1.15
Detecting the impact of sequencing errors on SAGE data. Bioinformatics (2001) 1.10
Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucleic Acids Res (2004) 1.06
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics (2004) 0.99
LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse. Bioinformatics (2004) 0.95
Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database. Nucleic Acids Res (2003) 0.93
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol (2004) 3.50
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proc Natl Acad Sci U S A (2010) 2.25
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics (2002) 2.22
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet (2010) 2.20
A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. PLoS Biol (2004) 2.20
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet (2007) 2.18
Translational control of intron splicing in eukaryotes. Nature (2008) 2.15
Neutral effect of recombination on base composition in Drosophila. Genet Res (2003) 2.11
Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res (2002) 2.04
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun (2011) 2.03
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci U S A (2004) 1.98
Vanishing GC-rich isochores in mammalian genomes. Genetics (2002) 1.86
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res (2013) 1.83
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet (2011) 1.63
Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol (2006) 1.62
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet (2008) 1.54
ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics (2004) 1.53
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet (2010) 1.53
Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res (2010) 1.48
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev (2011) 1.41
Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics (2011) 1.40
HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res (2005) 1.38
The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS Genet (2012) 1.38
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet (2004) 1.33
No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol Biol Evol (2005) 1.32
Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data. Genome Biol (2002) 1.32
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies. Nucleic Acids Res (2007) 1.28
Broadening of DNA replication origin usage during metazoan cell differentiation. EMBO Rep (2006) 1.26
Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci (2010) 1.25
XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat Genet (2013) 1.20
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics (2008) 1.18
Evidence that functional transcription units cover at least half of the human genome. Trends Genet (2004) 1.15
Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A (2005) 1.13
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics (2010) 1.12
Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res (2003) 1.11
Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation. Mol Biol Evol (2004) 1.09
Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J Mol Evol (2002) 1.06
Placenta-specific INSL4 expression is mediated by a human endogenous retrovirus element. Biol Reprod (2002) 1.03
MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record. Proc Biol Sci (2009) 1.03
On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter. BMC Syst Biol (2010) 1.03
Polymorphix: a sequence polymorphism database. Nucleic Acids Res (2005) 1.03
Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. BMC Biol (2013) 1.02
Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol (2009) 1.02
Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol (2012) 1.00
The relationship between DNA replication and human genome organization. Mol Biol Evol (2009) 1.00
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol (2013) 0.99
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics (2004) 0.99
SAGE analysis of mosquito salivary gland transcriptomes during Plasmodium invasion. Cell Microbiol (2006) 0.98
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol (2013) 0.95
Global transcription analysis of immature avian erythrocytic progenitors: from self-renewal to differentiation. Oncogene (2004) 0.94
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J Mol Evol (2006) 0.93
Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Genetics (2003) 0.92
Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat (2011) 0.91
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis. Mol Cell Proteomics (2007) 0.89
Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet (2009) 0.89
Adding self-renewal in committed erythroid progenitors improves the biological relevance of a mathematical model of erythropoiesis. J Theor Biol (2007) 0.88
Natural history of the ERVWE1 endogenous retroviral locus. Retrovirology (2005) 0.88
Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: insights into early anterior-posterior patterning of the chordate body plan. Dev Biol (2009) 0.87
Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA. Cold Spring Harb Protoc (2010) 0.87
Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form. FEMS Microbiol Lett (2003) 0.87
Paramecium tetraurelia: the renaissance of an early unicellular model. Cold Spring Harb Protoc (2010) 0.86
Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues. Gene (2007) 0.85
Heterochronic shifts explain variations in a sequentially developing repeated pattern: palatal ridges of muroid rodents. Evol Dev (2009) 0.85
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant. Oncogene (2005) 0.85
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. BMC Bioinformatics (2005) 0.84
The MEK-1/ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells. Oncogene (2003) 0.83
Towards experimental manipulation of stochasticity in gene expression. Prog Biophys Mol Biol (2012) 0.83
Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action. BMC Genomics (2007) 0.83
Serial analysis of gene expression in the silkworm, Bombyx mori. Genomics (2005) 0.82
SQUAT: A web tool to mine human, murine and avian SAGE data. BMC Bioinformatics (2008) 0.82
Differential miRNA expression profiles in proliferating or differentiated keratinocytes in response to gamma irradiation. BMC Genomics (2013) 0.82
The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol (2012) 0.82
Mathematical study of feedback control roles and relevance in stress erythropoiesis. J Theor Biol (2010) 0.81
Immunocytochemistry of Paramecium cytoskeletal structures. Cold Spring Harb Protoc (2010) 0.81
Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues. BMC Genomics (2006) 0.81
Mass culture of Paramecium tetraurelia. Cold Spring Harb Protoc (2010) 0.81
Maintaining clonal Paramecium tetraurelia cell lines of controlled age through daily reisolation. Cold Spring Harb Protoc (2010) 0.80
Mathematical model of the primary CD8 T cell immune response: stability analysis of a nonlinear age-structured system. J Math Biol (2011) 0.80
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions. BMC Genomics (2007) 0.79
Novel genes differentially expressed between posterior and median silk gland identified by SAGE-aided transcriptome analysis. Insect Biochem Mol Biol (2010) 0.79