Published in Genome Biol on August 07, 2006
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Determining promoter location based on DNA structure first-principles calculations. Genome Biol (2007) 1.44
Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. Genome Biol (2007) 1.43
Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics (2009) 1.33
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PLoS One (2014) 0.85
From plant genomes to protein families: computational tools. Comput Struct Biotechnol J (2013) 0.80
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Genome annotation assessment in Drosophila melanogaster. Genome Res (2000) 11.77
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Characterization of mammalian selenoproteomes. Science (2003) 9.07
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14
Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res (2012) 4.81
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
Comparative gene prediction in human and mouse. Genome Res (2003) 4.13
The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods (2012) 3.89
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
A combinatorial code for CPE-mediated translational control. Cell (2008) 3.23
Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature (2002) 3.01
Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol Cell (2005) 2.99
Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods (2013) 2.92
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Fast computation and applications of genome mappability. PLoS One (2012) 2.73
ASTD: The Alternative Splicing and Transcript Diversity database. Genomics (2008) 2.72
Improving gene annotation using peptide mass spectrometry. Genome Res (2006) 2.69
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett (2005) 2.68
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A (2012) 2.24
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Using geneid to identify genes. Curr Protoc Bioinformatics (2007) 2.04
Recent advances in gene structure prediction. Curr Opin Struct Biol (2004) 1.90
Comparative analysis of amino acid repeats in rodents and humans. Genome Res (2004) 1.78
The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat Struct Mol Biol (2009) 1.75
A general definition and nomenclature for alternative splicing events. PLoS Comput Biol (2008) 1.72
Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66
Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep (2004) 1.58
Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver. Mol Cell Biol (2009) 1.58
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res (2013) 1.51
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res (2006) 1.40
Comparison of splice sites in mammals and chicken. Genome Res (2004) 1.40
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol (2011) 1.31
Estimation of alternative splicing variability in human populations. Genome Res (2011) 1.27
Identifying protein-coding genes in genomic sequences. Genome Biol (2009) 1.26
Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res (2005) 1.24
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23
CPEB1 coordinates alternative 3'-UTR formation with translational regulation. Nature (2013) 1.23
Transcription factor map alignment of promoter regions. PLoS Comput Biol (2006) 1.22
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol (2013) 1.18
Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One (2012) 1.16
The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter". Front Genet (2012) 1.15
Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes. PLoS One (2008) 1.15
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol (2011) 1.12
The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol (2011) 1.05
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Nucleic Acids Res (2005) 1.01
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. Nucleic Acids Res (2008) 1.00
Splice site identification by idlBNs. Bioinformatics (2004) 1.00
Intron-centric estimation of alternative splicing from RNA-seq data. Bioinformatics (2012) 0.97
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Bioinformatics (2009) 0.97
Grape RNA-Seq analysis pipeline environment. Bioinformatics (2013) 0.96
Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster. Proc Natl Acad Sci U S A (2003) 0.94
Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation. Mol Ecol (2015) 0.92
Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biol (2006) 0.91
Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila. Genome Biol (2008) 0.90
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations. Bioinformatics (2007) 0.88
gff2aplot: Plotting sequence comparisons. Bioinformatics (2003) 0.87
Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics (2007) 0.86
CROC: finding chromosomal clusters in eukaryotic genomes. Bioinformatics (2009) 0.85
Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins. Mol Biol Evol (2009) 0.85
Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. J Mol Evol (2004) 0.84
The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells. Mol Immunol (2009) 0.83
[Long non-coding RNAs with enhancer-like function in human cells]. Med Sci (Paris) (2011) 0.80
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. Nucleic Acids Res (2013) 0.79
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics Chromatin (2010) 0.79
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection. Biomed Res Int (2013) 0.78
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. Nucleic Acids Res (2013) 0.78
Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Res (2013) 0.77
Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Hum Mutat (2009) 0.76
In silico meets in vivo. Genome Biol (2008) 0.75