Published in Nucleic Acids Res on November 11, 2006
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res (2011) 14.04
RefSeq: an update on mammalian reference sequences. Nucleic Acids Res (2013) 7.29
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Expressed pseudogenes in the transcriptional landscape of human cancers. Cell (2012) 4.22
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) 3.00
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res (2013) 2.77
A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat Commun (2014) 2.48
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res (2008) 2.17
Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol (2007) 2.07
hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions. BMC Evol Biol (2008) 1.80
Solving the Problem: Genome Annotation Standards before the Data Deluge. Stand Genomic Sci (2011) 1.54
The extinction dynamics of bacterial pseudogenes. PLoS Genet (2010) 1.53
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res (2011) 1.43
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics (2009) 1.26
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol (2013) 1.20
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation. BMC Genomics (2009) 1.17
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res (2009) 1.16
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics (2012) 1.12
GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes. Stand Genomic Sci (2009) 1.10
Asymmetric histone modifications between the original and derived loci of human segmental duplications. Genome Biol (2008) 1.09
Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet (2012) 1.07
Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. Genome Biol (2012) 1.07
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol (2009) 1.05
Filtering for compound heterozygous sequence variants in non-consanguineous pedigrees. PLoS One (2013) 1.05
Both selective and neutral processes drive GC content evolution in the human genome. BMC Evol Biol (2008) 1.02
Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics (2010) 1.02
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One (2012) 0.97
Genome-wide colonization of gene regulatory elements by G4 DNA motifs. Nucleic Acids Res (2009) 0.97
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. Hum Mol Genet (2013) 0.93
Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci U S A (2014) 0.88
Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota). BMC Genomics (2014) 0.88
Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol (2010) 0.87
Genome (re-)annotation and open-source annotation pipelines. Microb Biotechnol (2010) 0.87
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. BMC Genomics (2012) 0.86
PseudoGeneQuest - service for identification of different pseudogene types in the human genome. BMC Bioinformatics (2008) 0.86
Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss. BMC Biol (2013) 0.85
The human genome in the LINE of fire. Proc Natl Acad Sci U S A (2008) 0.85
Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures. BMC Genomics (2007) 0.83
Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons. Genome Res (2008) 0.83
RCPedia: a database of retrocopied genes. Bioinformatics (2013) 0.83
Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes. BMC Evol Biol (2010) 0.83
Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts. Philos Trans R Soc Lond B Biol Sci (2013) 0.82
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. Front Genet (2015) 0.82
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. Nucleic Acids Res (2007) 0.82
piRNAQuest: searching the piRNAome for silencers. BMC Genomics (2014) 0.82
Emergence and expansion of TFIIB-like factors in the plant kingdom. Gene (2013) 0.79
Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Hum Mol Genet (2016) 0.79
Strong association between pseudogenization mechanisms and gene sequence length. Biol Direct (2009) 0.78
Mouse genome annotation by the RefSeq project. Mamm Genome (2015) 0.78
Are Human Translated Pseudogenes Functional? Mol Biol Evol (2015) 0.78
Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. PLoS One (2012) 0.78
"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements. Mol Biol Evol (2016) 0.78
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. Nucleic Acids Res (2015) 0.77
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. Database (Oxford) (2013) 0.76
PGD: a pangolin genome hub for the research community. Database (Oxford) (2016) 0.75
Development of a robust DNA quality and quantity assessment qPCR assay for targeted next-generation sequencing library preparation. Int J Oncol (2016) 0.75
Computational Identification of Novel Genes: Current and Future Perspectives. Bioinform Biol Insights (2016) 0.75
On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human. BMC Genomics (2011) 0.75
Novel Role of 3'UTR-Embedded Alu Elements as Facilitators of Processed Pseudogene Genesis and Host Gene Capture by Viral Genomes. PLoS One (2016) 0.75
SinEx DB: a database for single exon coding sequences in mammalian genomes. Database (Oxford) (2016) 0.75
Efficient approach to correct read alignment for pseudogene abundance estimates. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
Ensembl 2005. Nucleic Acids Res (2005) 15.13
GenBank. Nucleic Acids Res (2006) 12.21
Organization of heterogeneous scientific data using the EAV/CR representation. J Am Med Inform Assoc (1999) 6.97
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
A genome-wide survey of human pseudogenes. Genome Res (2003) 4.34
Gene losses during human origins. PLoS Biol (2006) 3.17
Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res (2003) 3.03
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet (2004) 2.51
Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev (2004) 2.38
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol (2003) 2.19
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol (2004) 1.88
A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol (2006) 1.74
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. J Biol (2003) 1.57
Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res (2003) 1.48
HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res (2005) 1.38
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene (2003) 1.12
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Genomics (2003) 1.00
Reconstructing genetic networks in yeast. Nat Biotechnol (2003) 0.88
Ensembl: a genome infrastructure. Cold Spring Harb Symp Quant Biol (2003) 0.87
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
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
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell (2010) 8.79
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade. Cell (2013) 3.59
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell (2011) 2.80
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Genomics. Defining genes in the genomics era. Science (2003) 2.73
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins (2002) 2.72
Endocardial cells form the coronary arteries by angiogenesis through myocardial-endocardial VEGF signaling. Cell (2012) 2.71
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell (2004) 2.65
Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65
ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature (2010) 2.65
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol (2005) 2.54
Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet (2004) 2.51
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet (2010) 2.46
TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42
Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39
Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev (2004) 2.38
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38
Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol (2004) 2.37
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
The protein target list of the Northeast Structural Genomics Consortium. Proteins (2004) 2.31