Published in Nucleic Acids Res on August 09, 2013
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A (1987) 14.25
DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem (2001) 12.53
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol (2002) 11.79
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89
Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem (2007) 7.49
A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription. Science (2006) 6.71
Identification and distinct regulation of yeast TATA box-containing genes. Cell (2004) 6.27
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem Biol (2010) 5.61
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell (2005) 5.36
Histone variants--ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol (2010) 4.45
Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19
A model for the mechanism of human topoisomerase I. Science (1998) 4.10
Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat Genet (2010) 3.83
Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol (2005) 3.83
DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell (1993) 3.77
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (2007) 3.59
Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol (2012) 3.52
DNA topoisomerase II and its growing repertoire of biological functions. Nat Rev Cancer (2009) 3.05
Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell (2004) 2.99
Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q Rev Biophys (1998) 2.62
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol (2009) 2.58
DNA topoisomerase I is involved in both repression and activation of transcription. Nature (1993) 2.53
Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell (2012) 2.22
DNA topoisomerase IIbeta and neural development. Science (2000) 2.14
Topoisomerases and yeast rRNA transcription: negative supercoiling stimulates initiation and topoisomerase activity is required for elongation. Genes Dev (1992) 1.84
SWI/SNF chromatin remodeling requires changes in DNA topology. Mol Cell (2001) 1.72
Role of topoisomerase IIbeta in the expression of developmentally regulated genes. Mol Cell Biol (2006) 1.70
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. Genome Res (2011) 1.58
A complete set of nascent transcription rates for yeast genes. PLoS One (2010) 1.56
Transcriptional consequences of topoisomerase inhibition. Mol Cell Biol (2001) 1.55
BAF complexes facilitate decatenation of DNA by topoisomerase IIα. Nature (2013) 1.52
Formation of nucleosomes on positively supercoiled DNA. EMBO J (1991) 1.50
Genome-organizing factors Top2 and Hmo1 prevent chromosome fragility at sites of S phase transcription. Cell (2009) 1.48
Assembly of spaced chromatin involvement of ATP and DNA topoisomerase activity. EMBO J (1988) 1.47
Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. EMBO J (2006) 1.38
Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res (2004) 1.38
Aberrant lamination in the cerebral cortex of mouse embryos lacking DNA topoisomerase IIbeta. Proc Natl Acad Sci U S A (2003) 1.33
DNA topoisomerase IIalpha is required for RNA polymerase II transcription on chromatin templates. Nature (2001) 1.32
Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J (2010) 1.28
Comprehensive transcriptional analysis of the oxidative response in yeast. J Biol Chem (2008) 1.25
A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res (2011) 1.23
Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC? J Biol (2009) 1.22
Topoisomerase II: untangling its contribution at the centromere. Chromosome Res (2004) 1.22
Topoisomerase II: a fitted mechanism for the chromatin landscape. Nucleic Acids Res (2008) 1.13
Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast. Proc Natl Acad Sci U S A (2011) 1.12
A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses. Int Microbiol (2004) 1.10
Topoisomerase IIbeta activates a subset of neuronal genes that are repressed in AT-rich genomic environment. PLoS One (2008) 1.10
Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One (2011) 1.07
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. Bioinformatics (2007) 1.05
Chromatin fiber dynamics under tension and torsion. Int J Mol Sci (2010) 1.03
On the desoxyribonucleic acid content of sea urchin gametes. Experientia (1952) 1.03
Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state. Proc Natl Acad Sci U S A (2012) 1.02
Topoisomerase II is required for the production of long Pol II gene transcripts in yeast. Nucleic Acids Res (2012) 0.99
A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species. Nucleic Acids Res (2005) 0.99
Deviations from Chargaff's second parity rule in organellar DNA Insights into the evolution of organellar genomes. Gene (2006) 0.99
Failure to relax negative supercoiling of DNA is a primary cause of mitotic hyper-recombination in topoisomerase-deficient yeast cells. J Biol Chem (2002) 0.98
Topoisomerase IIbeta negatively modulates retinoic acid receptor alpha function: a novel mechanism of retinoic acid resistance. Mol Cell Biol (2008) 0.98
Topoisomerase function during replication-independent chromatin assembly in yeast. Mol Cell Biol (1997) 0.96
Polyamines, chromatin structure and transcription. Bioessays (1993) 0.95
Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes. EMBO J (2010) 0.95
DNA topoisomerase II and casein kinase II associate in a molecular complex that is catalytically active. J Biol Chem (1993) 0.95
Topological complexes between DNA and topoisomerase II and effects of polyamines. Biochemistry (1989) 0.94
Transcriptional inhibition by DNA torsional stress. Transcription (2011) 0.94
Poly(ADP-ribose) polymerases PARP1 and PARP2 modulate topoisomerase II beta (TOP2B) function during chromatin condensation in mouse spermiogenesis. Biol Reprod (2011) 0.93
DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae. PLoS Genet (2012) 0.90
Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion. J Mol Biol (2008) 0.90
Recruitment of cdc2 kinase by DNA topoisomerase II is coupled to chromatin remodeling. FASEB J (2001) 0.88
DNA topoisomerase II activity in nonreplicating, transcriptionally inactive, chicken late spermatids. EMBO J (1989) 0.85
The torsional state of DNA within the chromosome. Chromosoma (2011) 0.85
Topoisomerase IIbeta is required for lamina-specific targeting of retinal ganglion cell axons and dendrites. Development (2011) 0.83
Histone deacetylase inhibition redistributes topoisomerase IIβ from heterochromatin to euchromatin. Nucleus (2011) 0.82
Topoisomerase II is nonfunctional in polyamine-depleted cells. J Cell Biochem (1999) 0.81
Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation. Nat Commun (2013) 0.81
Expression and localization of DNA topoisomerase II during rat spermatogenesis. Mol Reprod Dev (1996) 0.79
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics Chromatin (2010) 0.79
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
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Enterotypes of the human gut microbiome. Nature (2011) 24.36
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
Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell (2004) 2.99
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
Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell (2013) 1.81
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
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc Natl Acad Sci U S A (2002) 1.71
Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA (2009) 1.66
Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66
Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol (2012) 1.64
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
A complete set of nascent transcription rates for yeast genes. PLoS One (2010) 1.56
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res (2013) 1.51
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression. J Cell Biol (2008) 1.40
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
Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. EMBO J (2006) 1.38
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol (2011) 1.31
DNA knots reveal a chiral organization of DNA in phage capsids. Proc Natl Acad Sci U S A (2005) 1.31
The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes. Genome Biol (2007) 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
Comprehensive transcriptional analysis of the oxidative response in yeast. J Biol Chem (2008) 1.25
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
Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast (2002) 1.19
Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. J Mol Biol (2004) 1.18
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
SRC1: an intron-containing yeast gene involved in sister chromatid segregation. Yeast (2002) 1.17
A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding. Nucleic Acids Res (2010) 1.17
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
The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast. Yeast (2008) 1.14
EGASP: Introduction. Genome Biol (2006) 1.13
Development of a real-time polymerase chain reaction assay for the diagnosis of human herpesvirus-6 infection and application to bone marrow transplant patients. J Virol Methods (2002) 1.13
Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to continuous oxidizing conditions are affected in the expression of specific sets of genes. J Biol Chem (2004) 1.13
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol (2011) 1.12
The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res (2010) 1.12
A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses. Int Microbiol (2004) 1.10
Regulon-specific control of transcription elongation across the yeast genome. PLoS Genet (2009) 1.10
Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One (2011) 1.07
The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol (2011) 1.05
Common gene expression strategies revealed by genome-wide analysis in yeast. Genome Biol (2007) 1.04
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
Topoisomerase II is required for the production of long Pol II gene transcripts in yeast. Nucleic Acids Res (2012) 0.99
Failure to relax negative supercoiling of DNA is a primary cause of mitotic hyper-recombination in topoisomerase-deficient yeast cells. J Biol Chem (2002) 0.98
Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Appl Environ Microbiol (2009) 0.98
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
Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes. EMBO J (2010) 0.95