Published in Genome Biol on July 16, 2010
Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol (2011) 2.11
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell (2015) 1.77
Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol (2012) 1.44
Protein expression regulation under oxidative stress. Mol Cell Proteomics (2011) 1.34
Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell (2011) 1.18
Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One (2011) 1.07
A key role for Chd1 in histone H3 dynamics at the 3' ends of long genes in yeast. PLoS Genet (2012) 1.02
Transcriptional elongation checkpoint control in development and disease. Genes Dev (2013) 0.98
High-resolution chromatin dynamics during a yeast stress response. Mol Cell (2015) 0.95
RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus (2014) 0.94
The Arabidopsis mediator complex subunits MED16, MED14, and MED2 regulate mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes. Plant Cell (2014) 0.89
Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases. Nucleic Acids Res (2014) 0.86
Dynamics of Nucleosome Positioning Maturation following Genomic Replication. Cell Rep (2016) 0.83
Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol (2014) 0.81
RNA polymerase II contributes to preventing transcription-mediated replication fork stalls. EMBO J (2014) 0.80
Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell (2016) 0.80
Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo. G3 (Bethesda) (2015) 0.79
A novel role for Cet1p mRNA 5'-triphosphatase in promoter proximal accumulation of RNA polymerase II in Saccharomyces cerevisiase. Genetics (2013) 0.78
Uniform distribution of elongating RNA polymerase II complexes in transcribed gene locus. J Biol Chem (2011) 0.76
Genomic insights into the different layers of gene regulation in yeast. Genet Res Int (2011) 0.76
The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast. Transcription (2012) 0.75
RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol (2016) 0.75
Temperature Shift Alters DNA Methylation and Histone Modification Patterns in Gonadal Aromatase (cyp19a1) Gene in Species with Temperature-Dependent Sex Determination. PLoS One (2016) 0.75
Functional role of histone variant Htz1 in the stress response to oleate in Saccharomyces cerevisiae. Biosci Rep (2015) 0.75
Multiplexed gene control reveals rapid mRNA turnover. Sci Adv (2017) 0.75
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Dissecting the regulatory circuitry of a eukaryotic genome. Cell (1998) 23.62
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006) 12.92
Divergent transcription from active promoters. Science (2008) 11.03
Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev (2000) 10.64
RNA polymerase is poised for activation across the genome. Nat Genet (2007) 9.57
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell (1988) 7.23
RNA exosome depletion reveals transcription upstream of active human promoters. Science (2008) 6.80
Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol (2007) 6.53
Dynamics of replication-independent histone turnover in budding yeast. Science (2007) 6.41
Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol (2005) 6.37
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol (1987) 5.93
Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell (2007) 5.13
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature (2009) 4.96
The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature (2004) 4.65
RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol Cell Biol (1986) 4.40
The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet (2009) 4.19
Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet (2008) 4.03
Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell (2006) 3.49
Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell (2006) 3.46
Transcription elongation and eukaryotic gene regulation. Oncogene (1990) 3.34
Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol Cell (2005) 3.15
A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol Cell (2008) 2.97
Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev (2005) 2.64
RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science (2009) 2.63
Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep (2009) 2.22
DNA melting on yeast RNA polymerase II promoters. Science (1993) 2.10
Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev (2006) 2.04
Regulation of yeast NRD1 expression by premature transcription termination. Mol Cell (2006) 1.82
Promoter proximal pausing on genes in metazoans. Chromosoma (2008) 1.64
Rheostat control of gene expression by metabolites. Mol Cell (2006) 1.53
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol (2010) 1.43
RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones. Proc Natl Acad Sci U S A (2010) 1.37
Control and signal processing by transcriptional interference. Mol Syst Biol (2009) 0.94
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Genome-scale identification of nucleosome positions in S. cerevisiae. Science (2005) 15.04
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
A module map showing conditional activity of expression modules in cancer. Nat Genet (2004) 8.57
Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
Stochastic protein expression in individual cells at the single molecule level. Nature (2006) 8.00
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 7.45
Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell (2005) 7.20
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79
Dynamics of replication-independent histone turnover in budding yeast. Science (2007) 6.41
Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol (2005) 6.37
Chromatin remodelling at promoters suppresses antisense transcription. Nature (2007) 6.11
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell (2003) 5.57
Global nucleosome occupancy in yeast. Genome Biol (2004) 5.49
Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (2010) 5.22
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol (2002) 5.04
Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. Mol Cell (2004) 5.01
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature (2004) 4.65
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature (2005) 4.33
Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (2009) 4.30
From signatures to models: understanding cancer using microarrays. Nat Genet (2005) 4.29
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res (2009) 3.99
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81
Immune inhibitory molecules LAG-3 and PD-1 synergistically regulate T-cell function to promote tumoral immune escape. Cancer Res (2011) 3.81
High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (2011) 3.53
Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J (2004) 3.50
Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci U S A (2005) 3.46
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A (2002) 3.28
gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair. Mol Cell (2005) 3.24
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell (2011) 3.19
The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol (2008) 3.17
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol (2010) 3.09
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
The CTD code. Nat Struct Biol (2003) 3.00
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A (2004) 2.99
A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell (2012) 2.86
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A (2004) 2.80
Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol Cell (2003) 2.74
Nucleosome positioning: how is it established, and why does it matter? Dev Biol (2009) 2.68
A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme. Science (2013) 2.67
Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet (2008) 2.67
Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. Cell (2009) 2.62
The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53
Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics (2007) 2.52
Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. Mol Cell (2006) 2.51
The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev (2006) 2.42
Distinct pathways for snoRNA and mRNA termination. Mol Cell (2006) 2.31
Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev (2005) 2.27
Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol (2011) 2.26
Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell (2011) 2.26
Proteasome involvement in the repair of DNA double-strand breaks. Mol Cell (2004) 2.17
Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol (2011) 2.11
Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem (2003) 2.10
Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol Cell Biol (2003) 2.08
Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol (2010) 2.07
The specificity and topology of chromatin interaction pathways in yeast. Mol Cell (2011) 2.04
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics (2004) 2.04
EHD2 and the novel EH domain binding protein EHBP1 couple endocytosis to the actin cytoskeleton. J Biol Chem (2003) 1.99
The Stanford Tissue Microarray Database. Nucleic Acids Res (2007) 1.96
Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast. PLoS Genet (2008) 1.93
Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem (2009) 1.89
Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood (2013) 1.86
Quantitative kinetic analysis of the bacteriophage lambda genetic network. Proc Natl Acad Sci U S A (2005) 1.76
Human and porcine early kidney precursors as a new source for transplantation. Nat Med (2002) 1.73
Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl Environ Microbiol (2011) 1.67
Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. PLoS One (2009) 1.66
The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol (2009) 1.64
Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol (2005) 1.64
Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell (2008) 1.61
Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell (2012) 1.61
Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell (2012) 1.61
Tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemistry. Mod Pathol (2002) 1.60
Practical approaches to analyzing results of microarray experiments. Am J Respir Cell Mol Biol (2002) 1.55