Published in Bioessays on May 30, 2014
Terminal NK cell maturation is controlled by concerted actions of T-bet and Zeb2 and is essential for melanoma rejection. J Exp Med (2015) 1.11
Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. Bioessays (2015) 0.95
Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation. PLoS Genet (2015) 0.79
"Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification. Bioessays (2015) 0.79
The search for cis-regulatory driver mutations in cancer genomes. Oncotarget (2015) 0.78
Ehrlichia chaffeensis TRP32 is a Nucleomodulin that Directly Regulates Expression of Host Genes Governing Differentiation and Proliferation. Infect Immun (2016) 0.76
Functional transcription factor target discovery via compendia of binding and expression profiles. Sci Rep (2016) 0.75
Binding Sites in the EFG1 Promoter for Transcription Factors in a Proposed Regulatory Network: A Functional Analysis in the White and Opaque Phases of Candida albicans. G3 (Bethesda) (2016) 0.75
Divergence and rewiring of regulatory networks for neural development between human and other species. Neurogenesis (Austin) (2016) 0.75
Shared transcription factors contribute to distinct cell fates. Transcription (2015) 0.75
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. Front Physiol (2016) 0.75
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. Elife (2017) 0.75
A CRISPR view of gene regulation. Curr Opin Syst Biol (2017) 0.75
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
Systematic localization of common disease-associated variation in regulatory DNA. Science (2012) 14.47
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13
Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell (2003) 10.42
The biology of chromatin remodeling complexes. Annu Rev Biochem (2009) 10.02
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet (2004) 9.57
The evolutionary significance of cis-regulatory mutations. Nat Rev Genet (2007) 9.35
Variation in transcription factor binding among humans. Science (2010) 9.33
Variation in genome-wide mutation rates within and between human families. Nat Genet (2011) 8.84
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell (1995) 7.17
Functional roles for noise in genetic circuits. Nature (2010) 6.96
Probing transcription factor dynamics at the single-molecule level in a living cell. Science (2007) 6.85
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30
Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol (2009) 5.23
Transcriptional regulation by the numbers: models. Curr Opin Genet Dev (2005) 5.20
Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet (2008) 5.08
Transcription factors: from enhancer binding to developmental control. Nat Rev Genet (2012) 5.00
Evolution of genetic redundancy. Nature (1997) 4.95
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature (2013) 4.47
The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet (2010) 4.46
A kinetic framework for a mammalian RNA polymerase in vivo. Science (2002) 4.42
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet (2013) 4.38
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet (2012) 4.37
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell (2004) 3.82
Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature (2010) 3.72
Epistasis and its implications for personal genetics. Am J Hum Genet (2009) 3.52
Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. Cell (2000) 3.50
Computational prediction of transcription-factor binding site locations. Genome Biol (2003) 3.39
Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet (2010) 3.29
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06
Uncovering cryptic genetic variation. Nat Rev Genet (2004) 3.01
Animal transcription networks as highly connected, quantitative continua. Dev Cell (2011) 2.87
Extensive variation in chromatin states across humans. Science (2013) 2.83
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet (2008) 2.67
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem (2005) 2.64
The transcription cycle of RNA polymerase II in living cells. J Cell Biol (2002) 2.59
CTCF and cohesin: linking gene regulatory elements with their targets. Cell (2013) 2.53
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet (2014) 2.42
Transcriptional enhancers in animal development and evolution. Curr Biol (2010) 2.41
Controlling gene expression in response to stress. Nat Rev Genet (2011) 2.33
Bringing genome-wide association findings into clinical use. Nat Rev Genet (2013) 2.32
Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell (2010) 2.29
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
Dynamic behavior of transcription factors on a natural promoter in living cells. EMBO Rep (2002) 2.21
Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell (2013) 2.16
Regulatory diversity among metazoan co-activator complexes. Nat Rev Mol Cell Biol (2004) 2.10
Thinking about genetic redundancy. Trends Genet (1993) 2.08
Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics (2006) 2.06
Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res (2009) 2.05
Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol (2007) 2.04
A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell (2012) 2.02
Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol (2012) 1.97
Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet (2010) 1.92
Widespread site-dependent buffering of human regulatory polymorphism. PLoS Genet (2012) 1.72
Qualifying the relationship between sequence conservation and molecular function. Genome Res (2008) 1.69
Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer. Dev Cell (2010) 1.61
Complexity in the signaling network: insights from the use of targeted inhibitors in cancer therapy. Genes Dev (2012) 1.60
Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet (2013) 1.57
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev (2012) 1.53
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell (2013) 1.52
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol (2010) 1.51
Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet (2011) 1.49
Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy. Bioessays (2011) 1.48
Genetic redundancy: new tricks for old genes. Cell (2009) 1.48
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A (2012) 1.39
The functional consequences of variation in transcription factor binding. PLoS Genet (2014) 1.38
Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet (2008) 1.36
Evolution of regulatory sequences in 12 Drosophila species. PLoS Genet (2009) 1.33
Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. Plant Cell (2007) 1.31
Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae. Genetics (2004) 1.30
Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. J Biol Chem (2007) 1.29
Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev (2009) 1.27
Abundant indispensable redundancies in cellular metabolic networks. Genome Biol Evol (2009) 1.23
Systematic functional regulatory assessment of disease-associated variants. Proc Natl Acad Sci U S A (2013) 1.22
Transcription factor Pip can enhance DNA binding by E47, leading to transcriptional synergy involving multiple protein domains. Mol Cell Biol (1998) 1.19
The physiological roles of histone deacetylase (HDAC) 1 and 2: complex co-stars with multiple leading parts. Biochem Soc Trans (2013) 1.18
Catalytic promiscuity and the divergent evolution of DNA repair enzymes. Chem Rev (2006) 1.18
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet (2013) 1.17
Transcription factor binding variation in the evolution of gene regulation. Trends Genet (2010) 1.14
In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev (2013) 1.12
Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos Trans R Soc Lond B Biol Sci (2013) 1.06
Evolutionary origins of transcription factor binding site clusters. Mol Biol Evol (2011) 1.05
Cis-regulatory mutations in the Caenorhabditis elegans homeobox gene locus cog-1 affect neuronal development. Genetics (2009) 1.05
Six Degrees of Epistasis: Statistical Network Models for GWAS. Front Genet (2012) 1.04
Global properties and functional complexity of human gene regulatory variation. PLoS Genet (2013) 1.02
Regulatory targets in the RNA polymerase II holoenzyme. Curr Opin Genet Dev (1998) 1.02
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol (2012) 0.99
Genetic redundancies and their evolutionary maintenance. Adv Exp Med Biol (2012) 0.96
Redundancy and the evolution of cis-regulatory element multiplicity. PLoS Comput Biol (2010) 0.95
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. BMC Genomics (2013) 0.93
Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. PLoS Genet (2014) 0.92
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Syst Biol (2010) 0.92