Published in Genome Res on March 01, 2017
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
Long noncoding RNA as modular scaffold of histone modification complexes. Science (2010) 15.23
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell (2008) 7.69
MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res (2004) 6.98
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
A transcriptional profile of aging in the human kidney. PLoS Biol (2004) 3.69
A genetic signature of interspecies variations in gene expression. Nat Genet (2006) 3.61
Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev (2007) 3.16
Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat Cell Biol (2008) 3.08
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A (2004) 2.99
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Accuracy of transpulmonary thermodilution versus gravimetric measurement of extravascular lung water. Crit Care Med (2004) 2.68
Genomics: ENCODE explained. Nature (2012) 2.62
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol (2012) 2.49
Determinants of nucleosome positioning. Nat Struct Mol Biol (2013) 2.47
Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46
High nucleosome occupancy is encoded at human regulatory sequences. PLoS One (2010) 2.43
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol (2008) 2.27
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet (2009) 2.22
EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16
A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol (2008) 2.12
Overlapping codes within protein-coding sequences. Genome Res (2010) 2.02
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet (2012) 1.89
Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res (2008) 1.83
Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A (2009) 1.81
Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res (2009) 1.72
Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol (2010) 1.72
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A (2008) 1.51
Reconstruction of cell lineage trees in mice. PLoS One (2008) 1.46
On the relation between promoter divergence and gene expression evolution. Mol Syst Biol (2008) 1.43
Reversal of aging by NFkappaB blockade. Cell Cycle (2007) 1.36
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Comput Biol (2008) 1.34
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell (2004) 1.32
Strategy of transcription regulation in the budding yeast. PLoS One (2007) 1.30
New insights into replication origin characteristics in metazoans. Cell Cycle (2012) 1.29
Revealing targeted therapy for human cancer by gene module maps. Cancer Res (2008) 1.29
Promoter sequence determines the relationship between expression level and noise. PLoS Biol (2013) 1.28
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol (2010) 1.25
Minimally cultured or selected autologous tumor-infiltrating lymphocytes after a lympho-depleting chemotherapy regimen in metastatic melanoma patients. J Immunother (2009) 1.25
A transcriptional program mediating entry into cellular quiescence. PLoS Genet (2007) 1.23
Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets. PLoS Biol (2009) 1.20
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res (2011) 1.19
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res (2010) 1.19
AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res (2004) 1.19
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci U S A (2013) 1.18
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol (2007) 1.18
Perianesthetic dental injuries: analysis of incident reports. J Clin Anesth (2004) 1.17
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res (2010) 1.15
Cell lineage analysis of the mammalian female germline. PLoS Genet (2012) 1.13
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res (2013) 1.08
Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol (2010) 1.07
Estimating cell depth from somatic mutations. PLoS Comput Biol (2008) 1.06
Stemness, cancer and cancer stem cells. Cell Cycle (2008) 1.02
Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res (2013) 1.00
t-SNARE phosphorylation regulates endocytosis in yeast. Mol Biol Cell (2002) 0.96
The grammar of transcriptional regulation. Hum Genet (2014) 0.95
Predicting disease risk using bootstrap ranking and classification algorithms. PLoS Comput Biol (2013) 0.94
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy. Bioinformatics (2009) 0.94
Possible role of recombinant activated factor VII (rFVIIa) in the control of hemorrhage associated with massive trauma. Can J Anaesth (2002) 0.93
Probabilistic discovery of overlapping cellular processes and their regulation. J Comput Biol (2005) 0.90
Outcome of patients with cystic fibrosis admitted to the intensive care unit: is invasive mechanical ventilation a risk factor for death in patients waiting lung transplantation? Heart Lung (2009) 0.90
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol (2013) 0.90
A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host. Gut Microbes (2015) 0.88
Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity. PLoS Comput Biol (2008) 0.88
Robust prediction of expression differences among human individuals using only genotype information. PLoS Genet (2013) 0.86
Mso1 is a novel component of the yeast exocytic SNARE complex. J Biol Chem (2005) 0.86
YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem (2002) 0.84
Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein. Proc Natl Acad Sci U S A (2013) 0.83
Nonlinear fitness consequences of variation in expression level of a eukaryotic gene. Mol Biol Evol (2012) 0.83
Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code. Proc Natl Acad Sci U S A (2008) 0.83
Reuse of concentrated animal feeding operation wastewater on agricultural lands. J Environ Qual (2008) 0.83
Outcome of patients having dermatomyositis admitted to the intensive care unit. Clin Rheumatol (2007) 0.80
Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site. Genome Res (2015) 0.80