Published in Genome Res on September 01, 2015
Categorical spectral analysis of periodicity in nucleosomal DNA. Nucleic Acids Res (2016) 0.77
DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells. Cell Res (2016) 0.75
Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome. Genome Res (2016) 0.75
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res (2016) 0.75
The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol (2017) 0.75
Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts. Epigenetics Chromatin (2017) 0.75
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature (1997) 44.55
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol (2010) 17.00
Genome-scale identification of nucleosome positions in S. cerevisiae. Science (2005) 15.04
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Nucleosome organization in the Drosophila genome. Nature (2008) 8.65
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89
The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature (1987) 7.23
Preparation of nucleosome core particle from recombinant histones. Methods Enzymol (1999) 6.46
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71
Determinants of nucleosome organization in primary human cells. Nature (2011) 5.50
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res (1988) 4.92
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell (1990) 3.75
Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol (2009) 3.43
Chromatin decouples promoter threshold from dynamic range. Nature (2008) 3.24
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics (2009) 3.05
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science (2011) 2.95
A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell (2012) 2.86
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol (2005) 2.85
Nucleosome positioning: how is it established, and why does it matter? Dev Biol (2009) 2.68
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science (2011) 2.50
Determinants of nucleosome positioning. Nat Struct Mol Biol (2013) 2.47
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol (2010) 2.40
A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res (2006) 2.24
Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell (2012) 2.22
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res (2000) 1.96
High-resolution genome-wide mapping of the primary structure of chromatin. Cell (2011) 1.89
Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena. Cell (1984) 1.82
Exonic transcription factor binding directs codon choice and affects protein evolution. Science (2013) 1.80
Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol (2010) 1.72
Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res (2010) 1.70
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res (2012) 1.65
Histones and chromatin structure in Tetrahymena macro- and micronuclei. Cold Spring Harb Symp Quant Biol (1978) 1.62
How the sequence of a gene can tune its translation. Cell (2010) 1.58
Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res (2011) 1.44
Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol (2007) 1.43
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol (2010) 1.25
Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science (2012) 1.22
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing. PLoS One (2012) 1.19
Transcribing through the nucleosome. Trends Biochem Sci (2014) 1.07
Canonical nucleosome organization at promoters forms during genome activation. Genome Res (2013) 1.05
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res (2013) 1.03
Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Res (2012) 0.96
Whole genome studies of Tetrahymena. Methods Cell Biol (2012) 0.96
Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell (2014) 0.96
Modulation of telomere length dynamics by the subtelomeric region of tetrahymena telomeres. Mol Biol Cell (2004) 0.93
Isolation and characterization of in vivo modified histones and an activity gel assay for identification of histone acetyltransferases. Methods Cell Biol (2000) 0.81
A comparison of in vitro nucleosome positioning mapped with chicken, frog and a variety of yeast core histones. J Mol Biol (2013) 0.77