Nucleosome positioning and gene regulation: advances through genomics
C Jiang, BF Pugh - Nature Reviews Genetics, 2009 - nature.com
Knowing the precise locations of nucleosomes in a genome is key to understanding how
genes are regulated. Recent'next generation'ChIP–chip and ChIP–Seq technologies have …
genes are regulated. Recent'next generation'ChIP–chip and ChIP–Seq technologies have …
Frontiers in molecular dynamics simulations of DNA
It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …
knowledge of its accessible conformational space remains limited. Structural data, primarily …
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition
Motivation: Enhancers are of short regulatory DNA elements. They can be bound with
proteins (activators) to activate transcription of a gene, and hence play a critical role in …
proteins (activators) to activate transcription of a gene, and hence play a critical role in …
iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition
Meiotic recombination is an important biological process. As a main driving force of
evolution, recombination provides natural new combinations of genetic variations. Rather …
evolution, recombination provides natural new combinations of genetic variations. Rather …
Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique
Motivation DNA replication is a key step to maintain the continuity of genetic information
between parental generation and offspring. The initiation site of DNA replication, also called …
between parental generation and offspring. The initiation site of DNA replication, also called …
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
The σ54 promoters are unique in prokaryotic genome and responsible for transcripting
carbon and nitrogen-related genes. With the avalanche of genome sequences generated in …
carbon and nitrogen-related genes. With the avalanche of genome sequences generated in …
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
Motivation: Nucleosome positioning participates in many cellular activities and plays
significant roles in regulating cellular processes. With the avalanche of genome sequences …
significant roles in regulating cellular processes. With the avalanche of genome sequences …
Identifying sigma70 promoters with novel pseudo nucleotide composition
Promoters are DNA regulatory elements located directly upstream or at the 5'end of the
transcription initiation site (TSS), which are in charge of gene transcription initiation. With the …
transcription initiation site (TSS), which are in charge of gene transcription initiation. With the …
G+ C content dominates intrinsic nucleosome occupancy
Background The relative preference of nucleosomes to form on individual DNA sequences
plays a major role in genome packaging. A wide variety of DNA sequence features are …
plays a major role in genome packaging. A wide variety of DNA sequence features are …
iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties
Nucleosome positioning has important roles in key cellular processes. Although intensive
efforts have been made in this area, the rules defining nucleosome positioning is still elusive …
efforts have been made in this area, the rules defining nucleosome positioning is still elusive …