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Model-based Analysis of ChIP-Seq (MACS)
TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
TLDR
A pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions is observed and is consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa.
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
TLDR
A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
TLDR
This work reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information, and demonstrates that the original Affymetrix probe set definitions are inaccurate.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Integrated Genomic Analyses of Ovarian Carcinoma
TLDR
It is reported that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1,BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes.
The genomic basis of adaptive evolution in threespine sticklebacks
TLDR
A high-quality reference genome assembly for threespine stickleback fish is developed and it is indicated that reuse of globally shared standing genetic variation has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation.
Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
TLDR
This work discusses how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data and develops a set of working standards and guidelines for ChIP experiments that are updated routinely.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
TLDR
The interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated gliobeasts, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
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