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Full-length transcriptome assembly from RNA-Seq data without a reference genome.
TLDR
The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
TLDR
The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Initial sequencing and comparative analysis of the mouse genome.
TLDR
The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Genome sequence, comparative analysis and haplotype structure of the domestic dog
TLDR
A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and 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.
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
TLDR
A comparative analysis of the human, mouse, rat and dog genomes is presented to create a systematic catalogue of common regulatory motifs in promoters and 3′ untranslated regions (3′ UTRs).
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
TLDR
Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish, and reconstructs much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
The ENCODE (ENCyclopedia Of DNA Elements) Project
TLDR
The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Whole-genome resequencing reveals loci under selection during chicken domestication
TLDR
The use of massively parallel sequencing is described to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens and their subsequent specialization into broiler (meat- producing) and layer (egg-producing) chickens.
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