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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. Expand
Initial sequencing and analysis of the human genome.
TLDR
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence. Expand
A second generation human haplotype map of over 3.1 million SNPs
TLDR
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated. Expand
Sequencing and comparison of yeast species to identify genes and regulatory elements
TLDR
A comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species, which inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. Expand
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. Expand
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to aExpand
Structure, Function and Diversity of the Healthy Human Microbiome
TLDR
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. Expand
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
TLDR
It is shown that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. Expand
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
TLDR
A new chimera detection tool called Chimera Slayer (CS), which detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. Expand
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. Expand
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