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Fast and accurate de novo genome assembly from long uncorrected reads.
TLDR
It is shown that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment-based, stand-alone consensus module called Racon. Expand
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
TLDR
The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects and are robust across datasets of varied complexity and sampling level. Expand
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
TLDR
It is shown that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. Expand
Comprehensive Characterization of Cancer Driver Genes and Mutations
TLDR
This study reports a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations, identifying 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Expand
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
TLDR
The results offer an explanation for the heterogeneity of TKI responses across individuals and suggest the possibility of personalizing therapy with BH3 mimetics to overcome BIM-polymorphism–associated TKI resistance. Expand
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
TLDR
Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties. Expand
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
TLDR
GraphMap is a mapping algorithm designed to analyse nanopore sequencing reads, which progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long reads with speed and high precision. Expand
The draft genome of sweet orange (Citrus sinensis)
TLDR
Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. Expand
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
TLDR
Somatic inactivation of FAT4 and ARID1A may be key tumorigenic events in a subset of gastric cancers, and cell adhesion was the most enriched biological pathway among the frequently mutated genes. Expand
Invariant NKT Cells Amplify the Innate Immune Response to Lipopolysaccharide1
TLDR
It is proposed that in addition to acting as a bridge to adaptive immunity, NKT cells act as an early amplification step in the innate immune response and that the rapid and complete initiation of this innate response depends on the early production of IFN-γ by N KT cells. Expand
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