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Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
Knowledge of the rate and nature of spontaneous mutation is fundamental to understanding evolutionary and molecular processes. In this report, we analyze spontaneous mutations accumulated overExpand
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The Ecoresponsive Genome of Daphnia pulex
The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions. We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases andExpand
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FragGeneScan: predicting genes in short and error-prone reads
The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmentalExpand
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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
We present RAPSearch2, a new memory-efficient implementation of the RAP search algorithm that uses a collision-free hash table to index a similarity search database. Expand
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Fragment assembly with short reads
We demonstrate that while it is feasible to assemble such short reads, the resulting contigs will require significant (if not prohibitive) finishing efforts. Expand
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Leaky Cauldron on the Dark Land: Understanding Memory Side-Channel Hazards in SGX
We report the first step toward systematic analyses of side-channel threats that SGX faces, focusing on the risks associated with its memory management. Expand
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The transcriptional diversity of 25 Drosophila cell lines.
Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. UnannotatedExpand
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Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis
In Arabidopsis thaliana, abundant 24 nucleotide small interfering RNAs (24 nt siRNA) guide the cytosine methylation and silencing of transposons and a subset of genes. 24 nt siRNA biogenesis requiresExpand
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De Novo Repeat Classification and Fragment Assembly
Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a newExpand
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RAPSearch: a fast protein similarity search tool for short reads
We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. Expand
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