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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25Expand
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Structure, Function and Diversity of the Healthy Human Microbiome
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remainsExpand
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Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potentialExpand
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Differential abundance analysis for microbial marker-gene surveys.
We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies onExpand
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GAGE: A critical evaluation of genome assemblies and assembly algorithms.
New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequencedExpand
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ARDB—Antibiotic Resistance Genes Database
  • Bo Liu, M. Pop
  • Biology, Medicine
  • Nucleic Acids Res.
  • 2 October 2008
TLDR
We have created a manually curated database—the Antibiotic Resistance Genes Database (ARDB)—unifying most of the publicly available information on antibiotic resistance. Expand
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Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
TLDR
We present a statistical method for comparing clinical metagenomic samples on the basis of count data (e.g. as obtained through sequencing) to detect differentially abundant features. Expand
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Metagenomic Analysis of the Human Distal Gut Microbiome
The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes as our own genome. We analyzed ∼78 millionExpand
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Evolution of genes and genomes on the Drosophila phylogeny
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genomeExpand
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The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease
Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs.Expand
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