The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Statistics for Spatial Data.

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Metagenomic biomarker discovery and explanation

羟氨苄青霉素引起大疱性类天疱疮样疹

http://www.jlakes.org/news/hal-200812-sdarticle.pdf

Hongbin Liu

Papers

Spawning time and egg development of the Japanese sardine and Japanese anchovy determined by the serial net sampling off southern Kyushu

Exploring the Influence Factors of Identifying Soil Texture Classes Using Multitemporal Landsat-8 and Sentinel-2 Data

Electromagnetic Design of HTS D-shaped Coils for a Toroidal-type Superconducting Magnet

The Spatial Variability of Temporal Changes in Soil Ph Affected by Topography and Fertilization

Upwelling ecosystem in the southern Taiwan Strait