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University of California System
US
3 researchers0 verified2 linked papers34,071 indexed citations
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2012 · Journal of Computational Biology · 27,638 citations
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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.
1989 · Biometrika · 6,433 citations
Regression and time series model selection in small samples
A bias correction to the Akaike information criterion, AIC, is derived for regression and autoregressive time series models. The correction is of particular use when the sample size is small, or when the number of fitted parameters is a moderate to large fraction of the sample size. The corrected method, called AICC, is asymptotically efficient if the true model is infinite dimensional. Furthermore, when the true model is of finite dimension, AICC is found to provide better model order choices than any other asymptotically efficient method. Applications to nonstationary autoregressive and mixed autoregressive moving average time series models are also discussed.