Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key
challenge in transcript quantification from RNA-Seq data is the handling of reads that map …

De novo assembly of RNA-seq data enables researchers to study transcriptomes without
the need for a genome sequence; this approach can be usefully applied, for instance, in …

Motivation: RNA-Seq is a promising new technology for accurately measuring gene expression
levels. Expression estimation with RNA-Seq requires the mapping of relatively short …

The population genetic perspective is that the processes shaping genomic variation can be
revealed only through simultaneous investigation of sequence polymorphism and …

Sequencing of multiple related species followed by comparative genomics analysis constitutes
a powerful approach for the systematic understanding of any genome. Here, we use the …

… Dewey is an assistant professor in the Department of Biostatistics and Medical
Informatics and the Department of Computer Sciences at the University of Wisconsin-Madison. …

Background Metazoan miRNAs regulate protein-coding genes by binding the 3′ UTR of
cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for …

Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The
method uses a non-parametric clustering of genes with compatible trees, and reconstructs …

This report of independent genome sequences of two natural populations of Drosophila
melanogaster (37 from North America and 6 from Africa) provides unique insight into forces …

De novo RNA-Seq assembly facilitates the study of transcriptomes for species without
sequenced genomes, but it is challenging to select the most accurate assembly in this context. To …