Upcoming challenges for multiple sequence alignment methods in the high-throughput era - This review focuses on recent trends in multiple sequence alignment tools.

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster - Motivation: In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common

An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions - Motivation: In both genome-wide association studies (GWAS) and pathway analysis, the modest sample size relative to the number of genetic mar

Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication - Motivation: ChIP–chip has been widely used for various genome-wide biological investigations.

Motif discovery and motif finding from genome-mapped DNase footprint data - Motivation: Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites.

Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus - Motivation: Mapping the antigenic and genetic evolution pathways of influenza A is of critical importance in the vaccine development and drug design of influenza virus.

k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage - Motivation: The clustering of expressed sequence tags (ESTs) is a crucial step in many sequence analysis studies that require a high level of redundancy.

Evidence for human microRNA-offset RNAs in small RNA sequencing data - MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate.

Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus - We identified 5 975 567 mono- and 6 995 122 di-nucleosome positions of the fungus Aspergillus fumigatus, which was detected at high resolution based on the DNA sequence data obtained from both mono- and di-nucleosomal DNA fragme

Plasmid-based lacZ{alpha} assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase - The preparation of a gapped pUC18 derivative, containing the lacZ reporter gene in the single-stranded region, is described.