Motif discovery and motif finding from genome-mapped DNase footprint data

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

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

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

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

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

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.

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data - Biclustering extends the traditional clustering techniques by attempting to find (all) subgroups of genes with similar expression patterns under to-be-identified subsets of experimental conditions when applied to gene expression data.

Copy number variation has little impact on bead-array-based measures of DNA methylation

Copy number variation has little impact on bead-array-based measures of DNA methylation - Motivation: Integration of various genome-scale measures of molecular alterations is of great interest to researchers aiming to better define disease processes or identify novel targets with clinical utility.

A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles

A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles - Motivation: Identification of core promoters is a key clue in understanding gene regulations.

PROMISE: a tool to identify genomic features with specific biological associations with multiple endpoint variables

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables - Motivation: In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a