bogdan's blog

R-Coffee: a method for multiple alignment of non-coding RNA

R-Coffee: a method for multiple alignment of non-coding RNA - R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align RNA sequences while exploiting secondary structure information.

Identification of soluble protein fragments by gene fragmentation and genetic selection

Identification of soluble protein fragments by gene fragmentation and genetic selection - We describe a new method, which identifies protein fragments for soluble expression in Escherichia coli from a randomly fragmented gene library. Inhibition of E.

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer - Gene transfer has been used to correct inherited immunodeficiencies, but in several patients integration of therapeutic retroviral vectors activated proto-oncogenes and caused leukemia.

Uncovering signal transduction networks from high-throughput data by integer linear programming

Uncovering signal transduction networks from high-throughput data by integer linear programming - Signal transduction is an important process that transmits signals from the outside of a cell to the inside to mediate sophisticated biological responses.

Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data

Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data - Motivation: Recently developed network component analysis (NCA) approach is promising for gene regulatory network reconstruction from microarray data.

Prediction of disordered regions in proteins based on the meta approach

Prediction of disordered regions in proteins based on the meta approach - Motivation: Intrinsically disordered regions in proteins have no unique stable structures without their partner molecules, thus these regions sometimes prevent high-quality structure determination.

A straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches - Motivation: The deluge of biological information from different genomic initiatives and the rapid advancement in biotechnologies have made bioinformatics tools an integral p

Expected gene-order distances and model selection in bacteria

Expected gene-order distances and model selection in bacteria - Motivation: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude.

Eukaryotic transcription factor binding sites - modeling and integrative search methods

Eukaryotic transcription factor binding sites--modeling and integrative search methods - A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks.