A knowledge-based approach to predict intragenic deletions or duplications

A knowledge-based approach to predict intragenic deletions or duplications - Motivation: Despite recent improvements in high-throughput or classic molecular biology approaches it is still challenging to identify intermediate resolution genomic variations (50 bp to 50 kb).

Powerful fusion: PSI-BLAST and consensus sequences

Powerful fusion: PSI-BLAST and consensus sequences - Motivation: A typical PSI-BLAST search consists of iterative scanning and alignment of a large sequence database during which a scoring profile is progressively built and refined.

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space - Motivation: RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard.

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mut

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis - Motivation: Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands - Motivation: DNA methylation plays important roles in biological processes and human diseases, especially cancers.

Discovering regulatory motifs in the Plasmodium genome using comparative genomics

Discovering regulatory motifs in the Plasmodium genome using comparative genomics - Motivation: Understanding gene regulation in Plasmodium, the causative agent of malaria, is an important step in deciphering its complex life cycle as well as leading to possible new targets for therapeutic ap

Bioimage informatics: a new area of engineering biology

Bioimage informatics: a new area of engineering biology - In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community.

A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors

A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors - We developed a functional selection system based on randomized genetic elements (GE) to identify potential regulators of hepatitis C virus (HCV) RNA translation, a process initiated by an inter

Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I

Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I - Tetraalkylammonium (TAA) derivatives have been reported to serve as stabilizers of asymmetrical cyanine dyes in aqueous solutions and to increase the yield and efficiency of polymerase chain reactio

Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification

Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification - Linear RNA amplification using T7 RNA polymerase is useful in genome-wide analysis of gene expression using DNA microarrays, but exponential amplification using polymerase chain reaction (PCR) is