De novo computational prediction of non-coding RNA genes in prokaryotic genomes

De novo computational prediction of non-coding RNA genes in prokaryotic genomes - Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology.

Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription

Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription - Most nucleic acid-based technologies rely upon sequence recognition between an oligonucleotide and its nucleic acid target.

Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells

Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells - Promoterless gene trap vectors have been widely used for high-efficiency gene targeting and random mutagenesis in embryonic stem (ES) cells.

A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases

A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases - Specialized DNA polymerases are involved in DNA synthesis during base-excision repair and translesion synthesis across a wide range of chemically modified DNA templates.

RNA polymerase III can drive polycistronic expression of functional interfering RNAs designed to resemble microRNAs

RNA polymerase III can drive polycistronic expression of functional interfering RNAs designed to resemble microRNAs - In both research and therapeutic applications of RNA interference, it is often advantageous to silence several targets simultaneously.

Analysis of splicing patterns by pyrosequencing

Analysis of splicing patterns by pyrosequencing - Several different mRNAs can be produced from a given pre-mRNA by regulated alternative splicing, or as the result of deregulations that may lead to pathological states.

The SNP ratio test: pathway analysis of genome-wide association datasets

The SNP ratio test: pathway analysis of genome-wide association datasets - Summary: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context.

Caleydo: connecting pathways and gene expression

Caleydo: connecting pathways and gene expression - Summary: Understanding the relationships between pathways and the altered expression of their components in disease conditions can be addressed in a visual data analysis process.

FRED--a framework for T-cell epitope detection

FRED--a framework for T-cell epitope detection - Summary: Over the last decade, immunoinformatics has made significant progress. Computational approaches, in particular the prediction of T-cell epitopes using machine learning methods, are at the core of modern vaccine design.

FBA-SimVis: interactive visualization of constraint-based metabolic models

FBA-SimVis: interactive visualization of constraint-based metabolic models - Summary: FBA-SimVis is a VANTED plug-in for the constraint-based analysis of metabolic models with special focus on the visual exploration of metabolic flux data resulting from model analysis.