Next generation software for functional trend analysis - Summary: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features.

QuickGO: a web-based tool for Gene Ontology searching - Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many year

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways - Motivation: Systematic analysis of connection between proteins, their cellular function and phenotypic manifestations in disease is a central problem of biological and clinical research.

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 - 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 - 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 - 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 - In both research and therapeutic applications of RNA interference, it is often advantageous to silence several targets simultaneously.

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.