Webserver for Aligning Non-Coding RNA Structure-WARJuly 13, 2008Finally a WAR with no conflict. We have to give a big electronic high five to the group from the University of Copenhagen who just introduced a very helpful web utility: WAR-Webserver for aligning structural RNAs is a very handy site that allows you to use the best algorithms for aligning and predicting the consensus […]
ChIPs and MeDIP: ChIP Antibody Selection TipsJuly 9, 2008Chromatin immunoprecipitation (ChIP) remains a powerful method to characterize in vivo binding of DNA hugging proteins like histones and transcription factors and more recently has been used effectively for DNA methylation studies. The ChIP technique has been around since the days of big hair and “Miami Vice,” so we won’t review it here much, but […]
PatMAn and the Magnificent Seven Methylation ClassifiersJune 16, 2008It seems pattern recognition and supervised learning techniques are being applied to epigenetics research a lot nowadays. These advanced computational techniques that have proven useful in everything from homeland security to financial modeling are lending a hand to some of the challenges in epigenetics research. Recently we’ve seen them applied to miRNA discovery and target […]
ChIP TipsJune 1, 2008There’s a reason chromosome immunoprecipitation (ChIP) continues to be used in labs all over the world. It works well. In fact, there aren’t too many ways to map minute-by-minute changes at a single promoter, or alternatively, follow a single transcription factor over the entire human genome. ChIP is very versatile and can yield significant insights […]
Pursuit of the Moving miRNA TargetApril 11, 2008Since 3’ UTRs were found to contain docking sites for miRNAs, labs with computational muscle around the world have been chipping away the target predication dilemma, but like any game, it’s hard to win when you don’t know the rules. It’s even harder when the rules are being rewritten weekly which is why we have […]