Sifting Through the Rubble: miRNA “Degradome” Sequencing for miRNA TargetsJanuary 26, 2009The miRNA target prediction field has developed rapidly over the last few years. New entrants like miRanda, PicTar, DIANA, and RNA22 have acted as oracles to the target seeking research community, but have often left scientists with more questions than answers, so experimental validation is still required. Taking advantage of the fact that Arognaute-mediated mRNA […]
LCM to Data: Navigating the Small Sample Obstacle Course in DNA Methylation ProfilingJanuary 25, 2009Tissue heterogeneity has pestered researchers desiring a closer look at tissue-specific genomics and epigenomics. Sure, laser capture microdissection (LCM) platforms have been really helpful in isolating very small and specific regions of tissue, but that’s only half the battle. Working with minute amounts of LCM samples, particularly when they’re derived from the battered formalin-fixed paraffin-embedded […]
CHARMed I’m Shore: Meet the Latest Hotspots for DNA MethylationJanuary 19, 2009Between reading Dilbert cartoons and refilling their Swingline staplers, many of corporate America’s finest day dream of holidays to distant islands, but they’re not alone. Researchers studying DNA methylation have made minimal attempts to hide their infatuation with CpG islands, after all, these regions tend to associate themselves with prestigious protein-coding regions of genes. An […]
CAGEd miRNAs: Taming Transcriptional InitiationJanuary 18, 2009Most primary miRNA transcripts remain a mystery because they’re generally degraded by the time they leave the comfort of the nucleus. Where do the transcripts start? Do they have a single “peak” of initiation, or are there a variety of sites where they’re likely to begin? Limitations in the currently available molecular biology tool set […]
Summitting With PeakSeq.It’s About MappabilityJanuary 10, 2009ChIP-seq continues to assault bioinformatics teams with avalanches of data, but the upside of using this powerful approach brings some challenges along with it. Modeling background accurately requires a few tweaks, so before you get all excited about the double black diamond peaks that you’re seeing in regulatory motifs, you might want to factor in […]
