Review Highlights Recent Advances in Computational Epigenetics


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A nice review article by Bock et. al. in Bioinformatics sheds light on some of the recent advances (2006-2007) being made in computational epigenetics. Some highlights:

  • The article provides a succinct introduction to epigenetics research for bioinformaticians that are new to the field, including explanations of mitotic vs. meiotic epigenetic inheritance, mechanisms of epigenetic regulation, and common techniques for genome-wide mapping of the epigenome.
  • CHIP-on-chip analysis is explored from a bioinformatics perspective, providing technical details on how this data can be efficiently analyzed with freely available tools.
  • The review provides a handy list of epigenome mapping projects and their current state as of October 2007.
  • The review notes some of the ways in which the ENCODE project has helped to develop more refined techniques for bioinformatics analysis of epigenetic data, such as new methods for using epigenetic information in promoter prediction.
  • One key challenge in computational epigenetics is the issue of public data storage. Hundreds of gigabytes of data can be generated routinely, and the ability to easily share the data on publicly accessible servers will be an ongoing issue.
  • Using epigenetic data for promoter prediction is increasingly becoming less relevant, therefore work is now being focus on advanced questions of transcriptional control, such as inferring tissue-specific signals and reconstructing transcriptional networks.
  • The concept of CpG islands are being refined based on new insight using genome-wide computational studies to better predict the location of CpG islands and DNA methylation.
  • Recent work in cancer epigenetics has shown the potential benefits of combining computational and experimental approaches in deciphering how epigenetics shapes cancer progression.
  • The authors expect that future computational studies in epigenetics will increasingly take into account the proteins that read and write epigenetic information, and that reduced costs in epigenome mapping will enable many studies of epigenetic variation in human populations.

And finally: “In conclusion, exciting times are ahead for research in computational epigenetics!”

References:

Bock C, Lengauer T. 2007. Bioinformatics Advance Access published online on November 17, 2007.

doi:10.1093/bioinformatics/btm546

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Backing up Research Data and Publications with Mozy


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I’m a regular reader of Derek Lowe’s In the Pipeline, an excellent blog written by an industry chemist that offers insight on careers in research, the ups and downs of life in the lab, and his unique perspective on pharmaceutical news. His recent post about the lengths that he went through to back up his dissertation during grad school was something many people can identify with in terms of the importance of some documents — whether it be research data or priceless digital photos of birthday parties and vacations.

Mozy 1

Mozy is a simple solution that I use to back up important files. Available for Windows 2000, XP, and Vista, and Mac OS X 10.4, Mozy automatically backs up files that you specify to a secure server. The great part is that Mozy works without assistance — you don’t have to remember to start the backup every so often. Mozy can be set to backup at certain times (such as the middle of the night), or when your computer has been idle for 30 minutes, for example.

Mozy 2

Mozy also has a convenient feature that allows you to backup common types of files, such as your iPhoto or iTunes library, Excel or PowerPoint documents, or application preferences. Other files and folders can also be selected manually.

The best part is that Mozy is completely free for up to 2 GB of files. Unlimited backup space is available for $4.95 per month. Use this link to get an additional 256 MB of free backup space.

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Bringing Your Research Lab’s Web Site into the 21st Century


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I have been asked by enough people for advice on making their lab web site “better” for various reasons, so I decided to put together a list of things that will have a tremendous impact on a researcher’s ability to provide readers with the information they’re looking for, convey a professional effort in its appearance, and keep journalists, students, and others coming back regularly for updates. With that said, here are my top 5 tips for bringing your research lab’s web site into the 21st century:

1. Offer RSS feeds for your own papers or papers within your specific speciality. An RSS feed is a simple and effective way for anyone to keep updated with your work without constantly checking your web site. They are easily set up and maintained, and can be added to any type of web site, including your lab’s home on the web.

2. Make an XML sitemap and submit it to Google. If you don’t want your research (probably publicly funded) to be widely disseminated, why are you doing it in the first place? One of the best ways to help people find your site is to get it in the search engines. The best way to do that? Make an XML sitemap and submit it Google using their handy webmaster tools. They’ll then know where each of your site’s pages are, and will check them regularly for updates. That means your pages will appear more quickly in search results, meaning your research will be easily found, and more likely to be cited in other papers. See XML-Sitemaps.com for more information.

3. Provide PDF reprints of your latest papers. Let’s face it: not everyone has the luxury of an institutional subscription for access to hundreds of journals. Why not offer simple PDF reprints of your latest papers right from your site? This not only makes your work more widely available (and more likely to be cited), it also makes it dead simple for prospective graduate students, for instance, to see what you’re actually working on right now. (Of course, this tip would be negated if all of your work was available in open access journals, but that’s not very likely.)

4. Update the site regularly. This tip may seem simple, but most researchers are “too busy” to follow it. How many lab web sites have you been to with the latest paper shown is 2 or 3 years old, yet they have 10-15 papers published over the last couple years? I’ve seen dozens of sites just like this, and I’m hoping it’s not yours. Just taking the time and effort to keep your site reflective of your lab’s current work is a step in the right direction.

5. Take the web site seriously. A large majority of the lab web sites that I have seen in recent years are absolute jokes in terms of their utility. Students, journalists, fellow researchers — they would all be equally dissatisfied with the experience. We’re talking about the way in which hundreds of thousands of people will be able to judge your life’s work, and you put up a simple page with a generic research outline (probably outdated based on your current work) and a CV and call it good? This is not good enough for today’s researchers. In fact, it wasn’t good enough five years ago either.I have heard grumblings from some professors that go something like, “I’m too busy to constantly update my web site,” or “I don’t know enough about that technical stuff to do it right.” I’m sorry, but these excuses just don’t float when a simple job like this can be contracted for $500 or less — an amount you probably spend on pipette tips in a month. Remember, this is your contact point for telling the world about your life’s work. Isn’t that important enough to make a solid effort?Now maybe if you do your web site well enough, and people can clearly understand the relevance and importance of your work, you will also be nominated for 2007 Time Person of the Year, just like epigenetics and imprinting researcher Dr. Randy Jirtle was. (See Dr. Jirtle’s site, Geneimprint.org, for a site done right.)

Putting the "Re” in Research


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Long-time readers may remember a time at which I mentioned that I was working on writing my first peer-reviewed research publication. Since then, I don’t think that I’ve mentioned it again. Well, to make a long story short, that work was put on the back burner, but is about to begin again, after repeating a series of experiments that was required after a previous result called for it.

All of this means that I won’t get to accomplish as much as I would have liked to as an undergraduate researcher, but it provides a much needed lesson for a researcher in training: this is how you can expect it to go. One of the former postdocs in the lab liked to say, “That’s the ‘re’ in research,” which isn’t the best thing to hear right after you learn that you’ll be repeating the experiment you just completed after months of work. Nevertheless, I can imagine that learning and accepting this reality even before I begin my graduate research will be a tremendous benefit in my future endeavors.
On a brighter note, shortly after arriving in the Skinner lab in 2004, I was involved in another project that now looks to be published in the next 3-4 months. That will be my first authorship in a peer-reviewed journal, and since it doesn’t relate to epigenetics, I doubt I will acknowledge it here when it finally does hit the press. But it does represent a major milestone in what I hope will be a future career in research, and at the very least, for that I can feel some sense of accomplishment.