One year of blogging

When I checked the date of my first blog post today, I was a bit surprised to find that it is exactly one year since I begin to blog on May 2, 2009. Altogether, I have written over 60 posts, slightly more than one per week. At this time, I feel it appropriate to summarize my thought on blogging in general, to provide a perspective to those who care to visit here and make comments.

• Why? The initial motivation was to use blog as a platform to express my personal views on issues I am interested in. As made clear in my first post, "this is Xiang-Jun's Corner on the Internet: all views are mine, and I am opinionated." Over the time, the blog posts have served as a convenient notebook (searchable and archived) either for my personal reference, or to refer others to a particular post (e.g., "On maintaining the 3DNA forum" when being asked a 3DNA-related question via email).
• What? "Random thoughts, mostly on scientific issues". I write only on issues I am familiar with and feel comfortable to say something, to the limit that I can respond quickly and concretely to users comments. I am always open to suggestions and will be prompt in acknowledging errors and making corrections. So far, the largest portion of the posts has been devoted to nucleic acid structures in general, and 3DNA-related topics in particular.
• How often? Due to time constraints, I will try to write one post per week at the minimum, maybe two, or in rare occasion three. Exceptions are possible, but by and large, I will aim for ~100 posts per year.
• Comment? Currently, the policy is set such that "Anyone - includes Anonymous Users" can make a comment, and the comments are moderated. So far, I have always approved all the comments as soon as I see them in my gmail alert, and follow up where appropriate. Note that due to global time difference, commenters may experience some lag in time.
• Does it work? Not unexpectedly, my blog has gradually attracted attentions from quite a broad audience, especially those interested in nucleic acid structures (3DNA), including leading scientists in the field (I know from emails I have received).
• Hot posts? According to Google Analytics, the most frequently visited nine posts are as follows (with posting date in parentheses):
  1. Curves+ vs 3DNA (Sunday, August 16, 2009)
  2. Does 3DNA work for RNA? (Friday, July 10, 2009)
  3. Two web-interfaces to 3DNA, and more (Sunday, July 5, 2009)
  4. Fit a least squares plane to a set of points (Saturday, August 22, 2009)
  5. Two 3DNA figures made into a textbook on structural biology (Sunday, May 3, 2009)
  6. Chemical diagram of Watson-Crick base-pairs (Saturday, January 23, 2010)
  7. What's special about the GpU dinucleotide platform? (Friday, April 2, 2010)
  8. Double helix groove width parameters from 3DNA (Saturday, September 5, 2009)
  9. How to calculate torsion angle? (Saturday, October 31, 2009)
  
  
  While some of the posts are well-expected to be in the list, a few of them (e.g., ls-plane fitting, calculation of torsion angle) could look a bit surprising. It does, however, verify an observation based on my personal experience and intuitive feeling about a technical niche that my expertise can make a difference.

Again, as I wrote in my first blog post, "Now the ball is rolling, and only time can tell where the destination will be -- but surely it will no longer stand where it was!" One year later, I can confidently say that the ball in rolling in the right direction, as I'd have hoped for. Of course, I know for sure more time and efforts are need to move to the next level, and I value your feedback!

C2B2 annual retreat; DNA shape matters

As in previous years, today's C2B2 annual retreat provided a good opportunity to know the projects going on, and to meet the people performing the researches in the broad area of computational biology and bioinformatics at Columbia. The depth and breadth of the topics covered, and the close collaborations among different labs were amazing; revealing the multidisciplinary nature of bioinformatics and systems biology. After lunch, there was only slightly more than 30 minutes left for poster session. I quickly walked around the posters and I only wished to have more time to read more carefully some of them and discuss with the presenters.

From a DNA structural perspective, of special note is the plenary talk by Dr. Tom Tullius, titled "Function follow form: the role of DNA shape in the working of human genome". I am aware of Dr. Tullius work on hydroxyl radical footprinting, and his 2009 Science paper on the correlation between local DNA topography (the shape of the backbone and grooves) with functional noncoding regions in the human genome. His talk connects naturally to the work by Rohs et al. (Nature, 2009) on the "The role of DNA shape in protein-DNA recognition" which shows that narrow DNA minor groove (associated with A-tracts and negative electrostatic potential) interacts preferably with arginine residues. The last talk by Dr. Richard Mann, titled "New insights into transcript factors specificity" echoed nicely with Dr. Tullius's presentation, emphasizing the importance of DNA shape.

Along the line, it is very interesting to note that Dr. Tullius mentioned a recently published paper titled "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis" by Stella et al., Genes Dev. 2010 Apr 15; 24(8):814-26. I happened to read this paper just a coupe of days ago and was impressed by the work. Additionally, I am happy to see that 3DNA's analyze/rebuild/fiber components combined together helped to pinpoint the fact that only three parameters – roll, twist, and slide – are needed to explain observed DNA shapes in Fis-DNA complexes. See also a related blog post, titled "Fiber, analyze and rebuild in 3DNA".

Overall, it is nice to see that the community has gradually realized that DNA structural features, not just (or in addition to) its base sequence, are a major player in protein/ligand-DNA recognition. From my (certainly not that extensive) understanding of the field, the impressive list of publications over the past few years by Dr. Remo Rohs (Barry Honig group at Columbia University) has played a significant role in "shaping" DNA.