added rna paper

Author: masarunakajima

_bibliography/papers.bib

@@ -3,6 +3,32 @@
 
 @string{aps = {American Physical Society,}}
 
+
+@article{nakajima2023counting,
+  title={Counting Distinguishable RNA Secondary Structures},
+  author={Nakajima, Masaru and Smith, Andrew D},
+  journal={Journal of Computational Biology},
+  year={2023},
+  publisher={Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…},
+  pdf={nakajima-smith-2023-counting-distinguishable-rna-secondary-structures.pdf},
+  abstract={RNA secondary structures are essential abstractions for understanding 
+  spacial folding behaviors of those macromolecules. Many secondary structure 
+  algorithms involve a common dynamic programming setup to exploit the property 
+  that secondary structures can be decomposed into substructures. Dirks et al. 
+  noted that this setup cannot directly address an issue of distinguishability 
+  among secondary structures, which arises for classes of sequences that admit 
+  nontrivial symmetry. Circular sequences are among these. We examine the problem 
+  of counting distinguishable secondary structures. Drawing from elementary results 
+  in group theory, we identify useful subsets of secondary structures. 
+  We then extend an algorithm due to Hofacker et al. for computing the sizes of 
+  these subsets. This yields a cubic-time algorithm to count distinguishable 
+  structures compatible with a given circular sequence. Furthermore, this general 
+  approach may be used to solve similar problems for which the RNA structures of 
+  interest involve symmetries.}
+}
+
+
+
 @article{nakajima2022development,
   title={Development of an interactive code for quick data analyses between STOR-M tokamak experimental plasma discharges},
   author={Nakajima, Masaru and Basu, Debjyoti and Melnikov, Alexander V and McColl, David and Xiao, Chijin},

_projects/dnmtools.md

@@ -27,3 +27,4 @@ My first task was to improve the efficienty of `dnmtools format`.
 I wrote the details in my [blog](../../blog/2023/revcomp-byte).
 The outcome was about 30 % reduction in computation time, which can be
 a lot when you are working with large files.
+