Publications

*Corresponding author

  1. Tavares RCA, Pyle AM, *Somarowthu S. (2019) Phylogenetic analysis with improved parameters reveals conservation in lncRNA structures. J Mol Biol (in press).

  2. *Somarowthu, S. Progress and Current Challenges in Modeling Large RNAs. (2016) J Mol Biol.;736-47.

  3. Liu, F., Somarowthu, S. & Pyle, A. M. (2017) Visualizing the secondary and tertiary architectural domains of lncRNA RepA. Nat Chem Biol. Jan 9. doi: 10.1038/nchembio.2272.

  4. Somarowthu, S., Legiewicz, M., Chillon, I., Marcia, M., Liu, F. & Pyle, A. M. (2015). HOTAIR forms an intricate and modular secondary  structure. Mol Cell 58, 353-61.

  5. Chillon, I., Marcia, M., Legiewicz, M., Liu, F., Somarowthu, S. & Pyle, A. M. (2015). Native Purification and Analysis of Long RNAs. Methods Enzymol 558, 3-37.

  6. Brodkin, H. R., DeLateur, N. A., Somarowthu, S., Mills, C. L., Novak, W. R., Beuning, P. J., Ringe, D. & Ondrechen, M. J. (2015).  Prediction of distal residue participation in enzyme catalysis. Protein Sci 24, 762-78.

  7. Somarowthu, S., Legiewicz, M., Keating, K. S. & Pyle, A. M. (2014). Visualizing the ai5gamma group IIB intron. Nucleic Acids Res 42, 1947-58.

  8. Wang, Z., Yin, P., Lee, J. S., Parasuram, R., Somarowthu, S. & Ondrechen, M. J. (2013). Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). BMC Bioinformatics 14 Suppl 3, S13.

  9. Marcia, M., Somarowthu, S. & Pyle, A. M. (2013). Now on display: a gallery of group II intron structures at different stages of catalysis. Mob DNA 4, 14.

  10. Marcia, M., Humphris-Narayanan, E., Keating, K. S., Somarowthu, S., Rajashankar, K. & Pyle, A. M. (2013). Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallogr D Biol Crystallogr 69, 2174-85.

  11. Somarowthu, S. & Ondrechen, M. J. (2012). POOL server: machine learning application for functional site prediction in proteins. Bioinformatics 28, 2078-9.

  12. Somarowthu, S., Yang, H., Hildebrand, D. G. & Ondrechen, M. J. (2011). High-performance prediction of functional residues in proteins with machine learning and computed input features. Biopolymers 95, 390-400.

  13. Somarowthu, S., Brodkin, H. R., D’Aquino, J. A., Ringe, D., Ondrechen, M. J. & Beuning, P. J. (2011). A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase. Biochemistry 50, 9283-95.

  14. Han, G. W., Ko, J., Farr, C. L., Deller, M. C., Xu, Q., Chiu, H. J., Miller, M. D., Sefcikova, J., Somarowthu, S., Beuning, P. J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. & Ondrechen, M. J. (2011). Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins 79, 2146-60.

  15. Parasuram, R., Lee, J. S., Yin, P., Somarowthu, S. & Ondrechen, M. J. (2010). Functional classification of protein 3D structures from predicted local interaction sites. J Bioinform Comput Biol 8 Suppl 1, 1-15.