Publications

*Corresponding author

20.*           Yankey A, Clark SC, Owens MC, Somarowthu S, Purification and structural characterization of the long noncoding RNAs. Methods in Mol Biol. 2021 (submitted)

 

19.            Mazina, O.M., S. Somarowthu, L.Y. Kadyrova, A.G. Baranovskiy, T.H. Tahirov, F.A. Kadyrov, and A.V. Mazin, Replication protein A binds RNA and promotes R-loop formation. J Biol Chem, 2020. 295(41): p. 14203-14213.

18.            Manigrasso, J., I. Chillon, V. Genna, P. Vidossich, S. Somarowthu, A.M. Pyle, M. De Vivo, and M. Marcia, Visualizing group II intron dynamics between the first and second steps of splicing. Nat Commun, 2020. 11(1): p. 2837.

17.            Shenoda, B.B., S. Ramanathan, R. Gupta, Y. Tian, R. Jean-Toussaint, G.M. Alexander, S. Addya, S. Somarowthu, A. Sacan, and S.K. Ajit, Xist attenuates acute inflammatory response by female cells. Cell Mol Life Sci, 2020.

16.*           Owens, M.C., S.C. Clark, A. Yankey, and S. Somarowthu, Identifying Structural Domains and Conserved Regions in the Long Non-Coding RNA lncTCF7. Int J Mol Sci, 2019. 20(19).

15.*          Tavares, R.C.A., A.M. Pyle, and S. Somarowthu, Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures. J Mol Biol, 2019. 431(8): p. 1592-1603.

14.*          Somarowthu, S., Progress and Current Challenges in Modeling Large RNAs. J Mol Biol, 2016. 428(5 Pt A): p. 736-747.

13.            Liu, F., S. Somarowthu, and A.M. Pyle, Visualizing the secondary and tertiary architectural domains of lncRNA RepA. Nat Chem Biol, 2017. 13(3): p. 282-289.

12.            Chillon, I., M. Marcia, M. Legiewicz, F. Liu, S. Somarowthu, and A.M. Pyle, Native Purification and Analysis of Long RNAs. Methods Enzymol, 2015. 558: p. 3-37.

11.            Somarowthu, S., M. Legiewicz, I. Chillon, M. Marcia, F. Liu, and A.M. Pyle, HOTAIR forms an intricate and modular secondary structure. Mol Cell, 2015. 58(2): p. 353-61.

10.          Brodkin, H.R., N.A. DeLateur, S. Somarowthu, C.L. Mills, W.R. Novak, P.J. Beuning, D. Ringe, and M.J. Ondrechen, Prediction of distal residue participation in enzyme catalysis. Protein Sci, 2015. 24(5): p. 762-78.

9.          Somarowthu, S., M. Legiewicz, K.S. Keating, and A.M. Pyle, Visualizing the ai5gamma group IIB intron. Nucleic Acids Res, 2014. 42(3): p. 1947-58.

8.          Marcia, M., E. Humphris-Narayanan, K.S. Keating, S. Somarowthu, K. Rajashankar, and A.M. Pyle, Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallogr D Biol Crystallogr, 2013. 69(Pt 11): p. 2174-85.

7.          Marcia, M., S. Somarowthu, and A.M. Pyle, Now on display: a gallery of group II intron structures at different stages of catalysis. Mob DNA, 2013. 4(1): p. 14.

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

5.          Somarowthu, S. and M.J. Ondrechen, POOL server: machine learning application for functional site prediction in proteins. Bioinformatics, 2012. 28(15): p. 2078-9.

4.          Somarowthu, S., H.R. Brodkin, J.A. D'Aquino, D. Ringe, M.J. Ondrechen, and P.J. Beuning, A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase. Biochemistry, 2011. 50(43): p. 9283-95.

3.          Han, G.W., J. Ko, C.L. Farr, M.C. Deller, Q. Xu, H.J. Chiu, M.D. Miller, J. Sefcikova, S. Somarowthu, P.J. Beuning, M.A. Elsliger, A.M. Deacon, A. Godzik, S.A. Lesley, I.A. Wilson, and M.J. Ondrechen, Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins, 2011. 79(7): p. 2146-60.

2.          Somarowthu, S., H. Yang, D.G. Hildebrand, and M.J. Ondrechen, High-performance prediction of functional residues in proteins with machine learning and computed input features. Biopolymers, 2011. 95(6): p. 390-400.

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