• Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason Wang, and Tamar Schlick, "CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking", PLoS ONE, DOI: 10.1371/journal.pone.0147097 (2016).
  • Louis Petingi, and Tamar Schlick, "Partitioning RNAs into pseudonotted and pseudoknot-free regions modeled as Dual Graphs", q-bio.QM,arXiv:1601.04259 (2016).
  • Naoto Baba, Shereef Elmetwaly, Namhee Kim, and Tamar Schlick, ”Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach”, Journal of Molecular Biology, doi:10.1016/j.jmb.2015.10.009 (2016).
  • Mai Zahran, Cigdem Sevim Bayrak, Shereef Elmetwaly, and Tamar Schlick, “RAG-3D: a search tool for RNA 3D substructures”, Nucl. Acids Res., doi: 10.1093/nar/gkv823 (2015).
  • Namhee Kim, Mai Zahran, and Tamar Schlick, "Computational Prediction of Riboswitch Tertiary Structures Including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling Approach", Methods Enzymol., 553, 115-35, DOI: 10.1016/bs.mie.2014.10.054 (2015).
  • Namhee Kim, Zhe Zheng, Shereef Elmetwaly and Tamar Schlick, "RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology", PLoS ONE, 9(9): e106074, DOI: 10.1371/journal.pone.0106074 (2014).
  • Namhee Kim, Christian Laing, Shereef Elmetwaly, Segun Jung, Jeremy Curuksu, and Tamar Schlick. Graph-based sampling for approximating global helical topologies of RNA. PNAS, 111(11):4079-84 (2014).
  • Christian Laing, Segun Jung, Namhee Kim, Shereef Elmetwaly, Mai Zahran, and Tamar Schlick. Predicting Helical Topologies in RNA Junctions as Tree Graphs. PLoS ONE, 8(8): e71947, DOI:10.1371/journal.pone.0071947 (2013).
  • Namhee Kim, Louis Petingi, and Tamar Schlick. Network Theory Tools for RNA Modeling. WSEAS Transactions on Math, 12(9): 941-955 (2013).
  • Namhee Kim, Niccole Fuhr and Tamar Schlick. Graph Applications to RNA Structure and Function. Chapter 3, pp. 23–51, In Biophysics of RNA Folding, Ed. R. Russel, Biophysics for the Life Sciences 3, Springer Verlag (2013).
  • Joseph Izzo, Namhee Kim, Shereef Elmetwaly, and Tamar Schlick. RAG: An Update to the RNA-As-Graphs Resource. BMC Bioinformatics, 12: 219 (2011).


For further information, please email Prof. T. Schlick at

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