References

• 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).

• Namhee Kim, Joseph Izzo, Shereef Elmetwaly, Hin Hark Gan and Tamar Schlick. Computational Generation and Screening of RNA Motifs in Large Nucleotide Sequence Pools. Nuc. Acids Res., doi:10.1093/nar/gkq282 (2010).
• Giulio Quarta, Namhee Kim, Joseph Izzo and Tamar Schlick. Analysis of Riboswitch Structure and Function by an Energy Landscape Framework. J. Mol. biol., 393: 993-1003 (2009).
• Namhee Kim, Hin Hark Gan and Tamar Schlick. A computational proposal for designing structured RNA pools for in vitro selection of RNAs. http://www.ncbi.nlm.nih.gov/pubmed/14962931RNA, 13:478-492 (2007).
• Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan and Tamar Schlick. RAGPOOLS: RNA-As-Graph-Pools -- A Web Server for Assisting the Design of Structured RNA Pools. Bioinformatics, 23:2959-2960 (2007).
• Jana Gevertz, Hin Hark Gan and Tamar Schlick. In Vitro RNA Random Pools are Not Structurally Diverse: A Computational Analysis. RNA 11: 853--863 (2005)
• Namhee Kim, N Shiffeldrim, Hin Hark Gan and Tamar Schlick. Candidates for novel RNA topologies. J. Mol. Biol., 341(5):1129-44 (2004).
• Julie Zorn, Hin Hark Gan, Nahum Shiffeldrim and Tamar Schlick. Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers., 73(3):340-7 (2004).
• Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, and Tamar Schlick. RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features. Bioinformatics, 20(8):1285-91 (2004).
• Hin Hark Gan, Samuela Pasquali, and Tamar Schlick. Exploring the repertoire of RNA secondary motifs using graph theory with implications for RNA design. Nucleic Acids Res., 31, 2926-2943 (2003).

For further information, please email Prof. T. Schlick at schlick@nyu.edu