Namhee Kim

     Assistant Research Scientist
     Computational Biology/Chemistry/Biomathematics Group (PI: Prof. Tamar Schlick)
     Department of Chemistry and Courant Institute of Mathematical Sciences
     New York University
     31 Washington Place, Main 1021
     New York, NY 10003
     Phone: (212) 998-3594
     Fax: (212) 995-4152
     Email: nk401@nyu.edu


Education

Ph.D. in Computational Biology, New York University

M.S. in Mathematics, Courant Institute of Mathematical Sciences

M.S. in Statistics, Seoul National University

B.S. in Mathematics, Seoul National University


Research Interests

Computational and mathematical biology

Network (Graph) modeling, simulation, and applications

RNA structure and function


Publications

1. N. Kim, C. Laing, S. Elmetwaly, S. Jung, J. Curuksu, and T. Schlick, Graph- Based Sampling for Approximating Global Helical Topologies of RNA, Proc Natl Acad Sci U S A 111(11):4079-4084 (2014) (Recommended by Faculty of 1000).

2. N. Kim, L. Petingi, and T. Schlick, Network Theory Tools for RNA Modeling, WSEAS Transactions on Math 12(9):941 (2013).

3. C. Laing, S. Jung, N. Kim, S. Elmetwaly, M. Zahran, and T. Schlick, Predicting Helical Topologies in RNA Junctions as Tree Graphs, PLoS One 8(8):e71947 (2013). pdf

4. N. Kim, K. N. Fuhr, and T. Schlick, Graph Applications to RNA Structure and Function, Chapter 3 for Biophysics of RNA Folding, Springer, ED. Rick Russell (2013).

5. N. Kim and T. Schlick, A New Toolkit for Modeling RNA from a Pseudo-torsional Space: Commentary on ``Discrete RNA Libraries from Pseudo-torsional Space'' by Humphris-Narayanan and Pyle (J. Mol. Biol. March 2012). J Mol Biol. 3;421(1):1-5 (2012).

6. J. A. Izzo*, N. Kim*, S. Elmetwaly, and T. Schlick, RAG: An Update to the RNA-As-Graphs Resource, BMC Bioinformatics, 12:219 (2011). (*: Equally contributed) pdf

7. N. Kim*, J. A. Izzo*, S. Elmetwaly*, H.H. Gan, and T. Schlick, Computational Generation and Screening of RNA Motifs in Large Nucleotide Sequence Pools, Nucleic Acids Res., 38:e139 (2010). (*: Equally contributed) pdf

8. G. Quarta*, N. Kim*, J. A. Izzo, and T. Schlick, Analysis of Riboswitch Structure and Function by an Energy Landscape Framework, J. Mol. Biol., 393:993 (2009). (*: Equally contributed) pdf

9. N. Kim, J.S. Shin, S. Elmetwaly, H.H. Gan, and T. Schlick, RAGPOOLS: RNA-As-Graph-Pools - A Web Server for Assisting the Design of Structured RNA Pools for In Vitro Selection, Bioinformatics 23:2959 (2007) pdf

10. N. Kim, H.H. Gan, and T. Schlick, A Computational Proposal for Designing Structured RNA Pools for In Vitro Selection of RNAs, RNA 13:478 (2007) pdf

11. N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick, Novel Candidates of RNA Topologies, J. Mol. Biol. 341:1129 (2004) pdf

12. D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H.H. Gan, and T. Schlick, RAG: RNA-As-Graphs web resource. BMC Bioinformatics 5:88 (2004) pdf

13. H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick, RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features, Bioinformatics 20:1285 (2004).pdf


Invited Presentations