MicroRNA

Review

Supervised learning methods for microRNA studies, Byoung-Tak Zhang and Jin-Wu Nam,Machine Learning for Bioinformatics,chapter 9, John Wiley & Sons, 2007. [-]
Genomics of microRNA, V. Narry Kim and Jin-Wu Nam, TRENDS in Genetics, 22(3):165-173, 2006. [PDF]

miRNA prediction

ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs, Jin-Wu Nam, Jin-Han Kim, Sung-Kyu Kim, Byoung-Tak Zhang, Nucleic Acids Research, 34:W455-W458, 2006. [PDF]
Human microRNA prediction through a probabilistic co-learning model of sequence and structure, Jin-Wu Nam, Ki-Roo Shin, Jinju Han, Yoontae Lee, V. Narry Kim, Byoung-Tak Zhang, Nucleic Acids Research, 33(11):3570-3581, 2005. [PDF]
Computational methods for identification of human microRNA precursors, J.-W. Nam, W.-J. Lee, and B.-T. Zhang, Lecture Notes in Artificial Intelligence, 3157:732-741, 2004. [PDF]
Two-step genetic programming for optimization of an RNA common-structure, J.-W. Nam, J.G. Joung, Y. S. Ahn and B.-T. Zhang, Lecture Notes in Computer Science, 3005:73-83, 2004. [PDF]

Target identification

miTarget: microRNA target-gene prediction using a Support Vector Machine, Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee and Byoung-Tak Zhang, BMC Bioinformatics, 7(1):411, 2006.[PDF]
A Kernel method for microRNA target prediction using sensible data and position-based features, S.-K. Kim, J.-W. Nam, W.-J. Lee, and B.-T. Zhang, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), pp. 46-52, 2005. [PDF]
Identification of Caenorhabditis elegans microRNA targets using a kernel method, W.-J. Lee, J.-W. Nam, S.-K. Kim, and B.-T. Zhang, Genomics & Informatics, 3(1):15-23, 2005. [PDF]

Expression analysis

• Co-evolutionary biclustering for miRNA expression profiles analysis, S.-J. Kim, J.-G, Joung and B.-T. Zhang, The 7th International Conference of Korean Society for Bioinformatics (BIOINFO 2006), pp. 60-65, 2006. [PDF]

Network & module identification

Discovery of microRNA-mRNA modules via population-based probabilistic learning, J.-G. Joung, K.-B. Hwang, J.-W. Nam, S.-J. Kim and B.-T. Zhang, Bioinformatics, 2007. (accepted) [-]

Processing model & Artificial design

Dinucleotide step parameterization of pre-miRNAs using multi-objective evolutionary algorithms, J.-W. Nam, I.-H. Lee, K.-B. Hwang, S.-B. Park, and B.-T. Zhang, Lecture Notes in Computer Science, EvoBio 2007, 2007. (accepted)[-]
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex, J. Han, Lee Y, K.H. Yeom, J.-W. Nam, I. Heo, J.-K. Rhee, S. Y. Sohn, Y. Cho, B.-T. Zhang and V.N. Kim, Cell, 125:887-901, 2006. [PDF]