An integrated approach to identify cis-regulatory modules in human genome
Data Set
The ChIP data considering sonication
format: ENCODE chr_begin_end ratio p_value ratio2The output of GITTAR for 4 TFs
The software
Won, K. J., Chepelev, I., Ren, B., Wang, W. (2009) Prediction of Regulatory Elements in Mammalian Genomes Using Chromatin Structure, BMC Bioinformatics , accepted
Won, K. J., Sandelin, A., Marstrand, T., and Krogh, A. (2008) Modeling Promoter Grammars with Evolving Hidden Markov Models, Bioinformatics , doi:10.1093/bioinformatics/btn254
Won, K. J., Hamelryck, T, Prugel-Bennett, A. and Krogh, A. (2007) An evolving method for learning HMM Structure: prediction of protein secondary structure. BMC Bioinformatics, 8:357
Won, K. J., Marstrand, T., and Krogh, A. (2006) Modelling eukaryotic promoters with an evolving HMM method, 8th International Bioinformatics 2006 Conference , selected to present
Won, K. J., Prugel-Bennett, A. and Krogh, A. (2006) Evolving the structure of Hidden Markov Models. IEEE Transactions on Evolutionary computation, vol. 10, no 1, pp.39-49, 2005
Won, K. J., Hamelryck, T, Prugel-Bennett, A. and Krogh, A. (2005) A Protein Secondary Structure Prediction using evolving HMMs. Young Bioinformaticians' Forum, Selected paper to present
Won, K. J., Hamelryck, T, Prugel-Bennett, A. and Krogh, A. (2005) Evolving Hidden Markov Models for Protein Secondary Structure Prediction. Proceedings of the 2005 IEEE Congress on Evolutionary Computation, pp. 33-40.
Won, K. J., Prugel-Bennett, A. and Krogh, A. (2004) The Block Hidden Markov Model for Biological Sequence Analysis. Lecture Notes in Artificial Intelligence vol. 3213, pp. 64-70.Won, K. J., Prugel-Bennett, A. and Krogh, A. (2004) Training HMM Structure with Genetic Algorithm for Biological Sequence Analysis. Bioinformatics. vol. 20, no. 18, pp:3613-3627
Old papers
Kyoung-Jae Won, Jae-Yong Seo, Jeong-Heum Yeon, Seong-Hyun Kim, Hong-Tae Jeon, “On Designing an Intelligent control system Using Immunized Neural Network”, The Magazine of the Institute of Electronics Engineers of Korea, pp 27-35, Dec. 1998
Jeong-Heum Yeon, Kyoung-Jae, Won, Il-Hun Jeong, Hong-Tae Jeon, “On Developing the Stable Learning Algorithm for Recurrent Neural Network Control System”, Journal of Fuzzy Logic and Intelligent Systems, Vol. 7, No. 3, pp.3-12, 1997
Kyoung-Jae Won, Seong-Hyun Kim, Hong-Tae Jeon, “Direct Adaptive Learning Control of a Robot Manipulator with Uncertain Dynamics using fuzzy-Neural Controller”, Proceedings of the 2nd Asian control Conference, pp.III-639~642, July 25, 1997, Seoul, Korea
Jae-Yong Seo, Kyoung-Jae Won, Seong-Hyun Kim, Hyun-Chan Cho, “On Designing a Robust Control System Using Immune Algorithm”, Journal of Fuzzy Logic and Intelligent Systems, pp. 12-20, Nov.1998
Seung-Jin Seo, Jae-Yong Seo, Kyoung-Jae Won, Jung-Heum Yon, Hong-Tae Jeon, “Wavelet Network for Stable Direct Adaptive Control of Nonlinear Systems”, The Magazine of the Institute of Electronics Engineers of Korea, pp. 51-57, Oct., 1997