Publications
Here are some papers I have published.
Book chapters
- "RNA Interference and microRNA", Qiu, S., and Lane, T., in Xiaohua Hu and Yi Pan (Eds.) Knowledge Discovery in Bioinformatics: Techniques, Methods and Applications, ISBN: 047177796X, John Wiley & Sons Inc., 2007.
- "siRNA Silencing Efficacy Prediction", Qiu, S., and Lane, T., in Frank Columbus (Eds.) Progress in RNAi Research, in press, Nova Publisers, 2008.
Journals
- Qiu, S., and Lane, T., "siRNA silencing efficacy prediction using the RNA string kernel" (to appear), International Journal of Computational Biology and Drug Design, 2007.
- Burge, J., Lane, T., Link, H., Qiu, S., and Clark, V. P., "Bayesian classification of fMRI data: evidence for altered neural networks in dementia" (in press), Human Brain Mapping, 2007.
- Qiu, S., and Lane, T., "Efficient search algorithms for RNAi target detection", The Journal of Supercomputing,, Vol. 42, No. 3, Springer, 2007.
- Qiu, S., and Lane, T., "Implications of phase transitions in knockdown networks of transitive RNAi", IEEE Transactions on Nanobioscience , Vol. 6, Issue 1, pp.68-76, 2007.
- Qiu, S., and Lane, T., "RNA string kernels for RNAi off-target evaluation", Int. Journal of Bioinformatics Research and Applications, Vol.2, No. 2, pp. 132-146, 2006.
- Qiu, S., Adema, C., and Lane, T., "A computational study of off-target effects of RNA interference", Nucleic Acids Research, Vol. 33, No. 6, pp. 1834-1847, 2005.
Conferences
- Qiu, S., and Lane, T., "The RNA string kernel for siRNA efficacy prediction" (best paper award winner, regular paper), Proc. 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE2007), IEEE, October 2007, Boston, MA.
- Qiu, S., Lane, T., and Buturovic, L., "A randomized string kernel and its applications to RNA interference", Proc. 22nd AAAI Conference on Artificial Intelligence (AAAI07), pp. 627-632, AAAI Press, July 2007, Vancouver, BC, Canada.
- Qiu, S., and Lane, T., "Efficient target detection for RNA interference" (best paper award winner), Proc. 1st International Conference on Grid and Pervasive Computing (GPC06) , Springer LNCS 3947, pp.22-31, Taichung, Taiwan, May 2006.
- Qiu, S., and Lane, T., "Phase transitions in the gene knockdown networks of transitive RNAi", Proc. 6th International Conf. Computational Science (ICCS06), Springer-Verlag LNCS 3992, pp. 895-903, Reading, UK, May 2006.
- Qiu, S., and Lane, T., "String kernels of imperfect matches for off-target detection in RNA interference",Proc. 5th International Conf. Computational Science (ICCS05), LNCS 3515, pp. 894-902, Springer-Verlag, Atlanta, GA, May 2005.
- Qiu, S., and Lane, T., "Parallel computation of RBF kernels for support vector classifiers" (full paper), Proc. 5th SIAM International Conf. Data Mining (SDM05) , pp. 334-345, SIAM, Newport Beach, California, April 2005.
- Layne., L.J., and Qiu., S., "Prediction for compound activity in large drug data sets using efficient machine learning approaches", Proc. 16th Information Resource Management Association Conference, San Diego, CA, May 2005.
- Qiu, S., and Li, S., "Efficient search of multimedia metadata on XML database systems using information retrieval approach", Proc. 21st IASTED International Conf. Applied Informatics (AI 2003), pp. 1239-1244, ACTA Press, Austria, Feb 2003.
Workshop presentations
- Qiu, S. and Lane, T., "Mismatch upper limit between siRNA and target mRNA: A computational estimation using a network model of transitive RNAi", scientific program and abstract of National IDeA Symposium of Biomedical Research Excellence (NISBRE), National Center for Research Resources (NCRR) of NIH, Washington D.C., July 2006.
- Lane, T., Qiu, S. and Zhao, W., "Computational modeling of RNA interference", scientific program and abstract of National IDeA Symposium of Biomedical Research Excellence (NISBRE), NCRR of NIH, Washington D.C., July 2006.
- Qiu, S., Lane, T., and Adema, C., "A computational study of off-target effects of RNA interference", 2005 Keystone Symposium on RNA Regulations, Breckenrige, Colorado, January 2005.
Technical reports
- Qiu, S., and Lane, T., "Multiple kernel learning for support vector regression", Tech. Report, TR-CS-2005-42, University of New Mexico, Dept. Computer Science, 2005.
- Burge, J., Clark, V. P., Lane, T., Link, H., and Qiu, S., "Evidence for altered neural networks in dementia", Tech. Report, TR-CS-2004-28, University of New Mexico, Dept. Computer Science, 2004.
- Qiu, S., and Lane, T., "Parallel kernel computation for high dimensional data and its application to fMRI image classification", Tech. Report, TR-CS-2004-12, University of New Mexico, Dept. Computer Science, 2004.