• Shulin Yang, Linda Shapiro, Michael Cunninghamy, Matthew Speltz, Craig Birgfeld, Indriyati Atmosukarto, Su-In Lee
  Skull Retrieval for Craniosynostosis Using Sparse Logistic Regression Models. Int'l Conference on Medical Image Computing and Computer Assisted Intervention 2012.

• Bilge Soran, Jenq-Neng Hwang, Su-In Lee, Linda Shapiro
  Tremor Detection Using Motion Filtering and SVM. International Conference on Pattern Recognition 2012

• RP Patwardhan et al.
  Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnology, 2012.

• Bilge Soran, Zhiyong Xie, Rosalia Tungaraza, Su-In Lee, Linda Shapiro, Thomas Grabowski.
  Parcellation of Human Inferior Parietal Lobule Based On Diffusion MRI. EMBC 2012.

• Shulin Yang, Linda Shapiro, Michael L Cunningham, Matthew Speltz, Su-In Lee.
  Classification and Interest Region Localization on Craniosynostosis Skulls. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011.

• I.M. Dykes, L.Tempest, S.I. Lee, and Eric Turner.
  Brn3a and Islet1 act epistatically to regulate the gene expression program of sensory differentiation, Journal of Neuroscience, 2011.

• S. Balakrishnan, H. Kamisetty, J.C. Carbonell, S.I. Lee, C.J. Langmead.
  Learning Generative Models for Protein Fold Families. PROTEINS: Structure, Function, and Bioinformatics, 2011.

• S. Balakrishnan, H. Kamisetty, J.C. Carbonell, S.I. Lee, C.J. Langmead.
  Learning Networks of Statistical Couplings in Protein Fold Families using L1-regularization. In Proceedings of 3DSIG 2010 Structural Bioinformatics and Computational Biophysics, 2010.

• Andrew J. Gentles*, Ash A. Alizadeh*, Su-In Lee, June H. Myklebust, Babak Shahbaba, Catherine M. Shachaf, Ronald Levy, Daphne Koller, Sylvia K. Plevritis.
  A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients. Blood. 2009 Oct 8; 114(15):3133-4. [PDF]

• Su-In Lee, Aimee M. Dudley, David Drubin, Pamela A. Silver, Nevan J. Krogan, Dana Pe'er and Daphne Koller.
  Learning a Prior on Regulatory Potential from eQTL Data. PLoS Genet 5(1): e1000358. doi:10.1371/journal.pgen.1000358. [PDF]

• Su-In Lee, Vassil Chatalbashev, David Vickrey and Daphne Koller.
  Learning a Meta-Level Prior for Feature Relevance from Multiple Related Tasks. In Proceedings of International Conference on Machine Learning (ICML 2007), Corvallis, OR, June 2007. [PDF]

• Su-In Lee*, Dana Pe'er*, Aimee M. Dudley, George M. Church and Daphne Koller.
  Identifying Regulatory Mechanisms using Individual Variation Reveals Key Role for Chromatin Modification. Proceedings of the National Academy of Sciences (PNAS), 2006 Sep; 103: 14062-14067. [PDF]

• Su-In Lee, Varun Ganapathi and Daphne Koller.
  Efficient Structure Learning of Markov Networks using L1-Regularization. In Proceedings of Neural Information Processing Systems (NIPS 19, 2007), Vancouver, British Columbia, December 2006. [PDF]

• Su-In Lee, Honglak Lee, Pieter Abbeel and Andrew Y. Ng.
  Efficient L1 Regularized Logistic Regression. In Proceedings of the Twenty-First National Conference on Artificial Intelligence (AAAI-06), Boston, MA, USA, July 2006. [PDF] [Software]

• James E. Galagan, Sarah E. Calvo, Christina Cuomo, Li-Jun Ma, Jennifer R. Wortman, Serafim Batzoglou, Su-In Lee, et al.
  Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 2005 Dec; 438(7071): 1105-1115. [PDF]

• Su-In Lee and Serafim Batzoglou.
  Application of Independent Component Analysis to Microarrays. Genome Biology, 2003 Oct; 4(11):R76. [PDF]

• Su-In Lee and Serafim Batzoglou.
  ICA-based Clustering of Genes from Microarray Expression Data. In Proceedings of Neural Information Processing Systems (NIPS 16, 2004), Vancouver, British Columbia, December 2003. [PDF]

• Su-In Lee and Soo-Young Lee.
  Top-Down Attention Control at Feature Selection. In Proceedings of IEEE International Workshop on Biologically Motivated Computer Vision (BMCV2000), May 2000.

• Su-In Lee and Soo-Young Lee.
  Biologically Inspired Neural Network Approach using Feature Extraction and Top-Down Selective Attention for Robust Optical Character Recognition. In Proceedings of Humantech Paper Competition held by Samsung Electronics, Inc., Jan 2000. - Gold prize (the first prize)

Softwares

Lirnet

Su-In Lee, Aimee M. Dudley, David Drubin, Pamela A. Silver, Nevan J. Krogan, Dana Pe'er and Daphne Koller. Learning a Prior on Regulatory Potential from eQTL Data. PLoS Genet 5(1): e1000358. doi:10.1371/journal.pgen.1000358.

[Link]

GenViewer

Visualization tool for genotype, expression and phenotype measurements from individuals – In preparation

[Link]

IRLA-LARS

Su-In Lee, Honglak Lee, Pieter Abbeel and Andrew Y. Ng. Efficient L1 Regularized Logistic Regression. In Proceedings of the Twenty-First National Conference on Artificial Intelligence (AAAI-06), Boston, MA, USA, July 2006.

[Link]