Computational Biology:

• Alexis Battle, Sara Mostafavi, Xiaowei Zhu, James B. Potash, Myrna M. Weissman, Courtney McCormick, Christian D. Haudenschild, Kenneth B. Beckman, Jianxin Shi, Rui Mei, Alexander E. Urban, Stephen B. Montgomery, Douglas F. Levinson, Daphne Koller, Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals, submitted.
• Alexis Battle, Hyunghoon Cho, Daphne Koller. Patterns of epistasis in complex traits and robust discovery from natural variation, submitted.
• Sara Mostafavi, Alexis Battle, Xiaowei Zhu, Alexander E. Urban, Douglas Levinson, Stephen Montgomery, Daphne Koller. Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge, submitted.
• Alexis Battle, Martin Jonikas, Peter Walter, Jonathan Weissman, Daphne Koller. Automated identification of pathways from quantitative genetic interaction data Molecular Systems Biology, 2010, 6, 379. (pubmed)
• Alexis Battle, Eran Segal, Daphne Koller. Probabilistic discovery of overlapping cellular processes and their regulation Journal of Computational Biology. Sep 2005, Vol. 12, No. 7: 909-927.
• Alexis Battle, Eran Segal, Daphne Koller. Probabilistic discovery of overlapping cellular processes and their regulation. RECOMB 2004.
• Eran Segal, Alexis Battle, Daphne Koller. Decomposing gene expression into cellular processes. Pacific Symposium on Biocomputing 2003.

Social Computation:

• Salman Ahmad, Alexis Battle, Zahan Malkani, Sepandar Kamvar. The Jabberwocky programming environment for structured social computation, in proceedings of ACM Symposium on User Interface Software and Technology (UIST), 2011.

fMRI:

• Alexis Battle, Gal Chechik, Daphne Koller. Temporal and cross-subject probabilistic models for fMRI prediction tasks. NIPS 19, 2006.

Machine Learning:

• Rajat Raina, Alexis Battle, Honglak Lee, Benjamin Packer, Andrew Ng. Self-taught learning: Transfer learning from unlabeled data. In Proceedings of the Twenty-fourth International Conference on Machine Learning, 2007.
• Honglak Lee, Alexis Battle, Rajat Raina, Andrew Ng. Efficient sparse coding algorithms. In NIPS 19, 2006.

Dialogue Systems:

• Oliver Lemon, Alexander Gruenstein, Alexis Battle, Elizabeth Bratt, and Stanley Peters. Multi-tasking in practical multi-modal dialogue systems in proceedings of Association for Computational Linguistics (ACL), 2002.

• Alexis Battle, Pranav Khaitan, Daphne Koller. PriorNet: A flexible pathway-based model of genetic variation in human disease, Machine Learning in Computational Biology workshop, Neural Information Processing Systems 2012.
• Alexis Battle, Sara Mostafavi, Xiaowei Zhu, Stephen B. Montgomery, James B. Potash, Myrna M. Weissman, Christian Haudenschild, Courtney McCormick, Rui Mei, Alexander E. Urban, Douglas F. Levinson, Daphne Koller. Characterizing the genetic basis of transcriptome diversity in a large RNA sequencing study, American Society for Human Genetics, San Francisco, November 2012.
• Alexis Battle, Hyunghoon Cho, Daphne Koller. Patterns of epistasis in complex traits and robust discovery from natural variation, RECOMB Regulatory and systems genomics, San Francisco, November 2012.
• Alexis Battle, Daphne Koller. Patterns of epistasis in complex traits and robust discovery from natural variation, Biology of Genomes, Cold Springs Harbor Laboratories, 2012.
• Alexis Battle. Combining data and networks to unravel the genetics of complex traits, University of Texas at Austin, invited talk, May 2012.
• Alexis Battle, Daphne Koller. Combining data and networks to unravel the genetics of complex traits, Keystone Symposium on Complex Traits, Breckenridge, 2012.
• Alexis Battle, Daphne Koller. Pathway-based models of genetic variation in human disease, Personal Genomes, Cold Springs Harbor Laboratories, 2011.
• Alexis Battle, Martin Jonikas, Peter Walter, Jonathan Weissman, Daphne Koller. Automatic identification of pathways from quantitative genetic interaction data, EMBO Workshop on Synthetic Lethality: From Yeast to Man, Vienna, 2011.
• Alexis Battle, Martin Jonikas, Peter Walter, Jonathan Weissman, Daphne Koller. Automated identification of pathways from quantitative genetic interaction data, Bay Area Yeast and Other Fungi Symposium, Berkeley, CA, 2010.
• Alexis Battle, Daphne Koller. Transfer learning for modeling genetic influence on multiple related diseases, Biomedical Computation At Stanford, 2010.