Multi-tasking and Collaborative Activities in Dialogue Systems. - Oliver Lemon; Alexander Gruenstein; Alexis J. Battle; Stanley Peters (SIGDIAL Workshop, 2002)

Decomposing Gene Expression into Cellular Processes. - Eran Segal; Alexis J. Battle; Daphne Koller (Pacific Symposium on Biocomputing, 2003)

Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation. - Alexis J. Battle; Eran Segal; Daphne Koller (J. Comput. Biol., 2005)

Temporal and Cross-Subject Probabilistic Models for fMRI Prediction Tasks. - Alexis J. Battle; Gal Chechik; Daphne Koller (NIPS, 2006)

Efficient sparse coding algorithms. - Honglak Lee; Alexis J. Battle; Rajat Raina; Andrew Y. Ng (NIPS, 2006)

Self-taught learning: transfer learning from unlabeled data. - Rajat Raina; Alexis J. Battle; Honglak Lee; Benjamin Packer; Andrew Y. Ng (ICML, 2007)

The jabberwocky programming environment for structured social computing. - Salman Ahmad; Alexis J. Battle; Zahan Malkani; Sepandar D. Kamvar (UIST, 2011)

Unraveling the genetics of disease using structured probabilistic models. - Alexis J. Battle (2013)

Sharing and Specificity of Co-expression Networks across 35 Human Tissues. - Emma Pierson; Daphne Koller; Alexis J. Battle; Sara Mostafavi (PLoS Comput. Biol., 2015)

FIRE: functional inference of genetic variants that regulate gene expression. - Nilah M. Ioannidis; Joe R. Davis; Marianne K. DeGorter; Nicholas B. Larson; Shannon K. McDonnell; Amy J. French; Alexis J. Battle; Trevor J. Hastie; Stephen N. Thibodeau; Stephen B. Montgomery; Carlos D. Bustamante; Weiva Sieh; et al. (Bioinform., 2017)

The impact of rare variation on gene expression across tissues. - Xin Li 130; Yungil Kim; Emily K. Tsang; Joe R. Davis; Farhan N. Damani; Colby Chiang; Gaelen T. Hess; Zachary Zappala; Benjamin J. Strober; Alexandra J. Scott; Amy Li; Andrea Ganna; et al. (Nat., 2017)