(w/ R. Sherwood, C. O'Donnell, T. Jaakkola and D. Gifford), Nature biotechnology 32 (2014),
Method for transcription factor binding estimates via analysis of DNAse-I seq data .
(w/ M. Edwards and D. Gifford), PLOS Comp. Bio. 10 (2014),
Method for controlling marginal overdispersion fo high-throughtput sequending data .
(w/ T. Jaakkola, D. Gifford), Proceedings of 20th ISMB (2012), (proceedings)
Technique for analyzing lineage-structured gene expression datasets using trace norm penalties
(w/ M. Segall), Proceedings of the ACS (2010) Technique for constructing human-memorizable decision rules based on drug discoery data.
(w/ M. Nagasaki, K. Kojima, S. Miyano), BMC Bioinformatics 10 (2009), (journal)
(w/ D. Avarez-Melis, T. Jaakkola), Preprint (arXiv)(supplemental data and code)
(w/ Y.Sun, T. Jaakkola), NIPS 2015, to appear. (preprint)(supplement)
(w/ Y. Sun, T. Jaakkola), NIPS workshop on networks (2014, Best student poster), AISTATS (2015), (preprint)
A method to recover both the distance and density on a graph using unweighted edges; shows an equivalence between the random walk and its continuum limit on a geometric graph.
(w/ A.D Shieh, E.M Airoldi), Proc. Natl. Acad. Sciences (2011), (journal)
Nonlinear dimensionality reduction by preserving cluster constraints defined by clustering
(w/ W. Li, D. Gifford, Q. Zhou et al), Nature biotechnology 32 (2014), 1223-1230. (journal)
(w/ K.A. Samerotte, E.M. Airoldi), PLOS one. 8 (2013),
( journal )
Universal Count Correction for High-Throughput Sequencing bitbucket
Discovery of directional and nondirectional pioneer transcription factors bitbucket