Multiple Alignment of Continuous Time Series. - Jennifer Listgarten; Radford M. Neal; Sam T. Roweis; Andrew Emili (NIPS, 2004)

A scalable robotic-based laboratory automation system for medium-sized biotechnology laboratories. - Peyman Najmabadi; Andrew A. Goldenberg; Andrew Emili (CASE, 2005)

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. - Sylvain Pitre; Frank K. H. A. Dehne; Albert Chan; James Cheetham; Alex Duong; Andrew Emili; Marinella Gebbia; Jack Greenblatt; Matthew Jessulat; Nevan J. Krogan; Xuemei Luo; Ashkan Golshani (BMC Bioinform., 2006)

A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. - Anitha Kannan; Andrew Emili; Brendan J. Frey (RECOMB, 2007)

Difference detection in LC-MS data for protein biomarker discovery. - Jennifer Listgarten; Radford M. Neal; Sam T. Roweis; Peter Wong; Andrew Emili (Bioinform., 2007)

Constructing Treatment Portfolios Using Affinity Propagation. - Delbert Dueck; Brendan J. Frey; Nebojsa Jojic; Vladimir Jojic; Guri Giaever; Andrew Emili; Gabe Musso; Robert Hegele (RECOMB, 2008)

Bacteriome.org - an integrated protein interaction database for E. coli. - Chong Su; José M. Peregrín-Alvarez; Gareth Butland; Sadhna Phanse; Vincent Fong; Andrew Emili; John Parkinson (Nucleic Acids Res., 2008)

Predicting protein functions by relaxation labelling protein interaction network. - Pingzhao Hu; Hui Jiang 001; Andrew Emili (BMC Bioinform., 2010)

Computational refinement of post-translational modifications predicted from tandem mass spectrometry. - Clement Chung; Jian Liu; Andrew Emili; Brendan J. Frey (Bioinform., 2011)

DAnCER: Disease-Annotated Chromatin Epigenetics Resource. - Andrei L. Turinsky; Brian Turner; Rosanne C. Borja; James A. Gleeson; Michael Heath; Shuye Pu; Thomas Switzer; Dong Dong; Yunchen Gong; Tuan On; Xuejian Xiong; Andrew Emili; et al. (Nucleic Acids Res., 2011)

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. - Clement Chung; Andrew Emili; Brendan J. Frey (Bioinform., 2013)

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. - James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; et al. (Bioinform., 2015)

Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. - Chen Xu; Bing Wang; Lin Yang; Lucas Zhongming Hu; Lanxing Yi; Yaxuan Wang; Shenglan Chen; Andrew Emili; Cuihong Wan (Genom. Proteom. Bioinform., 2022)

ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. - Lakshmipuram S. Swapna; Grant C. Stevens; Aline Sardinha-Silva; Lucas Zhongming Hu; Verena Brand; Daniel D. Fusca; Cuihong Wan; Xuejian Xiong; Jon P. Boyle; Michael E. Grigg; Andrew Emili; John Parkinson (PLoS Comput. Biol., 2024)