SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. - Paul Bertone; Yuval Kluger; Ning Lan; Deyou Zheng; Dinesh Christendat; Adelinda Yee; Aled M. Edwards; Cheryl H. Arrowsmith; Gaetano T. Montelione; Mark Gerstein (Nucleic Acids Res., 2001)

ExpressYourself: a modular platform for processing and visualizing microarray data - Nicholas M. Luscombe; Thomas E. Royce; Paul Bertone; Nathaniel Echols; Christine E. Horak; Joseph T. Chang; Michael Snyder 001; Mark Gerstein (Nucleic Acids Res., 2003)

Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. - Piotr Berman; Paul Bertone; Bhaskar DasGupta; Mark Gerstein; Ming-Yang Kao; Michael Snyder 001 (J. Comput. Biol., 2004)

Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. - Joel S. Rozowsky; Paul Bertone; Thomas E. Royce; Sherman Weissman; Michael Snyder 001; Mark Gerstein (BSB, 2005)

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research. - Frederick G. Sayward; Jin Yang; Kenneth Nelson; Ghia Euskirchen; Alexander E. Urban; Paul Bertone; John Rinn; Sherman Weissman; Mark Gerstein; Michael Snyder 001; Perry L. Miller (CISS, 2006)

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R. - Heidi Dvinge; Paul Bertone (Bioinform., 2009)

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. - Mali Salmon-Divon; Heidi Dvinge; Kairi Tammoja; Paul Bertone (BMC Bioinform., 2010)

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. - Nick Goldman; Paul Bertone; Siyuan Chen; Christophe Dessimoz; Emily M. LeProust; Botond Sipos; Ewan Birney (Nat., 2013)