Computer-produced Representation of dialectal variation: Initlal fricatives in Southern British English. - W. Nelson Francis; Jan Svartvik; Gerald M. Rubin (COLING, 1969)

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. - Uwe Ohler; Heinrich Niemann; Guo-chun Liao; Gerald M. Rubin (ISMB (Supplement of Bioinformatics), 2001)

Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars. - Ian Holmes; Gerald M. Rubin (Pacific Symposium on Biocomputing, 2002)

Biological and computational annotation of the Drosophila Genome Sequence. - Gerald M. Rubin (RECOMB, 2002)

Joint Nonparametric Alignment for Analyzing Spatial Gene Expression Patterns in Drosophila Imaginal Discs. - Parvez Ahammad; Cyrus L. Harmon; Ann Hammonds; Shankar Sastry 001; Gerald M. Rubin (CVPR (2), 2005)

Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. - Mark Yandell; Chris Mungall; Chris Smith; Simon Prochnik; Joshua S. Kaminker; George Hartzell; Suzanna Lewis; Gerald M. Rubin (PLoS Comput. Biol., 2006)

Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs. - Cyrus L. Harmon; Parvez Ahammad; Ann Hammonds; Richard Weiszmann; Susan E. Celniker; Shankar Sastry 001; Gerald M. Rubin (RECOMB, 2007)