A new approach to analyzing gene expression time series data. - Ziv Bar-Joseph; Georg K. Gerber; David K. Gifford; Tommi S. Jaakkola; Itamar Simon (RECOMB, 2002)

From promoter sequence to expression: a probabilistic framework. - Eran Segal; Yoseph Barash; Itamar Simon; Nir Friedman; Daphne Koller (RECOMB, 2002)

Continuous Representations of Time-Series Gene Expression Data. - Ziv Bar-Joseph; Georg K. Gerber; David K. Gifford; Tommi S. Jaakkola; Itamar Simon (J. Comput. Biol., 2003)

Deconvolving cell cycle expression data with complementary information. - Ziv Bar-Joseph; Shlomit Farkash; David K. Gifford; Itamar Simon; Roni Rosenfeld (ISMB/ECCB (Supplement of Bioinformatics), 2004)

MILANO - custom annotation of microarray results using automatic literature searches. - Ran Rubinstein; Itamar Simon (BMC Bioinform., 2005)

Continuous hidden process model for time series expression experiments. - Yanxin Shi; Michael Klutstein; Itamar Simon; Tom M. Mitchell; Ziv Bar-Joseph (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. - Yanxin Shi; Itamar Simon; Tom M. Mitchell; Ziv Bar-Joseph (RECOMB, 2008)

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. - Yanxin Shi; Michael Klutstein; Itamar Simon; Tom M. Mitchell; Ziv Bar-Joseph (J. Comput. Biol., 2009)

DECOD: fast and accurate discriminative DNA motif finding. - Peter Huggins; Shan Zhong; Idit Shiff; Rachel Beckerman; Oleg Laptenko; Carol Prives; Marcel H. Schulz; Itamar Simon; Ziv Bar-Joseph (Bioinform., 2011)