Genome-wide discovery of transcriptional modules from DNA sequence and gene expression

By Eran Segal, Roman Yelensky, Daphne Koller. Intelligent Systems in Molecular Biology, 2003

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Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. (2007, methodology): “Using a discriminative motif finder that we previously developed (Segal et al., 2003), we found that ncRNAs are enriched for specific DNA sequence motifs based on their site-specific expression patterns (p < 10 (9), Figure 3C).”
From signatures to models: understanding cancer using microarrays (2005, background): “Segal et al. 7 applied a module-level analysis to obtain a global view of the shared and unique molecular modules underlying human cancer.”
Graph theory and networks in Biology. (2006, background): “On the other hand, in [183, 184] a procedure is described which identifies modules of related genes in the transcriptional regulatory network of yeast as well as the regulators of each such module.”