Transcriptional regulatory code of a eukaryotic genome

By Christopher T. Harbison, D. B. Gordon, Tong Ihn Lee, Nicola J. Rinaldi, Kenzie D. MacIsaac, Timothy Danford, N. Hannett, J. Tagne, David B. Reynolds, Jane Yoo and 10 more. Nature, 2004

2,390 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4be810a3da26bd0d2002095eac5976e3f7e83580

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Citations in the corpus

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. (2008, background): “In addition, for many domain classes, and in organisms ranging from yeast to human, in vivo binding sites detected by ChIP-chip typically contain sequences that reflect those preferred in vitro (Carroll et al., 2005; Harbison et al., 2004).”
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005, methodology): “Since each of these collections of intergenic regions will typically contain binding sites for multiple TFs, we asked PhyloGibbs to search for three motifs, with a total number of sites equaling three times the number of annotated sites for the TF in [27].”
Differential network biology (2012, methodology): “For example, Harbison et al (2004) carried out a genome-wide analysis of transcription factor binding in the yeast S. cerevisiae using the technique of chromatin immunoprecipitation followed by microchip hybridization (ChIP-CHIP), with some of the data being collected under different stimulating…”
CEAS: cis-regulatory element annotation system (2006, methodology): “The current best de novo motif finding methods for ChIP–chip includes MEME (11), AlignACE (12), Mascan (13) and their combinations (14).”
STAMP: a web tool for exploring DNA-binding motif similarities (2007, neutral): “(13) and MacIsaac et al .”
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System (2008, neutral): “, [26– 29,32,35,52–60]).”
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE (2006, methodology): “PSAMs were inferred for PBM experiments using the microarray data fromMukherjee et al. (2004) and the feature sequence data from Harbison et al. (2004) as the two studies used the same array features.”
A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans (2012, methodology): “Finally, the Efg1 motif derived from our ChIP-chip data (RTGCATRW) closely resembles the TGCAGNNA consensus sequence of the S. cerevisiae ortholog, Sok2 (Harbison et al., 2004).”
A universal framework for regulatory element discovery across all genomes and data types. (2007, methodology): “Experimental (Gerber et al., 2004; Harbison et al., 2004) and computational approaches are emerging to meet these challenges.”