A universal framework for regulatory element discovery across all genomes and data types.

By Olivier Elemento, Noam Slonim, Saeed Tavazoie. Molecules and Cells, 2007

342 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bcc53286d8eab87bc9950b3026d01a0b70fc8b74

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In Biomedical Engineering

Olivier Elemento

In Molecular Biology

Citations in the corpus

Equitability, mutual information, and the maximal information coefficient (2013, background): “Not only does it naturally quantify the strength of relationships between arbitrary variables, its close connection to likelihood [44, 45] makes it a proper objective function for ﬁtting parameterized models to a wide variety of data sets [33, 34, 35, 36, 37].”
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons (2012, positive): “To do this, we used FIRE, a sensitive and unbiased tool for discovering RNA regulatory elements (Elemento et al., 2007).”
The mathematics of tanning (2009, neutral): “Interestingly, these RNA motifs were not significant in the S. cerevisiae orthologs of the 65 genes (the only 3' UTR motif reported for nucleolar proteins in the catalog by [43] is GAA.”
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System (2008, methodology): “We identified candidates for the sequence elements that mediate regulatory interactions with specific RBPs using two related computational methods: ‘‘finding informative regulatory elements’’ (FIRE), which searches for motifs with informative patterns of enrichment [89], and a newly developed method”
DNA methylation presents distinct binding sites for human transcription factors (2013, background): “We selected a total of 154 DNA motifs (Supplementary file 1A) with the following characteristics: (1) predicted to be potential TF-binding sites in promoter regions of the human genome (Xie et al., 2005; Yu et al., 2006; Elemento et al., 2007); (2) representative of a subset of the 460 DNA motifs th”
A neurodegeneration-specific gene expression signature and immune profile of acutely isolated microglia from an ALS mouse model (2013, positive): “We conducted expression comparisons and clustering using GenePattern analysis modules (Broad Institute), pathway analysis using DAVID and iPAGE (Goodarzi et al., 2009), motif analysis using FIRE (Elemento et al., 2007), and T cell microglia transcriptome analysis using iPAGE.”
Densely interconnected transcriptional circuits control cell states in human hematopoiesis (2011, neutral): “…(Hughes et al., 2000), MEME (Bailey and Elkan, 1995) and MDScan (Liu et al., 2002) (managed with TAMO software (Gordon et al., 2005)), FIRE (Elemento et al., 2007), Amadeus (Linhart et al., 2008) and SeedSearcher (Barash et al., 2002), resulting in 9489 motifs that were enriched among the…”