Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

By Xiaohui S. Xie, Jun Lu, E. Kulbokas, Todd R. Golub, Vamsi K. Mootha, Kerstin Lindblad-Toh, Eric S. Lander, Manolis Kellis. Nature, 2005

2,014 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/13ffc16cddf034c54e08daf578ab7935e62c6e41

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Citations in the corpus

miR2Disease: a manually curated database for microRNA deregulation in human disease (2008, neutral): “have been identified in mammalian cells (3,4).”
MiR-15a and miR-16-1 cluster functions in human leukemia (2008, background): “Two independent studies predicted that 20–30% of human genes could be controlled by miRNAs (8, 9).”
Transcripts Targeted by the MicroRNA-16 Family Cooperatively Regulate Cell Cycle Progression (2007, methodology): “We also measured highly significant enrichments with computationally predicted miRNA targets (34, 36, 52) in miRNA-down-regulated signatures.”
A mammalian microRNA expression atlas based on small RNA library sequencing. (2007, background): “The estimated number of miRNA genes in mammalian genomes has been steadily increasing, reaching currently tens of thousands (Berezikov et al., 2005; Xie et al., 2005; Rigoutsos et al., 2006).”
microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets (2005, background): “Previous analyses of microRNA targeting in vertebrates [6,8,13,15] and flies [5,14] suggested that a substantial fraction (10%–30%) of all protein-coding genes in both clades are regulated by microRNAs.”
Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. (2007, methodology): “…of miRNA:mRNA interactions have been revealed through elegant bioinformatics and experimental approaches (Lewis et al., 2005; Stark et al., 2003; Xie et al., 2005), but the limited number of validated miRNA targets reflects our incomplete knowledge of the ‘‘rules’’ of miRNA target prediction.”
A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes (2006, background): “Currently, over 400 human miRNAs, predicted to regulate as many as 30% of human transcripts, have been identified (John et al., 2004; Lai, 2004; Lewis et al., 2005; Xie et al., 2005).”
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, background): “Xie et al. [31] ended up testing ﬁve of our predicted miRNAs and validating four.”
Bioinformatic discovery of microRNA precursors from human ESTs and introns (2006, methodology): “Xie and colleagues [21] searched for target sites recognized by miRNAs and compiled 540 conserved and frequent 8-mer motifs by surveying 3' UTRs from human, mouse, rat and dog.”