Human-mouse genome comparisons to locate regulatory sites

By Wyeth W. Wasserman, M. Palumbo, W. Thompson, J. Fickett, Charles E. Lawrence. Nature Genetics, 2000

522 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/667d726dc1516fddab95e841cd0290e184942278

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In Molecular Biology

Citations in the corpus

Combining phylogenetic data with co-regulated genes to identify regulatory motifs (2003, background): “…sampler (Lawrence et al ., 1993), Consensus (Stormo and Hartzell, 1989; Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994, 1995), ANN-Spec (Workman and Stormo, 2000), AlignACE (Hughes et al ., 2000), Projection (Buhler and Tompa, 2002), MITRA (Eskin and Pevzner, 2002), and FootPrinter…”
The evolution of transcriptional regulation in eukaryotes. (2003, methodology): “This method can successfully identify previously unknown binding sites (Loots et al. 2000; Wasserman et al. 2000; Yuh et al. 2002).”
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes (2009, background): “…one-to-one conservation in orthologous sequences for TFBSs; and while this strategy is successful in cases like muscle-speciﬁc gene expression (13), in others we have TFs for which only a limited number of TFBSs is conserved (e.g. between human and mouse), and also when two orthologous genes…”
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals (2005, unknown): “21 miR-199b(†), miR-199a(†), miR-145(†), new(2) 48 GTATATAG 0.”
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. (2002, methodology): “One method that is very useful for identifying conserved DNA motifs is cross-species comparative sequence analysis (Hardison et al. 1997; Wasserman et al. 2000; Cliften et al. 2001).”
rVista for comparative sequence-based discovery of functional transcription factor binding sites. (2002, background): “Several recent studies have shown that noncoding regulatory sequences 2000; Loots et al. 2000; Wasserman et al. 2000).”
ConSite: web-based prediction of regulatory elements using cross-species comparison (2004, background): “This approach is known as phylogenetic footprinting : due to selective pressure, functional regulatory regions in non-coding sequence should be preferentially conserved compared to regions with no sequence-speciﬁc function (9,10).”
Non-coding nuclear DNA markers in phylogenetic reconstruction (2009, methodology): “The method most frequently applied for the determination of transcription factor binding sites within promoter regions is phylogenetic footprinting (Wasserman et al. 2000; Bulyk 2003; Weitzman 2003; Zhang and Gerstein 2003).”
Discovery of regulatory elements by a computational method for phylogenetic footprinting. (2002, background): “The same idea of using comparative analysis to identify conserved elements, but among only two or three species (particularly human and mouse), has recently become popular (Hardison et al. 1997; Jareborg et al. 1999; Dubchak et al. 2000; Wasserman et al. 2000; Mouchel et al. 2001; Wu et al. 2001).”
Identification of conserved regulatory elements by comparative genome analysis (2003, background): “Algorithms for the analysis of regulatory sequences have addressed the detection of over-represented patterns in the promoters of co-regulated genes [10], and the improved discrimination of regulatory modules [11], as well as comparative studies of orthologous promoters across collections of microbi”
Genomic strategies to identify mammalian regulatory sequences (2001, background): “did human–rodent comparative sequence analyses upstream of a set of 28 orthologous genes with upregulated expression in skeletal muscl”