Sequencing and comparison of yeast species to identify genes and regulatory elements

By Manolis Kellis, Nick Patterson, M. Endrizzi, Bruce W. Birren, Eric S. Lander. Nature, 2003

1,925 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c3dc6fefd792bd6bb34e069fa875e501a8d16ce9

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In Molecular Biology

Citations in the corpus

Genome evolution in yeasts (2004, background): “cerevisiae (the sensu stricto group), plus one more distant species, Saccharomyces kluyveri , in order to identify conserved regulatory element”
Heading for disaster: Fusarium graminearum on cereal crops. (2004, background): “When sequence assemblies for closely related Fusarium species become available, the reading frame conservation test (Kellis et al., 2003) also will be the most robust statistic for gene prediction.”
Plant cytochrome P450s from moss to poplar (2006, background): “Fungal genomes are also accumulating with the goal of comparative genomics of highly similar genomes, as in six species of Saccharomyces: S. cerevisiae, S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri (Kellis et al. 2003; Cliften et al. 2003).”
A universal framework for regulatory element discovery across all genomes and data types. (2007, methodology): “A comparison between our predicted motifs and the motifs discovered by an alignment-based approach (Kellis et al., 2003) further supports this conclusion (see Supplemental Results).”
Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination (2007, neutral): “Recently, two new bioinformatic approaches have been developed to identify UASs: phylogenetic footprinting (7,8) and clustering of co-regulated genes (9,10).”
Defining transcription modules using large-scale gene expression data (2004, methodology): “Finally, we compare the results with those of commonly used clustering methods that were applied to the same dataset, using an objective biological figure of merit (BFM), which is based on conservation of putative cis-regulatory elements between four related yeast species (Kellis et al., 2003).”
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005, methodology): “paradoxus we used data from the MIT group [16], while for S.”