Comparative analyses of multi-species sequences from targeted genomic regions

By James W. Thomas, J. Touchman, R. Blakesley, Gerald Bouffard, S. Beckstrom-Sternberg, Elliott H. Margulies, M. Blanchette, Adam C. Siepel, Pamela J. Thomas, Jennifer C Mcdowell and 61 more. Nature, 2003

664 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/0e0b09adf8694649ac04cd674a83a1fb0ac42512

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Citations in the corpus

Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA) (2008, background): “The sequences of both GBA and MTX1 have been shown through multispecies comparative sequence analyses [Thomas et al., 2003] to have conservation of the exonic regions in humans and nine mammalian species [LaMarca et al., 2004].”
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis (2003, methodology): “For both training and testing, we used portions of a multiple alignment consisting of nearly two megabases of human sequence, in the region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene (chromosome 7), and homologous sequence from eight other eutherian mammals (Thomas et al.”
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences (2003, neutral): “studies which have analyzed these sequences under the assumption of neutral selection [8, 41].”
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. (2005, background): “However, we have not found an enrichment for HCEs in a set of about 5000 alternatively retained cassette exons ( Sugnet et al. 2004 ), as compared with a background set of exons.”
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2004, positive): “Another highly successful approach to increasing the resolving power of comparative analyses is to use multispecies alignments combining both closely related and highly divergent organisms [14,22,23,24].”
The human phylome (2007, background): “However, phylogenies based on mitochondrial genes as well as the common presence of several mutational events and the insertion of MLTA0 elements support the clustering of primates and rodents to the exclusion of laurasatheria [41,44].”
Relaxed Phylogenetics and Dating with Confidence (2006, neutral): “The primate dataset was a subset of a 2,160,276 bp alignment of non-coding DNA from 19 mammals [41,42].”
Chromosome 21 and Down syndrome: from genomics to pathophysiology (2004, background): “The CNGs are highly conserved in mammals; from primates to monotremes, to marsupial”