Eh, Margulies Gm, Cooper G, Asimenos Dj, Thomas Cn, Dewey A, Siepel E, Birney D, Keefe As, Schwartz M, Hou
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Published in
Genome Research
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; com...
M, Blanchette Ed Green W, Miller David Haussler
Published in
Genome Research
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases cor...
H, Huang Nr, Zhang I, Holmes Jc, Mullikin A, Ureta-Vidal B, Paten M, Seringhaus D, Church K, Rosenbloom Wj, Kent
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Published in
Nature
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowle...
