Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, Clawson, Hiram, Spieth, John +8 more·2005·Genome Research
DOI 10.1101/gr.3715005

Cited by (4,072)

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  60. A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors
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