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Understanding genome browsing

How can genome browsers help researchers to infer biological knowledge from data that might be misleading?

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Figure 1: Illustrative screen shots from the current UCSC Genome Browser.


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Many people have made significant contributions to this manuscript. In particular, we wish to thank Mark Diekhans, Rachel Karchin, Donna Karolchik, Rachel Harte, Trey Lathe, Mary Mangan and Brooke Rhead for their insights. Bert Overduin and Deanna Church generously offered insights on how to perform similar analyses with the Ensembl and NCBI Map Viewer browsers, so that this paper might assist a broader community of users. This work was funded by the National Human Genome Research Institute (2 P41 HG002371-06 to UCSC Center for Genomic Science, 3 P41 HG002371-06S1 ENCODE supplement to UCSC Center for Genomic Science) and National Cancer Institute (contract no. N01-CO-12400 for Mammalian Gene Collection). M.S.C. is supported under National Institutes of Health GM-040478, and thanks Manuel Ares, Jr. for his mentorship and encouragement. We are grateful to the many researchers who have contributed tracks to the UCSC Genome Browser, as the value of any browser is determined by the underlying data.

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W.J.K. receives royalties from the sale of the UCSC Genome Browser source code to commercial entities. M.S.C. has no competing interests.

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Cline, M., Kent, W. Understanding genome browsing. Nat Biotechnol 27, 153–155 (2009).

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