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  Citing the UCSC Browser in a Publication or Web Page

Follow these citation guidelines when using applications from the Genome Browser tool suite or data from the UCSC Genome Browser database in a research work that will be published in a journal or on the Internet. In addition to the relevant paper, please include a reference to the Genome Browser website in your manuscript: http://archaea.ucsc.edu/. Be sure to mention the release date of the genome assembly used in your work to faciliate the examination of your data by reviewers and the readers.

The Archaeal UCSC Genome Browser:

Schneider, K.L., Pollard, K.S., Baertsch, R., Pohl, A., and Lowe, T.M. The UCSC Archaeal Genome Browser. Nucleic Acids Res. TBA (2006).

The original UCSC Genome Browser (focuses on vertebrates and model eukaryotes):

Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler, A. M., and Haussler, D. The Human Genome Browser at UCSC. Genome Res. 12(6), 996-1006 (2002).

UCSC Genome Browser database/data:

Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J., Haussler, D. and Kent, W.J. The UCSC Genome Browser Database. Nucl. Acids Res 31(1), 51-54 (2003).

Cite this paper for annotation data extracted from the Genome Browser database. Annotation tracks should also be credited according to their source, which can be found on the track's description page or on the Genome Browser Credits page.

BLAT alignment tool:

Kent, W.J. BLAT - The BLAST-Like Alignment Tool. Genome Res. 12(4), 656-664 (2002).

UCSC Table Browser:

Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D. and Kent, W.J. The UCSC Table Browser data retrieval tool. Nucl. Acids Res. 32(Suppl 1), D493-D496 (2004).

UCSC Proteome Browser:

Hsu, F., Pringle, T.H., Kuhn, R.M., Karolchik, D., Diekhans, M., Haussler, D., and Kent, W.J. The UCSC Proteome Browser. Nucl. Acids Res. 33(suppl 1), D454-D458 (2004).

Journal-quality screen shots of the Genome Browser can be produced by using the PDF/PS utility accessed via the top menu bar link on the tracks display page. When including a screen shot in your manuscript, reference http://genome.ucsc.edu in the caption and cite the Genome Browser paper in the manuscript. Don't forget to mention the genome assembly used to produce the image.