LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources von Karchin, Rachel, Diekhans, Mark, Kelly, Libusha, Thomas, Daryl J., Pieper, Ursula, Eswar, Narayanan, Haussler, David, Sali, Andrej

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UCSC Genome Browser Database: 2008 update von Karolchik, D, Kuhn, R.M, Baertsch, R, Barber, G.P, Clawson, H, Diekhans, M, Giardine, B, Harte, R.A, Hinrichs, A.S, Hsu, F, Kober, K.M, Miller, W, Pedersen, J.S, Pohl, A, Raney, B.J, Rhead, B, Rosenbloom, K.R, Smith, K.E, Stanke, M, Thakkapallayil, A, Trumbower, H, Wang, T, Zweig, A.S, Haussler, D, Kent, W.J

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UCSC Genome Browser Database: update 2009 von Kuhn, R.M, Karolchik, D, Zweig, A.S, Wang, T, Smith, K.E, Rosenbloom, K.R, Rhead, B, Raney, B.J, Pohl, A, Pheasant, M, Meyer, L, Hsu, F, Hinrichs, A.S, Harte, R.A, Giardine, B, Fujita, P, Diekhans, M, Dreszer, T, Clawson, H, Barber, G.P, Haussler, D, Kent, W.J

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UCSC Genome Browser Database: update 2006 von Hinrichs, A. S, Karolchik, D, Baertsch, R, Barber, G. P, Bejerano, G, Clawson, H, Diekhans, M, Furey, T. S, Harte, R. A, Hsu, F, Hillman-Jackson, J, Kuhn, R. M, Pedersen, J. S, Pohl, A, Raney, B. J, Rosenbloom, K. R, Siepel, A, Smith, K. E, Sugnet, C. W, Sultan-Qurraie, A, Thomas, D. J, Trumbower, H, Weber, R. J, Weirauch, M, Zweig, A. S, Haussler, D, Kent, W. J

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The UCSC Genome Browser Database von 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., Kent, W. J.

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The UCSC genome browser database: update 2007 von Kuhn, R M, Karolchik, D, Zweig, A S, Trumbower, H, Thomas, D J, Thakkapallayil, A, Sugnet, C W, Stanke, M, Smith, K E, Siepel, A, Rosenbloom, K R, Rhead, B, Raney, B J, Pohl, A, Pedersen, J S, Hsu, F, Hinrichs, A S, Harte, R A, Diekhans, M

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UCSC genome browser database: update 2007 von Kuhn, R.M, Karolchik, D, Zweig, A.S, Trumbower, H, Thomas, D.J, Thakkapallayil, A, Sugnet, C.W, Stanke, M, Smith, K.E, Siepel, A, Rosenbloom, K.R, Rhead, B, Raney, B.J, Pohl, A, Pedersen, J.S, Hsu, F, Hinrichs, A.S, Harte, R.A, Diekhans, M, Clawson, H, Bejerano, G, Barber, G.P, Baertsch, R, Haussler, D, Kent, W.J

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Tracking and coordinating an international curation effort for the CCDS Project von Harte, Rachel A, Farrell, Catherine M, Loveland, Jane E, Suner, Marie-Marthe, Wilming, Laurens, Aken, Bronwen, Barrell, Daniel, Frankish, Adam, Wallin, Craig, Searle, Steve, Diekhans, Mark, Harrow, Jennifer, Pruitt, Kim D

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UCSC Genome Browser database: update 2011 von Fujita, Pauline A, Rhead, Brooke, Zweig, Ann S, Hinrichs, Angie S, Karolchik, Donna, Cline, Melissa S, Goldman, Mary, Barber, Galt P, Clawson, Hiram, Coelho, Antonio, Diekhans, Mark, Dreszer, Timothy R, Giardine, Belinda M, Harte, Rachel A, Hillman-Jackson, Jennifer, Hsu, Fan, Kirkup, Vanessa, Kuhn, Robert M, Learned, Katrina, Li, Chin H, Meyer, Laurence R, Pohl, Andy, Raney, Brian J, Rosenbloom, Kate R, Smith, Kayla E, Haussler, David, Kent, W. James

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The UCSC Known Genes von Hsu, Fan, Kent, W. James, Clawson, Hiram, Kuhn, Robert M., Diekhans, Mark, Haussler, David

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UCSC Genome Browser database: update 2010 von Rhead, Brooke, Karolchik, Donna, Kuhn, Robert M, Hinrichs, Angie S, Zweig, Ann S, Fujita, Pauline A, Diekhans, Mark, Smith, Kayla E, Rosenbloom, Kate R, Raney, Brian J, Pohl, Andy, Pheasant, Michael, Meyer, Laurence R, Learned, Katrina, Hsu, Fan, Hillman-Jackson, Jennifer, Harte, Rachel A, Giardine, Belinda, Dreszer, Timothy R, Clawson, Hiram, Barber, Galt P, Haussler, David, Kent, W. James

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ENCODE whole-genome data in the UCSC Genome Browser: update 2012 von Rosenbloom, Kate R., Dreszer, Timothy R., Long, Jeffrey C., Malladi, Venkat S., Sloan, Cricket A., Raney, Brian J., Cline, Melissa S., Karolchik, Donna, Barber, Galt P., Clawson, Hiram, Diekhans, Mark, Fujita, Pauline A., Goldman, Mary, Gravell, Robert C., Harte, Rachel A., Hinrichs, Angie S., Kirkup, Vanessa M., Kuhn, Robert M., Learned, Katrina, Maddren, Morgan, Meyer, Laurence R., Pohl, Andy, Rhead, Brooke, Wong, Matthew C., Zweig, Ann S., Haussler, David, Kent, W. James

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The UCSC Kestrel parallel processor von Di Bias, A., Dahle, D.M., Diekhans, M., Grate, L., Hirschberg, J., Karplus, K., Keller, H., Kendrick, M., Mesa-Martinez, F.J., Pease, D., Rice, E., Schultz, A., Speck, D., Hughey, R.

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The UCSC Genome Browser database: extensions and updates 2011 von Dreszer, Timothy R., Karolchik, Donna, Zweig, Ann S., Hinrichs, Angie S., Raney, Brian J., Kuhn, Robert M., Meyer, Laurence R., Wong, Mathew, Sloan, Cricket A., Rosenbloom, Kate R., Roe, Greg, Rhead, Brooke, Pohl, Andy, Malladi, Venkat S., Li, Chin H., Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Harte, Rachel A., Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M., Fujita, Pauline A., Diekhans, Mark, Cline, Melissa S., Clawson, Hiram, Barber, Galt P., Haussler, David, James Kent, W.

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Cactus graphs for genome comparisons von Paten, Benedict, Diekhans, Mark, Earl, Dent, John, John St, Ma, Jian, Suh, Bernard, Haussler, David

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A discriminative framework for detecting remote protein homologies von Jaakkola, T, Diekhans, M, Haussler, D

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Combining local-structure, fold-recognition, and new fold methods for protein structure prediction von Karplus, Kevin, Karchin, Rachel, Draper, Jenny, Casper, Jonathan, Mandel-Gutfreund, Yael, Diekhans, Mark, Hughey, Richard

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Regions of extreme synonymous codon selection in mammalian genes von Schattner, Peter, Diekhans, Mark

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Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution von Hardison, Ross C, Roskin, Krishna M, Yang, Shan, Diekhans, Mark, Kent, W James, Weber, Ryan, Elnitski, Laura, Li, Jia, O'Connor, Michael, Kolbe, Diana, Schwartz, Scott, Furey, Terrence S, Whelan, Simon, Goldman, Nick, Smit, Arian, Miller, Webb, Chiaromonte, Francesca, Haussler, David

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What is the value added by human intervention in protein structure prediction? von Karplus, Kevin, Karchin, Rachel, Barrett, Christian, Tu, Spencer, Cline, Melissa, Diekhans, Mark, Grate, Leslie, Casper, Jonathan, Hughey, Richard

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