Detection of nonneutral substitution rates on mammalian phylogenies

Por Pollard, Katherine S., Hubisz, Melissa J., Rosenbloom, Kate R., Siepel, Adam
Publicado em 2010

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Por Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, Kent, Jim, Miller, Webb, Haussler, David
Publicado em 2006

UCSC Data Integrator and Variant Annotation Integrator

Por Hinrichs, Angie S., Raney, Brian J., Speir, Matthew L., Rhead, Brooke, Casper, Jonathan, Karolchik, Donna, Kuhn, Robert M., Rosenbloom, Kate R., Zweig, Ann S., Haussler, David, Kent, W. James
Publicado no Bioinformatics (2016)

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Por Blanchette, Mathieu, Kent, W. James, Riemer, Cathy, Elnitski, Laura, Smit, Arian F.A., Roskin, Krishna M., Baertsch, Robert, Rosenbloom, Kate, Clawson, Hiram, Green, Eric D., Haussler, David, Miller, Webb
Publicado em 2004

Forces Shaping the Fastest Evolving Regions in the Human Genome

Por Pollard, Katherine S, Salama, Sofie R, King, Bryan, Kern, Andrew D, Dreszer, Tim, Katzman, Sol, Siepel, Adam, Pedersen, Jakob S, Bejerano, Gill, Baertsch, Robert, Rosenbloom, Kate R, Kent, Jim, Haussler, David
Publicado em 2006

The UCSC Ebola Genome Portal

Por Haeussler, Maximilian, Karolchik, Donna, Clawson, Hiram, Raney, Brian J, Rosenbloom, Kate R., Fujita, Pauline A., Hinrichs, Angie S., Speir, Matthew L, Eisenhart, Chris, Zweig, Ann S., Haussler, David, Kent, W. James
Publicado no PLoS Curr (2014)

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

Por Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, Clawson, Hiram, Spieth, John, Hillier, LaDeana W., Richards, Stephen, Weinstock, George M., Wilson, Richard K., Gibbs, Richard A., Kent, W. James, Miller, Webb, Haussler, David
Publicado em 2005

The ENCODE Project at UC Santa Cruz

Por Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., Karolchik, Donna, Barber, Galt P., Harte, Rachel A., Hillman-Jackson, Jennifer, Kuhn, Robert M., Rhead, Brooke L., Smith, Kayla E., Thakkapallayil, Archana, Zweig, Ann S., Haussler, David, Kent, W. James
Publicado em 2007

ENCODE whole-genome data in the UCSC Genome Browser

Por Rosenbloom, Kate R., Dreszer, Timothy R., Pheasant, Michael, Barber, Galt P., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Wang, Ting, Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Learned, Katrina, Rhead, Brooke, Smith, Kayla E., Kuhn, Robert M., Karolchik, Donna, Haussler, David, Kent, W. James
Publicado em 2010

ENCODE Data in the UCSC Genome Browser: year 5 update

Por Rosenbloom, Kate R., Sloan, Cricket A., Malladi, Venkat S., Dreszer, Timothy R., Learned, Katrina, Kirkup, Vanessa M., Wong, Matthew C., Maddren, Morgan, Fang, Ruihua, Heitner, Steven G., Lee, Brian T., Barber, Galt P., Harte, Rachel A., Diekhans, Mark, Long, Jeffrey C., Wilder, Steven P., Zweig, Ann S., Karolchik, Donna, Kuhn, Robert M., Haussler, David, Kent, W. James
Publicado em 2013

The UCSC Genome Browser database: 2016 update

Por Speir, Matthew L., Zweig, Ann S., Rosenbloom, Kate R., Raney, Brian J., Paten, Benedict, Nejad, Parisa, Lee, Brian T., Learned, Katrina, Karolchik, Donna, Hinrichs, Angie S., Heitner, Steve, Harte, Rachel A., Haeussler, Maximilian, Guruvadoo, Luvina, Fujita, Pauline A., Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt P., Haussler, David, Kuhn, Robert M., Kent, W. James
Publicado no Nucleic Acids Res (2016)

The UCSC Genome Browser database: update 2010

Por 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
Publicado em 2010

ENCODE whole-genome data in the UCSC genome browser (2011 update)

Por Raney, Brian J., Cline, Melissa S., Rosenbloom, Kate R., Dreszer, Timothy R., Learned, Katrina, Barber, Galt P., Meyer, Laurence R., Sloan, Cricket A., Malladi, Venkat S., Roskin, Krishna M., Suh, Bernard B., Hinrichs, Angie S., Clawson, Hiram, Zweig, Ann S., Kirkup, Vanessa, Fujita, Pauline A., Rhead, Brooke, Smith, Kayla E., Pohl, Andy, Kuhn, Robert M., Karolchik, Donna, Haussler, David, Kent, W. James
Publicado em 2011

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Por Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, Burhans, Richard, King, David C., Baertsch, Robert, Blankenberg, Daniel, Kosakovsky Pond, Sergei L., Nekrutenko, Anton, Giardine, Belinda, Harris, Robert S., Tyekucheva, Svitlana, Diekhans, Mark, Pringle, Thomas H., Murphy, William J., Lesk, Arthur, Weinstock, George M., Lindblad-Toh, Kerstin, Gibbs, Richard A., Lander, Eric S., Siepel, Adam, Haussler, David, Kent, W. James
Publicado em 2007

The UCSC Genome Browser database: 2014 update

Por Karolchik, Donna, Barber, Galt P., Casper, Jonathan, Clawson, Hiram, Cline, Melissa S., Diekhans, Mark, Dreszer, Timothy R., Fujita, Pauline A., Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A., Heitner, Steve, Hinrichs, Angie S., Learned, Katrina, Lee, Brian T., Li, Chin H., Raney, Brian J., Rhead, Brooke, Rosenbloom, Kate R., Sloan, Cricket A., Speir, Matthew L., Zweig, Ann S., Haussler, David, Kuhn, Robert M., Kent, W. James
Publicado em 2014

The UCSC Genome Browser database: 2017 update

Por Tyner, Cath, Barber, Galt P., Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Eisenhart, Christopher, Fischer, Clayton M., Gibson, David, Gonzalez, Jairo Navarro, Guruvadoo, Luvina, Haeussler, Maximilian, Heitner, Steve, Hinrichs, Angie S., Karolchik, Donna, Lee, Brian T., Lee, Christopher M., Nejad, Parisa, Raney, Brian J., Rosenbloom, Kate R., Speir, Matthew L., Villarreal, Chris, Vivian, John, Zweig, Ann S., Haussler, David, Kuhn, Robert M., Kent, W. James
Publicado no Nucleic Acids Res (2017)

Toil enables reproducible, open source, big biomedical data analyses

Por Vivian, John, Rao, Arjun Arkal, Nothaft, Frank Austin, Ketchum, Christopher, Armstrong, Joel, Novak, Adam, Pfeil, Jacob, Narkizian, Jake, Deran, Alden D, Musselman-Brown, Audrey, Schmidt, Hannes, Amstutz, Peter, Craft, Brian, Goldman, Mary, Rosenbloom, Kate, Cline, Melissa, O’Connor, Brian, Hanna, Megan, Birger, Chet, Kent, W James, Patterson, David A, Joseph, Anthony D, Zhu, Jingchun, Zaranek, Sasha, Getz, Gad, Haussler, David, Paten, Benedict
Publicado no Nat Biotechnol (2017)

The UCSC Genome Browser database: update 2011

Por 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
Publicado em 2011

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

Por 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
Publicado em 2012

The UCSC Genome Browser database: extensions and updates 2011

Por 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.
Publicado em 2012