Using native and syntenically mapped cDNA alignments to improve de novo gene finding von Stanke, Mario, Diekhans, Mark, Baertsch, Robert, Haussler, David

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The UCSC Cancer Genomics Browser: update 2015 von Goldman, Mary, Craft, Brian, Swatloski, Teresa, Cline, Melissa, Morozova, Olena, Diekhans, Mark, Haussler, David, Zhu, Jingchun

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era von Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict

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The UCSC Genome Browser database: 2021 update von Navarro Gonzalez, Jairo, Zweig, Ann S, Speir, Matthew L, Schmelter, Daniel, Rosenbloom, Kate R, Raney, Brian J, Powell, Conner C, Nassar, Luis R, Maulding, Nathan D, Lee, Christopher M, Lee, Brian T, Hinrichs, Angie S, Fyfe, Alastair C, Fernandes, Jason D, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Benet-Pagès, Anna, Barber, Galt P, Haussler, David, Kuhn, Robert M, Haeussler, Maximilian, Kent, W James

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The UCSC Genome Browser database: 2018 update von Casper, Jonathan, Zweig, Ann S, Villarreal, Chris, Tyner, Cath, Speir, Matthew L, Rosenbloom, Kate R, Raney, Brian J, Lee, Christopher M, Lee, Brian T, Karolchik, Donna, Hinrichs, Angie S, Haeussler, Maximilian, Guruvadoo, Luvina, Navarro Gonzalez, Jairo, Gibson, David, Fiddes, Ian T, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Barber, Galt P, Armstrong, Joel, Haussler, David, Kuhn, Robert M, Kent, W James

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The UCSC Genome Browser database: 2023 update von Nassar, Luis R, Barber, Galt P, Benet-Pagès, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Brian T, Lee, Christopher M, Muthuraman, Pranav, Nguy, Beagan, Pereira, Tiana, Nejad, Parisa, Perez, Gerardo, Raney, Brian J, Schmelter, Daniel, Speir, Matthew L, Wick, Brittney D, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Haeussler, Maximilian, Kent, W James

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The UCSC Genome Browser database: 2022 update von Lee, Brian T, Barber, Galt P, Benet-Pagès, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Christopher M, Muthuraman, Pranav, Nassar, Luis R, Nguy, Beagan, Pereira, Tiana, Perez, Gerardo, Raney, Brian J, Rosenbloom, Kate R, Schmelter, Daniel, Speir, Matthew L, Wick, Brittney D, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Haeussler, Maximilian, Kent, W James

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Cactus: Algorithms for genome multiple sequence alignment von Paten, Benedict, Earl, Dent, Nguyen, Ngan, Diekhans, Mark, Zerbino, Daniel, Haussler, David

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UCSC Genome Browser enters 20th year von Lee, Christopher M, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Brian T, Nassar, Luis R, Powell, Conner C, Raney, Brian J, Rosenbloom, Kate R, Schmelter, Daniel, Speir, Matthew L, Zweig, Ann S, Haussler, David, Haeussler, Maximilian, Kuhn, Robert M, Kent, W James

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Long-read sequence assembly of the gorilla genome von Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.

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ENCODE data in the UCSC Genome Browser: year 5 update von 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

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Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation von Fiddes, Ian T, Armstrong, Joel, Diekhans, Mark, Nachtweide, Stefanie, Kronenberg, Zev N, Underwood, Jason G, Gordon, David, Earl, Dent, Keane, Thomas, Eichler, Evan E, Haussler, David, Stanke, Mario, Paten, Benedict

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The UCSC Cancer Genomics Browser: update 2013 von Goldman, Mary, Craft, Brian, Swatloski, Teresa, Ellrott, Kyle, Cline, Melissa, Diekhans, Mark, Ma, Singer, Wilks, Chris, Stuart, Josh, Haussler, David, Zhu, Jingchun

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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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Whole-Genome Alignment and Comparative Annotation von Armstrong, Joel, Fiddes, Ian T, Diekhans, Mark, Paten, Benedict

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Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells von Tunstall, Tate, Kock, Richard, Vahala, Jiri, Diekhans, Mark, Fiddes, Ian, Armstrong, Joel, Paten, Benedict, Ryder, Oliver A, Steiner, Cynthia C

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Transcriptional activity and strain-specific history of mouse pseudogenes von Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark

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CRAVAT: cancer-related analysis of variants toolkit von Douville, Christopher, Carter, Hannah, Kim, Rick, Niknafs, Noushin, Diekhans, Mark, Stenson, Peter D, Cooper, David N, Ryan, Michael, Karchin, Rachel

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CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer von Wong, Wing Chung, Kim, Dewey, Carter, Hannah, Diekhans, Mark, Ryan, Michael C., Karchin, Rachel

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Comparative analysis of pseudogenes across three phyla von Sisu, Cristina, Pei, Baikang, Leng, Jing, Frankish, Adam, Zhang, Yan, Balasubramanian, Suganthi, Harte, Rachel, Wang, Daifeng, Rutenberg-Schoenberg, Michael, Clark, Wyatt, Diekhans, Mark, Rozowsky, Joel, Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark B.

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