Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic von Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie S., De Maio, Nicola, Gozashti, Landen, Lanfear, Robert, Haussler, David, Corbett-Detig, Russell

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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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Visualizing and interpreting cancer genomics data via the Xena platform von Goldman, Mary J., Craft, Brian, Hastie, Mim, Repečka, Kristupas, McDade, Fran, Kamath, Akhil, Banerjee, Ayan, Luo, Yunhai, Rogers, Dave, Brooks, Angela N., Zhu, Jingchun, 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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Linear assembly of a human centromere on the Y chromosome von Jain, Miten, Olsen, Hugh E, Turner, Daniel J, Stoddart, David, Bulazel, Kira V, Paten, Benedict, Haussler, David, Willard, Huntington F, Akeson, Mark, Miga, Karen H

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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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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons von Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes von Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E., Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J., Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M., Liu, Kelvin J., Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M., Vollger, Mitchell R., Monlong, Jean, Garrison, Erik, Eichler, Evan E., Salama, Sofie, Haussler, David, Green, Richard E., Akeson, Mark, Phillippy, Adam, Miga, Karen H., Carnevali, Paolo, Jain, Miten, Paten, Benedict

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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage von Putnam, Nicholas H, O'Connell, Brendan L, Stites, Jonathan C, Rice, Brandon J, Blanchette, Marco, Calef, Robert, Troll, Christopher J, Fields, Andrew, Hartley, Paul D, Sugnet, Charles W, Haussler, David, Rokhsar, Daniel S, Green, Richard E

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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: 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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HAL: a hierarchical format for storing and analyzing multiple genome alignments von Hickey, Glenn, Paten, Benedict, Earl, Dent, Zerbino, Daniel, Haussler, David

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Earth BioGenome Project: Sequencing life for the future of life von Lewin, Harris A., Robinson, Gene E., Kress, W. John, Baker, William J., Coddington, Jonathan, Crandall, Keith A., Durbin, Richard, Edwards, Scott V., Forest, Félix, Gilbert, M. Thomas P., Goldstein, Melissa M., Grigoriev, Igor V., Hackett, Kevin J., Haussler, David, Jarvis, Erich D., Johnson, Warren E., Patrinos, Aristides, Richards, Stephen, Castilla-Rubio, Juan Carlos, van Sluys, Marie-Anne, Soltis, Pamela S., Xu, Xun, Yang, Huanming, Zhang, Guojie

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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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Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution von Pollen, Alex A., Bhaduri, Aparna, Andrews, Madeline G., Nowakowski, Tomasz J., Meyerson, Olivia S., Mostajo-Radji, Mohammed A., Di Lullo, Elizabeth, Alvarado, Beatriz, Bedolli, Melanie, Dougherty, Max L., Fiddes, Ian T., Kronenberg, Zev N., Shuga, Joe, Leyrat, Anne A., West, Jay A., Bershteyn, Marina, Lowe, Craig B., Pavlovic, Bryan J., Salama, Sofie R., Haussler, David, Eichler, Evan E., Kriegstein, Arnold R.

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Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser von Cline, Melissa S., Craft, Brian, Swatloski, Teresa, Goldman, Mary, Ma, Singer, Haussler, David, Zhu, Jingchun

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The Human Pangenome Project: a global resource to map genomic diversity von Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David

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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis von Fiddes, Ian T., Lodewijk, Gerrald A., Mooring, Meghan, Bosworth, Colleen M., Ewing, Adam D., Mantalas, Gary L., Novak, Adam M., van den Bout, Anouk, Bishara, Alex, Rosenkrantz, Jimi L., Lorig-Roach, Ryan, Field, Andrew R., Haeussler, Maximilian, Russo, Lotte, Bhaduri, Aparna, Nowakowski, Tomasz J., Pollen, Alex A., Dougherty, Max L., Nuttle, Xander, Addor, Marie-Claude, Zwolinski, Simon, Katzman, Sol, Kriegstein, Arnold, Eichler, Evan E., Salama, Sofie R., Jacobs, Frank M.J., Haussler, David

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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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