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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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: 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: 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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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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Stability of SARS-CoV-2 phylogenies von Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R, Hinrichs, Angie S, Fernandes, Jason D, Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell

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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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The UCSC Genome Browser database: 2025 update von Perez, Gerardo, Barber, Galt P, Benet-Pages, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Christopher M, Nassar, Luis R, Raney, Brian J, Speir, Matthew L, van Baren, Marijke J, Vaske, Charles J, Haussler, David, Kent, W James, Haeussler, Maximilian

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

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Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level von Goya, Stephanie, Ruis, Christopher, Neher, Richard A, Meijer, Adam, Aziz, Ammar, Hinrichs, Angie S, von Gottberg, Anne, Roemer, Cornelius, Amoako, Daniel G, Acuña, Dolores, McBroome, Jakob, Otieno, James R, Bhiman, Jinal N, Everatt, Josie, Muñoz-Escalante, Juan C, Ramaekers, Kaat, Duggan, Kate, Presser, Lance D, Urbanska, Laura, Venter, Marietjie, Wolter, Nicole, Peret, Teresa C T, Salimi, Vahid, Potdar, Varsha, Borges, Vítor, Viegas, Mariana

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The UCSC Genome Browser von Karolchik, Donna, Hinrichs, Angie S., Kent, W. James

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GenArk: towards a million UCSC genome browsers von Clawson, Hiram, Lee, Brian T, Raney, Brian J, Barber, Galt P, Casper, Jonathan, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Christopher M, Nassar, Luis R, Perez, Gerardo, Wick, Brittney, Schmelter, Daniel, Speir, Matthew L, Armstrong, Joel, Zweig, Ann S, Kuhn, Robert M, Kirilenko, Bogdan M, Hiller, Michael, Haussler, David, Kent, W James, Haeussler, Maximilian

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The UCSC Genome Browser database: 2019 update von Haeussler, Maximilian, Zweig, Ann S, Tyner, Cath, Speir, Matthew L, Rosenbloom, Kate R, Raney, Brian J, Lee, Christopher M, Lee, Brian T, Hinrichs, Angie S, Gonzalez, Jairo Navarro, Gibson, David, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt P, Haussler, David, Kuhn, Robert M, Kent, W James

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A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees von McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, Kramer, Alexander, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish

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Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementati... von Kramer, Alexander M, Thornlow, Bryan, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie S, Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell

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The UCSC Genome Browser database: 2017 update von 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

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The UCSC Genome Browser database: 2016 update von 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

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The UCSC Genome Browser database: 2015 update von Rosenbloom, Kate R, Armstrong, Joel, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Dreszer, Timothy R, Fujita, Pauline A, Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A, Heitner, Steve, Hickey, Glenn, Hinrichs, Angie S, Hubley, Robert, Karolchik, Donna, Learned, Katrina, Lee, Brian T, Li, Chin H, Miga, Karen H, Nguyen, Ngan, Paten, Benedict, Raney, Brian J, Smit, Arian F A, Speir, Matthew L, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Kent, W James

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The UCSC Genome Browser database: 2014 update von 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

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G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes von Lemay, Danielle G, Martin, William F, Hinrichs, Angie S, Rijnkels, Monique, German, J Bruce, Korf, Ian, Pollard, Katherine S

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