The UCSC genome browser database: 2023 update

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

Publikováno v: Nucleic Acids Res. 51, D1188–D1195 (2023)
Nucleic acids research, vol 51, iss D1

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data,

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https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=66861

Towards complete and error-free genome assemblies of all vertebrate species

Autor: Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim

Publikováno v: Nature, 592, 737-746
Nature
Rhie, A, McCarthy, S A, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, B J, Chaisson, M, Gedman, G L, Cantin, L J, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, S C, Lama, T M, Grutzner, F, Warren, W C, Balakrishnan, C N, Burt, D, George, J M, Biegler, M T, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, A F, Franchini, P, Detrich, H W, Svardal, H, Wagner, M, Naylor, G J P, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, B T, Pesout, T, Houck, M, Misuraca, A, Kingan, S B, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, R E, Putnam, N H, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, R E, Guan, D, London, S E, Clayton, D F, Mello, C V, Friedrich, S R, Lovell, P V, Osipova, E, Al-Ajli, F O, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, R S, Makova, K D, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, B P, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, R H S, Crawford, A J, Gilbert, M T P, Zhang, G, Venkatesh, B, Murphy, R W, Koepfli, K-P, Shapiro, B, Johnson, W E, Di Palma, F, Marques-Bonet, T, Teeling, E C, Warnow, T, Graves, J M, Ryder, O A, Haussler, D, O’Brien, S J, Korlach, J, Lewin, H A, Howe, K, Myers, E W, Durbin, R, Phillippy, A M & Jarvis, E D 2021, ' Towards complete and error-free genome assemblies of all vertebrate species ', Nature, vol. 592, no. 7856, pp. 737-746 . https://doi.org/10.1038/s41586-021-03451-0
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Nature, 592, 7856, pp. 737-746

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d50f2a74ee7e66ef185d231bcebbd6ea
https://doi.org/10.1038/s41586-021-03451-0

The UCSC Genome Browser database: 2021 update

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

Publikováno v: Nucleic acids research, vol 49, iss D1
Nucleic Acids Research

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become availabl

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https://escholarship.org/uc/item/0qk9n5s0

The UCSC SARS-CoV-2 Genome Browser

Autor: Maximilian Haeussler, Jairo Navarro Gonzalez, Russ Corbet-Detig, Daniel Schmelter, Kate R. Rosenbloom, Ann S. Zweig, Nathan Maulding, Brian T. Lee, W. James Kent, Alastair C. Fyfe, Arjun A. Rao, Santrupti Nerli, Luis R Nassar, Manuel Ares, David Haussler, Hiram Clawson, Brian J. Raney, Todd M. Lowe, Angie S. Hinrichs, Jason D Fernandes

Publikováno v: Nature genetics, vol 52, iss 10
Nature genetics
Nature Genetics

BackgroundResearchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9e979ac1386e97001df9893d421a1907
https://doi.org/10.1101/2020.05.04.075945