The UCSC Genome Browser database: 2022 update

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

Publikováno v: Nucleic acids research, vol 50, iss D1
Nucleic Acids Research

The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic data

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a810a05c2e772e61cca39e68ad73c7cf
https://doi.org/10.1093/nar/gkab959

Variant Interpretation: UCSC Genome Browser Recommended Track Sets

Autor: Brian T. Lee, Luis R Nassar, Daniel Schmelter, Jairo Navarro Gonzalez, Kate R. Rosenbloom, Jonathan Casper, Christopher Lee, W. James Kent, Hiram Clawson, Robert M. Kuhn, Anna Benet-Pagès, Gerardo Perez, Brian J. Raney, Ann S. Zweig, Maximillian Haeussler

The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The da

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9d0258daf0f72d6ac15733e889e64a7
https://doi.org/10.22541/au.162547326.67836758/v1

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Autor: Deborah C. Mash, Kevin S. Smith, Lappalainen T, Jeffrey A. Thomas, Rajinder Kaul, Paul Flicek, Maghboeba Mosavel, Yuxin Zou, Barbara E. Stranger, Brandon L. Pierce, Yanyu Liang, Andrew R. Hamel, Lihua Jiang, Marcus Hunter, Jimmie B. Vaught, Hae Kyung Im, John M. Rouhana, François Aguet, Ferran Reverter, Jason Bridge, Farzana Jasmine, Scott D. Jewell, William F. Leinweber, Gad Getz, Jonah Einson, Kevin Myer, SE Castel, Barbara E. Engelhardt, Stephen B. Montgomery, Brunilda Balliu, Gary Walters, Helen M. Moore, Daniel Nachun, Zerbino, Lori E. Brigham, Gao Wang, Farhad Hormozdiari, Pejman Mohammadi, Kasper D. Hansen, Nicole A. Teran, Fred A. Wright, Bryan Gillard, Sarah Kim-Hellmuth, CC Powell, Susan E. Koester, Wucher, Aaron Graubert, Duyen T. Nguyen, Shin Lin, Mike Moser, John A. Stamatoyannopoulos, Liqun Qi, Princy Parsana, Peter Hickey, Latarsha J. Carithers, Saboor Shad, Eric R. Gamazon, Jennifer A. Doherty, Stephen J. Trevanion, Kane Hadley, Kate R. Rosenbloom, Anita H. Undale, Robert E. Handsaker, Debra Bradbury, Shankara Anand, Meng Wang, David E. Tabor, Karna Robinson, S. Gabriel, Esti Yeger-Lotem, Kimberly Ramsey, Mary Barcus, Daniel G. MacArthur, Yuan He, Nancy Roche, Alvaro N. Barbeira, Ayellet V. Segrè, Dan Sheppard, Souvik Das, AR Little, Nathan S. Abell, Xiaoquan Wen, Elise D. Flynn, Nicole M. Ferraro, Hua Tang, Jared L. Nedzel, Jessica Wheeler, Abhi Rao, Meier, Thomas Juettemann, Sandra Linder, Bruce A. Roe, Daniel J. Cotter, David A. Davis, Christopher Johns, Lin Chen, Seva Kashin, Muhammad G. Kibriya, Ana Viñuela, Ellen Todres, Ashis Saha, Matthew Stephens, Chiara Sabatti, Manolis Kellis, Laura A. Siminoff, Phillip Branton, Xiao Li, Michael Snyder, Kathryn Demanelis, Gen Li, Barbara A. Foster, Leslie H. Sobin, Simona Volpi, Magali Ruffier, Christopher D. Brown, Ping Guan, Benjamin J. Strober, Alexis Battle, Michael J. Gloudemans, Silva Kasela, Manuel Muñoz-Aguirre, Ellen Karasik, OM deGoede, Roderic Guigó, Michael Washington, Alisa McDonald, Andrew A. Brown, Meritxell Oliva, Kieron Taylor, Nancy J. Cox, Daniel C. Rohrer, Paul J. Hoffman, Gene Kopen, Qin Li, Andrew D Skol, Rodrigo Bonazzola, Tiffany Eulalio, Mark H. Johnson, Laure Fresard, Lindsay F. Rizzardi, Abhiram Rao, T Krubit, W. J. Kent, Alan Kwong, Anna M. Smith, Pedro G. Ferreira, HM Gardiner, Andrew P. Feinberg, Rick Hasz, Lei Hou, Marta Melé, Andrew B. Nobel, Katherine H. Huang, Laura Barker, Maximilian Haeussler, Kristin G. Ardlie, Concepcion R. Nierras, Christopher Lee, Joshua M. Akey, Eskin E, Jeffrey McLean, Donald F. Conrad, Jin Billy Li, YoSon Park, Serghei Mangul, Emmanouil T. Dermitzakis, Brian Jo, D Garrido-Martin

The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing. Some human genetic variants affect the amount of RNA produced and the splicing of gene transcripts, crucial steps in development and ma

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::750f7e68291b1839a3351deae498ad1b
http://hdl.handle.net/2445/195117

A vast resource of allelic expression data spanning human tissues

Autor: Nancy J. Cox, Sayantan Das, Abhi Rao, Pejman Mohammadi, Alan Kwong, Brandon L. Pierce, Yanyu Liang, Yuxin Zou, Anna M. Smith, Matthew Stephens, Chiara Sabatti, Yuan He, Kasper D. Hansen, Lei Hou, Meritxell Oliva, W. James Kent, Stacey Gabriel, Andrew R. Hame, Tanya Krubit, Gary Walters, Lori E. Brigham, Gao Wang, Kevin S. Smith, Michael J. Gloudemans, Barbara E. Engelhardt, Yongjin Park, Nicole A. Teran, David A. Davis, Thomas Juettemann, Kimberley Ramsey, Fred A. Wright, Lin Chen, Valentin Wucher, Benjamin J. Strober, Duyen T. Nguyen, Eleazar Eskin, Kane Hadley, Deborah C. Mash, Michael Snyder, Sarah Kim-Hellmuth, Laura A. Siminoff, Maghboeba Mosavel, Shin Lin, Richard Hasz, Daniel C. Rohrer, Latarsha J. Carithers, Kevin Myer, Rajinder Kaul, Andrew D. Skol, Bryan Gillard, Dana R. Valley, Philip A. Branton, Stephane E. Castel, Robert E. Handsaker, Debra Bradbury, Meng Wang, Mary Barcus, Xiaoquan Wen, Hua Tang, Daniel J. Cotter, Lihua Jiang, Jason Bridge, Ashis Saha, Gen Li, Susan E. Koester, Qin Li, Mark H. Johnson, Barbara E. Stranger, Jimmie B. Vaught, Hae Kyung Im, Paul Flicek, Marcus Hunter, François Aguet, Elise D. Flynn, Sandra Linder, Nancy Roche, Daniel R. Zerbino, Xiao Li, Barbara A. Foster, Stephen B. Montgomery, Daniel Nachun, Serghei Mangul, Emmanouil T. Dermitzakis, Brian Jo, Simona Volpi, Farzana Jasmine, Scott D. Jewell, Jonah Einson, Tuuli Lappalainen, Farhad Hormozdiari, John M. Rouhana, Ana Viñuela, Daniel G. MacArthur, William F. Leinweber, Gad Getz, Peter Hickey, Eric R. Gamazon, Brunilda Balliu, Jennifer A. Doherty, Christopher D. Brown, Roderic Guigó, Gene Kopen, Rodrigo Bonazzola, Pedro G. Ferreira, Andrew P. Feinberg, Shankara Anand, Helen M. Moore, Paul J. Hoffman, Heather M. Gardiner, Ping Guan, Ferran Reverter, Jin Billy Li, Tiffany Eulalio, Joseph Wheeler, Alvaro N. Barbeira, Jared L. Nedzel, Seva Kashin, Laure Fresard, Lindsay F. Rizzardi, Abhiram Rao, Muhammad G. Kibriya, David Tabor, Leslie H. Sobin, A. Roger Little, Stephen J. Trevanion, Nicole M. Ferraro, Kate R. Rosenbloom, John A. Stamatoyannopoulos, Liqun Qi, Princy Parsana, Ayellet V. Segrè, Dan Sheppard, Nathan S. Abell, Kathryn Demanelis, Manolis Kellis, Silva Kasela, Xin Li, Conner C. Powell, YoSon Park, Michael Washington, Magali Ruffier, Saboor Shad, Christopher Johns, Jeffrey A. Thomas, Andrew Brown, Alisa McDonald, Karna Robinson, Esti Yeger-Lotem, Manuel Muñoz-Aguirre, Kieron Taylor, Marta Melé, Diego Garrido-Martín, Brian Roe, Michael T. Moser, Andrew B. Nobel, Alexis Battle, Maximilian Haeussler, Concepcion R. Nierras, Ellen Karasik, Sam Meier, Anita H. Undale, Ellen Todres, Aaron Graubert, Joshua M. Akey, Jeffrey McLean, Donald F. Conrad, Olivia M. De Goede, Katherine H. Huang, Laura Barker, Kristin G. Ardlie, Christopher Lee

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-12 (2020)
Genome Biology

Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 mi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::90fddfebf856337cc6189fbe1de49662
http://hdl.handle.net/10230/45398

The UCSC Genome Browser database: 2019 update

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

Publikováno v: Nucleic acids research, vol 47, iss D1
Nucleic Acids Research

The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and featur

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b09bf5efd53bf5e6a10a036c127068a9
https://doi.org/10.1093/nar/gky1095