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1. The UCSC Genome Browser database: 2022 update

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Databases, Genetic, Genome, Human, Humans, Phylogeny, Polymerase Chain Reaction, SARS-CoV-2, User-Computer Interface, Web Browser, Exome Sequencing, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

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 datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.

Published
2022

2. The UCSC Genome Browser database: 2021 update

Author

Gonzalez, Jairo Navarro, 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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Emerging Infectious Diseases, Animals, COVID-19, Computational Biology, Data Curation, Databases, Genetic, Epidemics, Genome, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, SARS-CoV-2, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

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 available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

Published
2021

3. The UCSC Genome Browser database: 2021 update.

Author

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, and Kent, W James

Subjects
Animals, Humans, Mice, Computational Biology, Genomics, Genome, Internet, Software, Databases, Genetic, Epidemics, Molecular Sequence Annotation, Data Curation, COVID-19, SARS-CoV-2, Developmental Biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

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 available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

Published
2021

4. The UCSC SARS-CoV-2 Genome Browser.

Author

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

Subjects
Humans, Pneumonia, Viral, Coronavirus Infections, Genome, Viral, Internet, Databases, Genetic, Pandemics, Betacoronavirus, COVID-19, SARS-CoV-2, Biological Sciences, Medical and Health Sciences, Developmental Biology
Published
2020

5. UCSC Genome Browser enters 20th year

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer, Human Genome, Databases, Genetic, Genome, Human, Genomics, Humans, Internet, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.

Published
2020

6. The UCSC Genome Browser database: 2019 update

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Chromosome Mapping, Databases, Genetic, Genome, Genome, Human, Genomics, Humans, Molecular Sequence Annotation, Software, Web Browser, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

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 features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.

Published
2019

7. The UCSC Genome Browser database: 2018 update

Author

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, Gonzalez, Jairo Navarro, Gibson, David, Fiddes, Ian T, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Barber, Galt P, Armstrong, Joel, Haussler, David, Kuhn, Robert M, and Kent, W James

Subjects
Genetics, Human Genome, CRISPR-Cas Systems, Data Display, Databases, Genetic, Gene Regulatory Networks, Genome, Genome, Human, Humans, Molecular Sequence Annotation, Terminology as Topic, User-Computer Interface, Web Browser, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

Published
2018

8. The UCSC Genome Browser database: 2017 update

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Computational Biology, Databases, Genetic, Genome, Genomics, Humans, Molecular Sequence Annotation, Search Engine, Software, Web Browser, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

Published
2017

9. UCSC Data Integrator and Variant Annotation Integrator

Author

Hinrichs, Angie S, Raney, Brian J, Speir, Matthew L, Rhead, Brooke, Casper, Jonathan, Karolchik, Donna, Kuhn, Robert M, Rosenbloom, Kate R, Zweig, Ann S, Haussler, David, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Cancer, Animals, Databases, Genetic, Genome, Genomics, Humans, Internet, Software, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

UnlabelledTwo new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.Availability and implementationThe web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license.Contactangie@soe.ucsc.eduSupplementary informationSupplementary data are available at Bioinformatics online.

Published
2016

10. The UCSC Genome Browser database: 2016 update

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Animals, Databases, Genetic, Disease, Genes, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

Published
2016

11. The UCSC Genome Browser database: 2015 update

Author

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 FA, Speir, Matthew L, Zweig, Ann S, Haussler, David, Kuhn, Robert M, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Animals, Cricetinae, Databases, Nucleic Acid, Dogs, Ebolavirus, Gene Expression, Genome, Genomics, Internet, Mice, Molecular Sequence Annotation, Phenotype, Rats, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

Published
2015

12. The UCSC Genome Browser database: 2014 update

Author

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, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Alleles, Animals, Databases, Genetic, Genome, Genome, Human, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Sequence Alignment, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Published
2014

13. Forces Shaping the Fastest Evolving Regions in the Human Genome

Author

Pollard, Katherine S, Salama, Sofie R, King, Bryan, Kern, Andrew D, Dreszer, Tim, Katzman, Sol, Siepel, Adam, Pedersen, Jakob S, Bejerano, Gill, Baertsch, Robert, Rosenbloom, Kate R, Kent, Jim, and Haussler, David

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Animals, Base Pairing, Base Sequence, Conserved Sequence, Evolution, Molecular, Genome, Human, Humans, Molecular Sequence Data, Recombination, Genetic, Regulatory Elements, Transcriptional, Selection, Genetic, Sequence Analysis, DNA, Species Specificity, Developmental Biology
Abstract

Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements are dramatically changed in human but not in other primates, with seven times more substitutions in human than in chimp. The accelerated elements, and in particular the top five, show a strong bias for adenine and thymine to guanine and cytosine nucleotide changes and are disproportionately located in high recombination and high guanine and cytosine content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, there is some evidence of directional selection in the regions containing the two most accelerated regions. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.

Published
2006

14. The impact of rare variation on gene expression across tissues

Author

Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun

Subjects
Disease susceptibility -- Genetic aspects, Genetic variation -- Observations, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]

Published
2017
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15. Dynamic landscape and regulation of RNA editing in mammals

Author

Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko

Subjects
Genetic research, Mammals -- Genetic aspects, RNA processing -- Research, Genetic regulation, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]

Published
2017
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16. Landscape of X chromosome inactivation across human tissues

Author

Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir

Subjects
Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]

Published
2017
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17. Genetic effects on gene expression across human tissues

Author

Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, Roger A., Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, James W., Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Brown, Andrew A., Nguyen, Duyen Y., Sullivan, Timothy J., Addington, Anjene, Koester, Susan, Lockhart, Nicole C., Roe, Bryan, Valley, Dana, Gewirtz, Ariel D. H., He, Amy Z., Quon, Gerald, Ripke, Stephan, Shimko, Tyler C., Teran, Nicole A., Zhang, Hailei, Bustamante, Carlos D., and Guigó, Roderic

Published
2017
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18. Variant interpretation: UCSC Genome Browser Recommended Track Sets

Author

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

Published
2022
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19. A comparative encyclopedia of DNA elements in the mouse genome

Author

Yue, Feng, Cheng, Yong, Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Thurman, Robert E., Kaul, Rajinder, Rynes, Eric, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Amrhein, Henry, Fisher-Aylor, Katherine, Antoshechkin, Igor, DeSalvo, Gilberto, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Zaleski, Chris, Dobin, Alex, Prieto, Pablo, Lagarde, Julien, Bussotti, Giovanni, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Byron, Rachel, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Kellis, Manolis, Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Jain, Deepti, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Kawli, Trupti, Boyle, Alan P., Euskirchen, Ghia, Kundaje, Anshul, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Erickson, Drew T., Kirkup, Vanessa M., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Lacerda de Sousa, Beatriz, Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, James Kent, W., Ramalho Santos, Miguel, Herrero, Javier, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Haugen, Eric, Dunn, Douglas, Reynolds, Alex P., Neph, Shane, Humbert, Richard, Scott Hansen, R., De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Eichler, Evan E., Orkin, Stuart H., Levasseur, Dana, Papayannopoulou, Thalia, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Blobel, Gerd A., Cao, Xiaoyi, Zhong, Sheng, Wang, Ting, Good, Peter J., Lowdon, Rebecca F., Adams, Leslie B., Zhou, Xiao-Qiao, Pazin, Michael J., Feingold, Elise A., Wold, Barbara, Taylor, James, Mortazavi, Ali, Weissman, Sherman M., Stamatoyannopoulos, John A., Snyder, Michael P., Guigo, Roderic, Gingeras, Thomas R., Gilbert, David M., Hardison, Ross C., Beer, Michael A., and Ren, Bing

Subjects
Man -- Genetic aspects, Genetic research, Human beings -- Genetic aspects, Genomes -- Comparative analysis, Mice -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases., Author(s): Feng Yue [1, 2]; Yong Cheng [3]; Alessandra Breschi [4]; Jeff Vierstra [5]; Weisheng Wu [6]; Tyrone Ryba [7]; Richard Sandstrom [5]; Zhihai Ma [3]; Carrie Davis [8]; Benjamin [...]

Published
2014
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20. The UCSC Genome Browser database: 2022 update

Author

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

Published
2021
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21. Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Author

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

Published
2021
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22. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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23. The UCSC Genome Browser database: 2021 update

Author

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

Published
2020
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24. A Quantitative Proteome Map of the Human Body

Author

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

Published
2020
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25. The UCSC Genome Browser database: extensions and updates 2013

Author

Meyer, Laurence R., Zweig, Ann S., Hinrichs, Angie S., Karolchik, Donna, Kuhn, Robert M., Wong, Matthew, Sloan, Cricket A., Rosenbloom, Kate R., Roe, Greg, Rhead, Brooke, Raney, Brian J., Pohl, Andy, Malladi, Venkat S., Li, Chin H., Lee, Brian T., Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Heitner, Steve, Harte, Rachel A., Haeussler, Maximilian, Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M., Fujita, Pauline A., Dreszer, Timothy R., Diekhans, Mark, Cline, Melissa S., Clawson, Hiram, Barber, Galt P., Haussler, David, and Kent, James W.

Published
2013
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26. ENCODE Data in the UCSC Genome Browser: year 5 update

Author

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, and Kent, James W.

Published
2013
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27. UCSC Genome Browser database: 2022 update.

Author

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, and Wick, Brittney D

Published
2022
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28. The UCSC Genome Browser database: extensions and updates 2011

Author

Dreszer, Timothy R., Karolchik, Donna, Zweig, Ann S., Hinrichs, Angie S., Raney, Brian J., Kuhn, Robert M., Meyer, Laurence R., Wong, Mathew, Sloan, Cricket A., Rosenbloom, Kate R., Roe, Greg, Rhead, Brooke, Pohl, Andy, Malladi, Venkat S., Li, Chin H., Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Harte, Rachel A., Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M., Fujita, Pauline A., Diekhans, Mark, Cline, Melissa S., Clawson, Hiram, Barber, Galt P., Haussler, David, and James Kent, W.

Published
2012
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29. ENCODE whole-genome data in the UCSC Genome Browser: update 2012

Author

Rosenbloom, Kate R., Dreszer, Timothy R., Long, Jeffrey C., Malladi, Venkat S., Sloan, Cricket A., Raney, Brian J., Cline, Melissa S., Karolchik, Donna, Barber, Galt P., Clawson, Hiram, Diekhans, Mark, Fujita, Pauline A., Goldman, Mary, Gravell, Robert C., Harte, Rachel A., Hinrichs, Angie S., Kirkup, Vanessa M., Kuhn, Robert M., Learned, Katrina, Maddren, Morgan, Meyer, Laurence R., Pohl, Andy, Rhead, Brooke, Wong, Matthew C., Zweig, Ann S., Haussler, David, and Kent, W. James

Published
2012
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30. The UCSC Genome Browser database: update 2011

Author

Fujita, Pauline A., Rhead, Brooke, Zweig, Ann S., Hinrichs, Angie S., Karolchik, Donna, Cline, Melissa S., Goldman, Mary, Barber, Galt P., Clawson, Hiram, Coelho, Antonio, Diekhans, Mark, Dreszer, Timothy R., Giardine, Belinda M., Harte, Rachel A., Hillman-Jackson, Jennifer, Hsu, Fan, Kirkup, Vanessa, Kuhn, Robert M., Learned, Katrina, Li, Chin H., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Rosenbloom, Kate R., Smith, Kayla E., Haussler, David, and Kent, W. James

Published
2011
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31. ENCODE whole-genome data in the UCSC genome browser (2011 update)

Author

Raney, Brian J., Cline, Melissa S., Rosenbloom, Kate R., Dreszer, Timothy R., Learned, Katrina, Barber, Galt P., Meyer, Laurence R., Sloan, Cricket A., Malladi, Venkat S., Roskin, Krishna M., Suh, Bernard B., Hinrichs, Angie S., Clawson, Hiram, Zweig, Ann S., Kirkup, Vanessa, Fujita, Pauline A., Rhead, Brooke, Smith, Kayla E., Pohl, Andy, Kuhn, Robert M., Karolchik, Donna, Haussler, David, and Kent, W. James

Published
2011
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32. The UCSC SARS-CoV-2 Genome Browser

Author

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

Published
2020
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33. Comparative Genomic Analysis Using the UCSC Genome Browser

Author

Karolchik, Donna, primary, Bejerano, Gill, additional, Hinrichs, Angie S., additional, Kuhn, Robert M., additional, Miller, Webb, additional, Rosenbloom, Kate R., additional, Zweig, Ann S., additional, Haussler, David, additional, and Kent, W. James, additional

Published
2007
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34. UCSC Genome Browser enters 20th year

Author

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

Published
2019
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36. ENCODE whole-genome data in the UCSC Genome Browser

Author

Rosenbloom, Kate R., Dreszer, Timothy R., Pheasant, Michael, Barber, Galt P., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Wang, Ting, Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Learned, Katrina, Rhead, Brooke, Smith, Kayla E., Kuhn, Robert M., Karolchik, Donna, Haussler, David, and Kent, W. James

Published
2010
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37. The UCSC Genome Browser database: update 2010

Author

Rhead, Brooke, Karolchik, Donna, Kuhn, Robert M., Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Diekhans, Mark, Smith, Kayla E., Rosenbloom, Kate R., Raney, Brian J., Pohl, Andy, Pheasant, Michael, Meyer, Laurence R., Learned, Katrina, Hsu, Fan, Hillman-Jackson, Jennifer, Harte, Rachel A., Giardine, Belinda, Dreszer, Timothy R., Clawson, Hiram, Barber, Galt P., Haussler, David, and Kent, W. James

Published
2010
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38. The UCSC Genome Browser database: 2017 update

Author

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., and Kent, W. James

Subjects
Genome, Human Genome, Computational Biology, Molecular Sequence Annotation, Genomics, Biological Sciences, Web Browser, Search Engine, Databases, Genetic, Information and Computing Sciences, Databases, Genetic, Genetics, Database Issue, Animals, Humans, natural sciences, Environmental Sciences, Software, Developmental Biology
Abstract

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

Published
2016

39. The ENCODE Project at UC Santa Cruz

Author

Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., Karolchik, Donna, Barber, Galt P., Harte, Rachel A., Hillman-Jackson, Jennifer, Kuhn, Robert M., Rhead, Brooke L., Smith, Kayla E., Thakkapallayil, Archana, Zweig, Ann S., Haussler, David, and Kent, W. James

Published
2007

40. An encyclopedia of mouse DNA elements (Mouse ENCODE)

Author

Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, and Adams, Leslie B

Published
2012
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41. The UCSC Genome Browser database: 2019 update

Author

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

Published
2018
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42. Genetic effects on gene expression across human tissues

Author

Haugen, Eric, He, Yuan, Chen, Lin S., Dermitzakis, Emmanouil T., Branton, Philip A., Nobel, Andrew B., Park, YoSon, McLean, Jeffrey A., Neri, Fidencio J., Tabor, David E., Saha, Ashis, Sobin, Leslie, Doherty, Jennifer A., Rosenbloom, Kate R., Quan, Jie, Strober, Benjamin J., Liu, Yaping, Valley, Dana, Basha, Omer, Barshir, Ruth, Trowbridge, Casandra A., Segrè, Ayellet V., Skol, Andrew, Karasik, Ellen, Bridge, Jason, Kent, W. James, Chiang, Colby, Damani, Farhan N., Karczewski, Konrad J., Barcus, Mary E., Oliva, Meritxell, Papasaikas, Panagiotis, Nelson, Jemma, Linke, Caroline, Paten, Benedict, Gelfand, Ellen T., Zhu, Jingchun, Wright, Fred A., Smith, Kevin S., Halow, Jessica, Kim-Hellmuth, Sarah, Salvatore, Michael, Hunter, Steven, Noble, Michael S., Goldman, Mary, Nguyen, Duyen Y., Singh, Shilpi, Rohrer, Daniel C., Cox, Nancy J., Hickey, Peter F., Battle, Alexis, Claussnitzer, Melina, Molinie, Benoit, Aguet, François, Balliu, Brunilda, Thomas, Jeffrey A., Hormozdiari, Farhad, Hou, Lei, Kaul, Rajinder, Peterson, Christine B., Lin, Jessica, Barker, Laura K., Brown, Christopher D., Guan, Ping, Lee, Kristen, Gloudemans, Michael J., Ripke, Stephan, Moser, Michael T., Muñoz-Aguirre, Manuel, Haeussler, Maximilian, Vatanian, Negin, Gewirtz, Ariel D.H., Castel, Stephane E., Monlong, Jean, Scott, Alexandra J., Stamatoyannopoulos, John, Ruffier, Magali, Zappala, Zachary, Li, Xiao, Ferreira, Pedro G., Nierras, Concepcion R., Yeger-Lotem, Esti, Wen, Xiaoquan, Struewing, Jeffery P., Delaneau, Olivier, Tukiainen, Taru, Tomaszewski, Maria M., Jo, Brian, Park, Yongjin, Martin, Casey, Bogu, Gireesh K., Pierce, Brandon L., Zhou, Yi-Hui, Eskin, Eleazar, Reverter, Ferran, Guigó, Roderic, Teran, Nicole A., Lek, Monkol, Leinweber, William F., Ardlie, Kristin G., Kopen, Gene, Ongen, Halit, Lonsdale, John T., Hall, Ira M., Bustamante, Carlos D., Quon, Gerald, Han, Buhm, Mohammadi, Pejman, Nicolae, Dan L., Kellis, Manolis, Vivian, John, Robinson, Karna L., Davis, David A., Washington, Michael, Montroy, Robert G., Craft, Brian, Wang, Gao, Garrido-Martín, Diego, Taylor, Kieron, Linder, Sandra, Hadley, Kane, Addington, Anjene M., Davis, Joe R., Siminoff, Laura A., Miklos, Mark, Tsang, Emily K., Diegel, Morgan, Mash, Deborah C., McDowell, Ian C., Lockhart, Nicole C., Payne, Anthony J., Abell, Nathan S., Cummings, Beryl B., Wheeler, Joseph, Matose, Takunda, Demanelis, Kathryn, Gliner, Genna, Stephens, Matthew, McDonald, Alisa, Rao, Abhi, Foster, Barbara A., Frésard, Laure, Brown, Andrew A., Zhang, Rui, Rinaldi, Nicola J., Gillard, Bryan M., Zerbino, Daniel R., Sabatti, Chiara, Moore, Helen M., Hasz, Richard, Brigham, Lori E., Zaugg, Judith B., Jian, Ruiqi, Conrad, Donald F., Snyder, Michael P., Im, Hae Kyung, Wu, Fan, MacArthur, Daniel G., Liu, Boxiang, Gamazon, Eric R., Jiang, Lihua, Sammeth, Michael, Johns, Christopher, Maurano, Matthew T., Hansen, Kasper D., Kang, Eun Yong, Myer, Kevin, Tang, Hua, Johnson, Mark, Fernando, Marian S., Smith, Anna M., Urbut, Sarah, Gould, Sarah E., Van Wittenberghe, Nicholas, Lee, Christopher M., Engelhardt, Barbara E., Panousis, Nikolaos, Palowitch, John J., Kibriya, Muhammad G., Sheppard, Dan, McCarthy, Mark I., Ndungu, Anne W., Valentino, Kimberly M., Sodaei, Reza, Sandstrom, Richard, Parsana, Princy, Kim, Yungil, Kumar, Rachna, Chan, Joanne, Little, A. Roger, Shimko, Tyler C., Volpi, Simona, Li, Qin, Akey, Joshua M., Walters, Gary, Roe, Bryan, Undale, Anita H., Van De Bunt, Martijn, Getz, Gad, Li, Jin Billy, Mangul, Serghei, Feinberg, Andrew P., Sul, Jae Hoon, Rizzardi, Lindsay F., Nguyen, Duyen T., Stranger, Barbara E., Um, Ki Sung, Flicek, Paul, Trevanion, Stephen J., Vaught, Jimmie B., Lockart, Nicole C., Nedzel, Jared L., Handsaker, Robert E., Hunter, Marcus, Xi, Hualin S., Bates, Daniel, Howald, Cedric, Roche, Nancy V., Koester, Susan, Huang, Katherine H., Sullivan, Timothy J., Wang, Meng, Shabalin, Andrey A., Shad, Saboor, Hariharan, Pushpa, He, Amy Z., Qi, Liqun, Lappalainen, Tuuli, Li, Xin, Carithers, Latarsha J., Mestichelli, Bernadette, Kashin, Seva, Li, Gen, Jasmine, Farzana, Juettemann, Thomas, Montgomery, Stephen B., Zhang, Hailei, Traino, Heather M., Mosavel, Maghboeba, Koester, Susan E., Lin, Shin, Jewell, Scott D., Johnson, Audra, and Wang, Li

Abstract

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.

Published
2017
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43. The UCSC Genome Browser database: 2018 update

Author

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

Published
2017
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45. Analyses of deep mammalian sequence alignment and constraint predictions for 1% of the human genome

Author

Margulies, Elliott H., Schwartz, Ariel S., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Taylor, James, Nikolaev, Sergey, Montoya-Burgos, Juan I., Minmei Hou, Dewey, Colin N., Siepel, Adam, Birney, Ewan, Keefe, Damian, Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Massingham, Tim, Ureta-Vidal, Abel, Paten, Benedict; Stone, Eric A., Bickel, Peter, Mullikin, James C., Holmes, Ian, Rosenbloom, Kate R., Brown, James B., Goldman, Nick, Hardison, Ross, Miller, Webb, Haussler, David, Antonarakis, Stylianos E., Batzoglou, Serafim, Kent, W.James, Pachter, Lior, Green, Eric D., and Sidow, Arend

Subjects
Mammals -- Genetic aspects, Nucleotide sequence -- Analysis, Biological diversity -- Analysis, Health
Abstract

The sequence analyses of functional elements involving sequence generation, alignment and evolutionary constraint of 23 mammalian species are carried out using quantitative and qualitative methods. The constraint regions and the elements are found to be nonoverlapping.

Published
2007

46. The UCSC Genome Browser database: 2016 update

Author

Speir, Matthew L., primary, Zweig, Ann S., additional, Rosenbloom, Kate R., additional, Raney, Brian J., additional, Paten, Benedict, additional, Nejad, Parisa, additional, Lee, Brian T., additional, Learned, Katrina, additional, Karolchik, Donna, additional, Hinrichs, Angie S., additional, Heitner, Steve, additional, Harte, Rachel A., additional, Haeussler, Maximilian, additional, Guruvadoo, Luvina, additional, Fujita, Pauline A., additional, Eisenhart, Christopher, additional, Diekhans, Mark, additional, Clawson, Hiram, additional, Casper, Jonathan, additional, Barber, Galt P., additional, Haussler, David, additional, Kuhn, Robert M., additional, and Kent, W. James, additional

Published
2015
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47. The UCSC Genome Browser database: 2015 update

Author

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

Published
2014
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48. Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome

Author

Nilsson, Carol L., primary, Mostovenko, Ekaterina, additional, Lichti, Cheryl F., additional, Ruggles, Kelly, additional, Fenyö, David, additional, Rosenbloom, Kate R., additional, Hancock, William S., additional, Paik, Young-Ki, additional, Omenn, Gilbert S., additional, LaBaer, Joshua, additional, Kroes, Roger A., additional, Uhlén, Matthias, additional, Hober, Sophia, additional, Végvári, Ákos, additional, Andrén, Per E., additional, Sulman, Erik P., additional, Lang, Frederick F., additional, Fuentes, Manuel, additional, Carlsohn, Elisabet, additional, Emmett, Mark R., additional, Moskal, Joseph R., additional, Berven, Frode S., additional, Fehniger, Thomas E., additional, and Marko-Varga, György, additional

Published
2014
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50. The UCSC Ebola Genome Portal

Author

Haeussler, Maximilian, primary, Karolchik, Donna, additional, Clawson, Hiram, additional, Raney, Brian J, additional, Rosenbloom, Kate R., additional, Fujita, Pauline A., additional, Hinrichs, Angie S., additional, Speir, Matthew L, additional, Eisenhart, Chris, additional, Zweig, Ann S., additional, Haussler, David, additional, and Kent, W. James, additional

Published
2014
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