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Your search keyword '"Rosenbloom, Kate R."' showing total 5 results
Start Over Author "Rosenbloom, Kate R." Publication Type Magazines
5 results on '"Rosenbloom, Kate R."'

1. 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

Abstract

The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

Published
2020
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3. 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

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

Author

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

Abstract

We describe the utility of integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the “missing proteins”, novel proteoforms, and PTMs. On one hand, databases in combination with bioinformatic tools are efficiently utilized to establish microarray-based transcript analysis and supply rapid protein identifications in clinical samples. On the other hand, sequence libraries are the foundation of targeted protein identification and quantification using mass spectrometric and immunoaffinity techniques. The results from combining proteoENCODEdb searches with experimental mass spectral data indicate that some alternative splicing forms detected at the transcript level are in fact translated to proteins. Our results provide a step toward the directives of the C-HPP initiative and related biomedical research.

Published
2015
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5. 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

Abstract

To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

Published
2012
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