8 results on '"Dreszer T"'
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2. The UCSC Genome Browser database: extensions and updates 2011
- Author
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Dreszer, T. R., primary, Karolchik, D., additional, Zweig, A. S., additional, Hinrichs, A. S., additional, Raney, B. J., additional, Kuhn, R. M., additional, Meyer, L. R., additional, Wong, M., additional, Sloan, C. A., additional, Rosenbloom, K. R., additional, Roe, G., additional, Rhead, B., additional, Pohl, A., additional, Malladi, V. S., additional, Li, C. H., additional, Learned, K., additional, Kirkup, V., additional, Hsu, F., additional, Harte, R. A., additional, Guruvadoo, L., additional, Goldman, M., additional, Giardine, B. M., additional, Fujita, P. A., additional, Diekhans, M., additional, Cline, M. S., additional, Clawson, H., additional, Barber, G. P., additional, Haussler, D., additional, and James Kent, W., additional
- Published
- 2011
- Full Text
- View/download PDF
3. ENCODE whole-genome data in the UCSC Genome Browser: update 2012
- Author
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Rosenbloom, K. R., primary, Dreszer, T. R., additional, Long, J. C., additional, Malladi, V. S., additional, Sloan, C. A., additional, Raney, B. J., additional, Cline, M. S., additional, Karolchik, D., additional, Barber, G. P., additional, Clawson, H., additional, Diekhans, M., additional, Fujita, P. A., additional, Goldman, M., additional, Gravell, R. C., additional, Harte, R. A., additional, Hinrichs, A. S., additional, Kirkup, V. M., additional, Kuhn, R. M., additional, Learned, K., additional, Maddren, M., additional, Meyer, L. R., additional, Pohl, A., additional, Rhead, B., additional, Wong, M. C., additional, Zweig, A. S., additional, Haussler, D., additional, and Kent, W. J., additional
- Published
- 2011
- Full Text
- View/download PDF
4. The UCSC Genome Browser database: update 2011
- Author
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Fujita, P. A., primary, Rhead, B., additional, Zweig, A. S., additional, Hinrichs, A. S., additional, Karolchik, D., additional, Cline, M. S., additional, Goldman, M., additional, Barber, G. P., additional, Clawson, H., additional, Coelho, A., additional, Diekhans, M., additional, Dreszer, T. R., additional, Giardine, B. M., additional, Harte, R. A., additional, Hillman-Jackson, J., additional, Hsu, F., additional, Kirkup, V., additional, Kuhn, R. M., additional, Learned, K., additional, Li, C. H., additional, Meyer, L. R., additional, Pohl, A., additional, Raney, B. J., additional, Rosenbloom, K. R., additional, Smith, K. E., additional, Haussler, D., additional, and Kent, W. J., additional
- Published
- 2010
- Full Text
- View/download PDF
5. ENCODE whole-genome data in the UCSC Genome Browser
- Author
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Rosenbloom, K. R., primary, Dreszer, T. R., additional, Pheasant, M., additional, Barber, G. P., additional, Meyer, L. R., additional, Pohl, A., additional, Raney, B. J., additional, Wang, T., additional, Hinrichs, A. S., additional, Zweig, A. S., additional, Fujita, P. A., additional, Learned, K., additional, Rhead, B., additional, Smith, K. E., additional, Kuhn, R. M., additional, Karolchik, D., additional, Haussler, D., additional, and Kent, W. J., additional
- Published
- 2009
- Full Text
- View/download PDF
6. The UCSC Genome Browser database: update 2010
- Author
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Rhead, B., primary, Karolchik, D., additional, Kuhn, R. M., additional, Hinrichs, A. S., additional, Zweig, A. S., additional, Fujita, P. A., additional, Diekhans, M., additional, Smith, K. E., additional, Rosenbloom, K. R., additional, Raney, B. J., additional, Pohl, A., additional, Pheasant, M., additional, Meyer, L. R., additional, Learned, K., additional, Hsu, F., additional, Hillman-Jackson, J., additional, Harte, R. A., additional, Giardine, B., additional, Dreszer, T. R., additional, Clawson, H., additional, Barber, G. P., additional, Haussler, D., additional, and Kent, W. J., additional
- Published
- 2009
- Full Text
- View/download PDF
7. The ENCODE Uniform Analysis Pipelines.
- Author
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Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, and Cherry JM
- Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses., Competing Interests: Conflict of interest. None declared
- Published
- 2023
- Full Text
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8. Forces shaping the fastest evolving regions in the human genome.
- Author
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Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, and Haussler D
- Subjects
- Animals, Base Pairing, Base Sequence, Conserved Sequence, Humans, Molecular Sequence Data, Recombination, Genetic, Regulatory Elements, Transcriptional genetics, Sequence Analysis, DNA, Species Specificity, Evolution, Molecular, Genome, Human genetics, Selection, Genetic
- 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., Competing Interests: Competing interests. The authors have declared that no competing interests exist.
- Published
- 2006
- Full Text
- View/download PDF
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