| 1. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Franke, James A., et al.
(author)
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The GGCMI Phase 2 emulators : Global gridded crop model responses to changes in CO2, temperature, water, and nitrogen (version 1.0)
- 2020
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In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:9, s. 3995-4018
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Journal article (peer-reviewed)abstract
- Statistical emulation allows combining advantageous features of statistical and process-based crop models for understanding the effects of future climate changes on crop yields. We describe here the development of emulators for nine process-based crop models and five crops using output from the Global Gridded Model Intercomparison Project (GGCMI) Phase 2. The GGCMI Phase 2 experiment is designed with the explicit goal of producing a structured training dataset for emulator development that samples across four dimensions relevant to crop yields: Atmospheric carbon dioxide (CO2) concentrations, temperature, water supply, and nitrogen inputs (CTWN). Simulations are run under two different adaptation assumptions: That growing seasons shorten in warmer climates, and that cultivar choice allows growing seasons to remain fixed. The dataset allows emulating the climatological-mean yield response of all models with a simple polynomial in mean growing-season values. Climatological-mean yields are a central metric in climate change impact analysis; we show here that they can be captured without relying on interannual variations. In general, emulation errors are negligible relative to differences across crop models or even across climate model scenarios; errors become significant only in some marginal lands where crops are not currently grown. We demonstrate that the resulting GGCMI emulators can reproduce yields under realistic future climate simulations, even though the GGCMI Phase 2 dataset is constructed with uniform CTWN offsets, suggesting that the effects of changes in temperature and precipitation distributions are small relative to those of changing means. The resulting emulators therefore capture relevant crop model responses in a lightweight, computationally tractable form, providing a tool that can facilitate model comparison, diagnosis of interacting factors affecting yields, and integrated assessment of climate impacts.
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