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- Birney, Ewan, et al.
(författare)
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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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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)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. |
- Jansson, Jesper, et al.
(författare)
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Determining the consistency of resolved triplets and fan triplets
- 2017
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Ingår i: Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783319569697 ; 10229 LNCS, s. 82-98
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Konferensbidrag (refereegranskat)abstract
- The R+−F+− Consistency problem takes as input two sets R+ and R− of resolved triplets and two sets F+ and F− of fan triplets, and asks for a distinctly leaf-labeled tree that contains all elements in R+ ∪ F+ and no elements in R− ∪ F− as embedded subtrees, if such a tree exists. This paper presents a detailed characterization of how the computational complexity of the problem changes under various restrictions. Our main result is an efficient algorithm for dense inputs satisfying R− = ∅ whose running time is linear in the size of the input and therefore optimal.
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