| 1. |
- Ma, Tao, et al.
(author)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Journal article (peer-reviewed)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 2. |
- Sodergren, Erica, et al.
(author)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Journal article (peer-reviewed)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 3. |
- Song, Han Hee, et al.
(author)
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Clustered Embedding of Massive Social Networks
- 2012
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In: Proceedings of the 12th ACM SIGMETRICS/PERFORMANCE joint international conference on Measurement and Modeling of Computer Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450310970 ; , s. 331-342
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Conference paper (other academic/artistic)abstract
- The explosive growth of social networks has created numerous exciting research opportunities. A central concept in the analysis of social networks is a proximity measure, which captures the closeness or similarity between nodes in a social network. Despite much research on proximity measures, there is a lack of techniques to eciently and accurately compute proximity measures for large-scale social networks. In this paper, we develop a novel dimensionality reduction technique, called clustered spectral graph embedding, to embed the graphs adjacency matrix into a much smaller matrix. The embedded matrix together with the embedding subspaces capture the essential clustering and spectral structure of the original graph and allows a wide range of analysis tasks to be performed in an ecient and accurate fashion. To evaluate our technique, we use three large real-world social network datasets: Flickr, LiveJournal and MySpace, with up to 2 million nodes and 90 million links. Our results clearly demonstrate the accuracy, scalability and exibility of our approach in the context of three importantsocial network analysis tasks: proximity estimation, missing link inference, and link prediction.
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