Automated Author ProfileYiu, Siu-Ming
Yiu, Siu-Ming
Current S-Index
Sum of Dataset Indices for all datasets
Average Dataset Index per Dataset
Average Dataset Index per dataset
Total Datasets
Total datasets for this author
Average FAIR Score
Average FAIR Score per dataset
Total Citations
Total citations to the author's datasets
Total Mentions
Total mentions of the author's datasets
S-Index Interpretation
The S-Index (Sharing Index) is a comprehensive metric that represents the cumulative impact of all your datasets. It is calculated as the sum of Dataset Index scores across all your claimed datasets.
What it means:
- A higher S-index indicates greater overall impact of your datasets relative to typical datasets in their fields of research
- The S-Index grows as you add more datasets or as existing datasets gain more citations and mentions
- It provides a single number to track your research data impact over time
Current S-Index: 8.1 (sum of 3 datasets Dataset Index scores)
More information here.
S-Index Over Time
Cumulative Citations Over Time
Cumulative Mentions Over Time
Datasets
Assemblathon 2 is a genome assembly contest where participating teams attempted to assemble genomes for three vertebrate species using a mixture of next-generation sequencing data. In total, 43 assemblies were submitted for three species (15 for bird, 16 for fish, and 12 for snake). These assemblies were assessed using a wide variety of statistical approaches as well as using experimental data from Fosmid sequences and optical maps.
Authors
- Bradnam, Keith, R ;
- Fass, Joseph, N ;
- Alexandrov, Anton ;
- Baranay, Paul ;
- Bechner, Michael ;
- Birol, Inanç ;
- Boisvert, Sébastien ;
- Chapman, Jarrod, A ;
- Chapuis, Guillaume ;
- Chikhi, Rayan ;
- Chitsaz, Hamidreza ;
- Chou, Wen-Chi ;
- Corbeil, Jacques ;
- Del Fabbro, Cristian ;
- Docking, T.Roderick, R ;
- Durbin, Richard ;
- Earl, Dent ;
- Emrich, Scott ;
- Fedotov, Pavel ;
- Fonseca, Nuno, A ;
- Ganapathy, Ganeshkumar ;
- Gibbs, Richard, A ;
- Gnerre, Sante ;
- Godzaridis, Élénie ;
- Goldstein, Steve ;
- Haimel, Matthias ;
- Hall, Giles ;
- Haussler, David ;
- Hiatt, Joseph, B ;
- Ho, Isaac ;
- Howard, Jason, T ;
- Hunt, Martin ;
- Jackman, Shaun, D ;
- Jaffe, David, B ;
- Jarvis, Erich, D ;
- Jiang, Huaiyang ;
- Kazakov, Sergey ;
- Kersey, Paul, J ;
- Kitzman, Jacob, O ;
- Knight, James, R ;
- Koren, Sergey ;
- Lam, Tak-Wah ;
- Lavenier, Dominique ;
- Laviolette, François ;
- Li, Yingrui ;
- Li, Zhenyu ;
- Liu, Binghang ;
- Liu, Yue ;
- Luo, Ruibang ;
- MacCallum, Iain ;
- MacManes, Matthew, D ;
- Maillet, Nicolas ;
- Melnikov, Sergey ;
- Naquin, Delphine ;
- Ning, Zemin ;
- Otto, Thomas, D ;
- Paten, Benedict ;
- Paulo, Octávio, S ;
- Phillippy, Adam, M ;
- Pina-Martins, Francisco ;
- Place, Michael ;
- Przybylski, Dariusz ;
- Qin, Xiang ;
- Qu, Carson ;
- Ribeiro, Filipe, J ;
- Richards, Stephen ;
- Rokhsar, Daniel, S ;
- Ruby, J.Graham ;
- Scalabrin, Simone ;
- Schatz, Michael, C ;
- Schwartz, David, C ;
- Sergushichev, Alexey ;
- Sharpe, Ted ;
- Shaw, Timothy, I ;
- Shendure, Jay ;
- Shi, Yujian ;
- Simpson, Jared, T ;
- Song, Henry ;
- Tsarev, Fedor ;
- Vezzi, Francesco ;
- Vicedomini, Riccardo ;
- Vieira, Bruno, M ;
- Wang, Jun ;
- Worley, Kim, C ;
- Yin, Shuangye ;
- Yiu, Siu-Ming ;
- Yuan, Jianying ;
- Zhang, Guojie ;
- Zhang, Hao ;
- Zhou, Shiguo ;
- Korf, Ian, F
SOAPdenovo2 is the latest de novo genome assembly package from BGIs SOAP (short oligonucleotide analysis package) suite of tools (homepage here: http://soap.genomics.org.cn/). Compared to SOAPdenovo1, this new version has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closure, and is optimized for large genomes.
Using new sequencing data from the YH (Homo sapiens) diploid genome the first sequenced Han Chinese individual, an updated assembly was produced (see dataset here: doi:10.5524/100038), with the N50 scores for the contig and scaffold being 3-fold and 50-fold longer, respectively, than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 times lower during the point of largest memory consumption.
Benchmarking with Assemblathon1 and GAGE datasets shows that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo1 and is competitive to other assemblers on both assembly length and accuracy.
In order to facilitate readers to repeat and recreate these findings, configured packages with the compressed pipelines containing all of the necessary shell scripts and tools are available from the BGI FTP server (ftp://public.genomics.org.cn/BGI/SOAPdenovo2).
The latest version of SOAPdenovo2 is available from Sourceforge: http://soapdenovo2.sourceforge.net/
These pipelines are available from our data platform as Galaxy workflows: http://galaxy.cbiit.cuhk.edu.hk/
Authors
- Luo, Ruibang ;
- Liu, Binghang ;
- Xie, Yinlong ;
- Li, Zhenyu ;
- Huang, Weihua ;
- Yuan, Jianying ;
- He, Guangzhu ;
- Chen, Yanxiang ;
- Pan, Qi ;
- Liu, Yunjie ;
- Tang, Jingbo ;
- Wu, Gengxiong ;
- Zhang, Hao ;
- Shi, Yujian ;
- Liu, Yong ;
- Yu, Chang ;
- Wang, Bo ;
- Lu, Yao ;
- Han, Changlei ;
- Cheung, David ;
- Yiu, Siu-Ming ;
- Peng, Shaoliang ;
- Xiaoqian, Zhu ;
- Liu, Guangming ;
- Liao, Xiangke ;
- Li, Yingrui ;
- Yang, Huanming ;
- Wang, Jian ;
- Lam, Tak-Wah, W ;
- Wang, Jun
The giant panda (Ailuropoda melanoleuca) is considered a symbol of China and is a much loved animal all around the world. It is also one of the worlds most endangered species, making it a flagship species for conservation efforts. As the first fully sequenced Ursidae and the second fully sequenced carnivore after the dog, the whole genome sequence and annotation data provide an unparalleled amount of information to aid in understanding the genetic and biological underpinnings of this unique species, and will help contribute to disease control and conservation efforts.In 2008, BGI completed a first draft of the genome sequence of a three-year old female giant panda named Jingjing, who was used as a model for the 2008 Olympics in Beijing, China (doi: 10.1038/nature08696). Using second-generation Illumina GA sequencing data, the first de novo genome assembly was created using short-read sequencing technology. Here you will find the giant panda genome sequence assembly as well as annotation information, such as gene structure and function, non-coding RNAs, and repeat elements. Also presented are polymorphism information detected in the diploid genome, including SNPs, indels, and structural variations (SVs). The assembly was done using SOAPdenovo software and the panda genome data is visualized via MapView, which is powered by the Google Web Toolkit.
Authors
- Li, Ruiqiang ;
- Fan, Wei ;
- Tian, Geng ;
- Zhu, Hongmei ;
- He, Lin ;
- Cai, Jing ;
- Huang, Quanfei ;
- Cai, Qingle ;
- Li, Bo ;
- Bai, Yinqi ;
- Zhang, Zhihe ;
- Zhang, Yaping ;
- Wang, Wen ;
- Li, Jun ;
- Wei, Fuwen ;
- Li, Heng ;
- Jian, Min ;
- Li, Jianwen ;
- Zhang, Zhaolei ;
- Nielsen, Rasmus ;
- Li, Dawei ;
- Gu, Wanjun ;
- Yang, Zhentao ;
- Xuan, Zhaoling ;
- Ryder, Oliver, A ;
- Leung, Frederick, Chi-Ching ;
- Zhou, Yan ;
- Cao, Jianjun ;
- Sun, Xiao ;
- Fu, Yonggui ;
- Fang, Xiaodong ;
- Guo, Xiaosen ;
- Wang, Bo ;
- Hou, Rong ;
- Shen, Fujun ;
- Mu, Bo ;
- Ni, Peixiang ;
- Lin, Runmao ;
- Qian, Wubin ;
- Wang, Guodong ;
- Yu, Chang ;
- Nie, Wenhui ;
- Wang, Jinhuan ;
- Wu, Zhigang ;
- Liang, Huiqing ;
- Min, Jiumeng ;
- Wu, Qi ;
- Cheng, Shifeng ;
- Ruan, Jue ;
- Wang, Mingwei ;
- Shi, Zhongbin ;
- Wen, Ming ;
- Liu, Binghang ;
- Ren, Xiaoli ;
- Zheng, Huisong ;
- Dong, Dong ;
- Cook, Kathleen ;
- Shan, Gao ;
- Zhang, Hao ;
- Kosiol, Carolin ;
- Xie, Xueying ;
- Lu, Zuhong ;
- Zheng, Hancheng ;
- Li, Yingrui ;
- Steiner, Cynthia, C ;
- Lam, Tommy, Tsan-Yuk ;
- Lin, Siyuan ;
- Zhang, Qinghui ;
- Li, Guoqing ;
- Tian, Jing ;
- Gong, Timing ;
- Liu, Hongde ;
- Zhang, Dejin ;
- Fang, Lin ;
- Ye, Chen ;
- Zhang, Juanbin ;
- Hu, Wenbo ;
- Xu, Anlong ;
- Ren, Yuanyuan ;
- Zhang, Guojie ;
- Bruford, Michael, W ;
- Li, Qibin ;
- Ma, Lijia ;
- Guo, Yiran ;
- An, Na ;
- Hu, Yujie ;
- Zheng, Yang ;
- Shi, Yongyong ;
- Li, Zhiqiang ;
- Liu, Qing ;
- Chen, Yanling ;
- Zhao, Jing ;
- Qu, Ning ;
- Zhao, Shancen ;
- Tian, Feng ;
- Wang, Xiaoling ;
- Wang, Haiyin ;
- Xu, Lizhi ;
- Liu, Xiao ;
- Vinar, Tomas ;
- Wang, Yajun ;
- Lam, Tak-Wah ;
- Yiu, Siu-Ming ;
- Liu, Shiping ;
- Zhang, Hemin ;
- Li, Desheng ;
- Huang, Yan ;
- Wang, Xia ;
- Yang, Guohua ;
- Jiang, Zhi ;
- Wang, Junyi ;
- Qin, Nan ;
- Li, Li ;
- Li, Jingxiang ;
- Bolund, Lars ;
- Kristiansen, Karsten ;
- Wong, Gane, Ka-Shu ;
- Olson, Maynard ;
- Zhang, Xiuqing ;
- Li, Songgang ;
- Yang, Huanming ;
- Wang, Jian ;
- Wang, Jun