Automated Author ProfileHuang, Quanfei
Huang, Quanfei
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: 11.2 (sum of 6 datasets Dataset Index scores)
More information here.
S-Index Over Time
Cumulative Citations Over Time
Cumulative Mentions Over Time
Datasets
The software is a pipeline for mitochondrial protein annotation in mixed bulk samples. The pipeline annotates mitochondrial genes using homolog prediction with TBLASTN based on known complete mitochondrial genomes from GenBank RefSeq. The BLAST results were then used to determine gene ontology (e.g., mRNA and coding sequence regions) using Genewise. Annotation results include gff format annotation file, DNA and protein sequences of annotated genes. Compared to other mitochondrial annotation pipelines, the MT_annotation_BGI pipeline is easier to run a batch of annotation tasks with high speed and precision. For additional methodological details see the published paper using an example of bulk insect data suitable for running on this pipeline (see dataset here: doi:10.5524/100045).
Authors
- Li, Yiyuan ;
- Liu, Shanlin ;
- Yang, Qing ;
- Su, Xu ;
- Zhou, Lili ;
- Tang, Min ;
- Fu, Ribei ;
- Li, Jiguang ;
- Huang, Quanfei
The Chinese rhesus macaque (Macaca mulatta lasiota) is a subspecies of rhesus macaques that mainly resides in western and central China. Due to their anatomical and physiological similarity with human beings, macaques are a common laboratory model. Also, as several macaques species have been sequenced, such as the Indian rhesus macaque and the crab-eating macaque, examination of the Chinese rhesus macaque (CR) genome offers interesting insights into the entire Macaca genus.The DNA sample for data sequencing and analyses was obtained from a five-year old female CR from southwestern China. The genome was sequenced on the IlluminaGAIIx platform, from which 142-Gb of high-quality sequence, representing 47-fold genome coverage for CR. The total size of the assembled CR genome was about 2.84 Gb, providing 47-fold on average. Scaffolds were assigned to the chromosomes according to the synteny displayed with the Indian rhesus macaque and human genome sequences. About 97% of the CR scaffolds could be placed onto chromosomes.
Authors
- Yan, Guangmei ;
- Zhang, Guojie ;
- Fang, Xiaodong ;
- Zhang, Yanfeng ;
- Li, Cai ;
- Ling, Fei ;
- Cooper, David, N ;
- Li, Qiye ;
- Li, Yan ;
- van Gool, Alain, J ;
- Du, Hongli ;
- Chen, Jiesi ;
- Chen, Ronghua ;
- Zhang, Pei ;
- Huang, Zhiyong ;
- Thompson, John, R ;
- Meng, Yuhuan ;
- Bai, Yinqi ;
- Wang, Jufang ;
- Zhuo, Min ;
- Wang, Tao ;
- Huang, Ying ;
- Wei, Liqiong ;
- Li, Jianwen ;
- Wang, Zhiwen ;
- Hu, Haofu ;
- Le, Liang ;
- Stenson, Peter, D ;
- Li, Bo ;
- Liu, Xiaoming ;
- Ball, Edward, V ;
- An, Na ;
- Huang, Quanfei ;
- Zhang, Yong ;
- Fan, Wei ;
- Zhang, Xiuqing ;
- Li, Yingrui ;
- Wang, Wen ;
- Katze, Michael, G ;
- Su, Bing ;
- Nielsen, Rasmus ;
- Yang, Huanming ;
- Wang, Jun ;
- Wang, Xiaoning ;
- Wang, Jian
The crab-eating macaque (Macaca fascicularis), also known as the Java macaque or long-tailed macaque, is a species of primate located throughout Southeast Asia. Due to the frequent usage of the genus Macaca in scientific research, the sequence the crab-eating macaque furthers our understanding on how it differs from other macaque species, like the Chinese rhesus macaque and the Indian rhesus macaque. This is especially relevant considering the recent trend of using crab-eating macaque (CE) and Chinese rhesus macaques rather than the Indian rhesus macaque as laboratory models.The DNA sample for genome sequencing and analyses was from a female CE that was a captive-bred descendent of a CE from Vietnam. The genome was sequenced on the IlluminaGAIIx platform, and we obtained 162-Gb of high-quality sequence, representing 54-fold coverage. The sequencing data were processed with Illumina custom computational pipelines. The genome was de novo assembled using SOAPdenovo program based on the de Bruijn graph algorithm methods. The total size of the assembled genome was about 2.85 Gb, providing 54-fold coverage on average. The scaffolds were assigned to the chromosomes according to the synteny displayed with the Indian rhesus macaque and human genome sequences. About 92% of the CE scaffolds could be placed onto chromosomes.
Authors
- Yan, Guangmei ;
- Zhang, Guojie ;
- Fang, Xiaodong ;
- Zhang, Yanfeng ;
- Li, Cai ;
- Ling, Fei ;
- Cooper, David, N ;
- Li, Qiye ;
- Li, Yan ;
- van Gool, Alain, J ;
- Du, Hongli ;
- Chen, Jiesi ;
- Chen, Ronghua ;
- Zhang, Pei ;
- Huang, Zhiyong ;
- Thompson, John, R ;
- Meng, Yuhuan ;
- Bai, Yinqi ;
- Wang, Jufang ;
- Zhuo, Min ;
- Wang, Tao ;
- Huang, Ying ;
- Wei, Liqiong ;
- Li, Jianwen ;
- Wang, Zhiwen ;
- Hu, Haofu ;
- Le, Liang ;
- Stenson, Peter, D ;
- Li, Bo ;
- Liu, Xiaoming ;
- Ball, Edward, V ;
- An, Na ;
- Huang, Quanfei ;
- Zhang, Yong ;
- Fan, Wei ;
- Zhang, Xiuqing ;
- Li, Yingrui ;
- Wang, Wen ;
- Katze, Michael, G ;
- Su, Bing ;
- Nielsen, Rasmus ;
- Yang, Huanming ;
- Wang, Jun ;
- Wang, Xiaoning ;
- Wang, Jian
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
Available here is genomic data for the polyploid plant Brassica rapa ssp. pekinensis line Chiifu-401-42, a Chinese cabbage. As there are several oil and vegetable crop species in the Brassica family, this genome is of great agricultural relevance. It also provides an important resource for studying the evolution of polyploid genomes.The Brassica rapa Genome Sequencing Project Consortium assembled a 283.8 Mb genome estimated to cover >98% of the gene space. Using 72X coverage of paired short read sequences generated by Illumina GA II technology and 199,452 BAC-end sequences, 159 super scaffolds were produced, representing 90% of the assembled sequences with an N50 scaffold size of 1.97 Mb. Using genetic mapping of 1,427 markers in B. rapa, ten pseudo chromosomes that included 90% of the assembly were produced. A total of 41,174 protein-coding genes in the B. rapa genome were modeled, and the genome was found to have undergone genome triplication.
Authors
- Wang, Xiaowu ;
- Wang, Hanzhong ;
- Wang, Jun ;
- Sun, Rifei ;
- Wu, Jian ;
- Liu, Shengyi ;
- Bai, Yinqi ;
- Mun, Jeong-Hwan ;
- Bancroft, Ian ;
- Cheng, Feng ;
- Huang, Sanwen ;
- Li, Xixiang ;
- Hua, Wei ;
- Wang, Junyi ;
- Wang, Xiyin ;
- Freeling, Michael ;
- Pires, J.Chris ;
- Paterson, Andrew, H ;
- Chalhoub, Boulos ;
- Wang, Bo ;
- Hayward, Alice ;
- Sharpe, Andrew, G ;
- Park, Beom-Seok ;
- Weisshaar, Bernd ;
- Liu, Binghang ;
- Li, Bo ;
- Liu, Bo ;
- Tong, Chaobo ;
- Song, Chi ;
- Duran, Christopher ;
- Peng, Chunfang ;
- Geng, Chunyu ;
- Koh, Chushin ;
- Lin, Chuyu ;
- Edwards, David ;
- Mu, Desheng ;
- Shen, Di ;
- Soumpourou, Eleni ;
- Li, Fei ;
- Fraser, Fiona ;
- Conant, Gavin ;
- Lassalle, Gilles ;
- King, Graham, J ;
- Bonnema, Guusje ;
- Tang, Haibao ;
- Wang, Haiping ;
- Belcram, Harry ;
- Zhou, Heling ;
- Hirakawa, Hideki ;
- Abe, Hiroshi ;
- Guo, Hui ;
- Wang, Hui ;
- Jin, Huizhe ;
- Parkin, Isobel, AP ;
- Batley, Jacqueline ;
- Kim, Jeong-Sun, S ;
- Just, Jérémy ;
- Li, Jianwen ;
- Xu, Jiaohui ;
- Deng, Jie ;
- Kim, Jin, A ;
- Li, Jingping ;
- Yu, Jingyin ;
- Meng, Jinling ;
- Wang, Jinpeng ;
- Min, Jiumeng ;
- Poulain, Julie ;
- Wang, Jun ;
- Hatakeyama, Katsunori ;
- Wu, Kui ;
- Wang, Li ;
- Fang, Lu ;
- Trick, Martin ;
- Links, Matthew, G ;
- Zhao, Meixia ;
- Jin, Mina ;
- Ramchiary, Nirala ;
- Drou, Nizar ;
- Berkman, Paul, J ;
- Cai, Qingle ;
- Huang, Quanfei ;
- Li, Ruiqiang ;
- Tabata, Satoshi ;
- Cheng, Shifeng ;
- Zhang, Shu ;
- Zhang, Shujiang ;
- Huang, Shunmou ;
- Sato, Shusei ;
- Sun, Silong ;
- Kwon, Soo-Jin, J ;
- Choi, Su-Ryun, R ;
- Lee, Tae-Ho, H ;
- Fan, Wei ;
- Zhao, Xiang ;
- Tan, Xu ;
- Xu, Xun ;
- Wang, Yan ;
- Qiu, Yang ;
- Yin, Ye ;
- Li, Yingrui ;
- Du, Yongchen ;
- Liao, Yongcui ;
- Lim, Yongpyo ;
- Narusaka, Yoshihiro ;
- Wang, Yupeng ;
- Wang, Zhenyi ;
- Li, Zhenyu ;
- Wang, Zhiwen ;
- Xiong, Zhiyong ;
- Zhang, Zhonghua ;
- , Brassica Rapa Genome Sequencing Project Consortium
Here we present genomic data for the domestic cucumber (Cucumis sativus var. sativus L.). The cucumber is a member of the Cucurbitaceae or cucurbit family, a family of great agricultural and horticultural importance that also includes species such as melons, gourds and squashes. A biologically interesting as well as an economically relevant species, it is used as a model system for plant sex determination and vascular biology studies.The domestic cucumber has seven pairs of chromosomes and a haploid genome of 367 Mb, a smaller genome for the Cucurbitaceae family. The genome was sequenced and assembled with N50 contig and scaffold sizes of 19.8 Kb and 1.14 Mb, respectively. Using the genetic map, 72.8% of the assembled sequences were anchored onto the 7 chromosomes. A total of 26,682 genes were predicted in the current cucumber genome.
Authors
- Huang, Sanwen ;
- Li, Ruiqiang ;
- Zhang, Zhonghua ;
- Li, Li ;
- Gu, Xingfang ;
- Fan, Wei ;
- Lucas, William, J ;
- Wang, Xiaowu ;
- Xie, Bingyan ;
- Ni, Peixiang ;
- Ren, Yuanyuan ;
- Zhu, Hongmei ;
- Li, Jun ;
- Lin, Kui ;
- Jin, Weiwei ;
- Fei, Zhangjun ;
- Li, Guangcun ;
- Staub, Jack ;
- Kilian, Andrzej ;
- van der Vossen, Edwin, AG ;
- Wu, Yang ;
- Guo, Jie ;
- He, Jun ;
- Jia, Zhiqi ;
- Ren, Yi ;
- Tian, Geng ;
- Lu, Yao ;
- Ruan, Jue ;
- Qian, Wubin ;
- Wang, Mingwei ;
- Huang, Quanfei ;
- Li, Bo ;
- Xuan, Zhaoling ;
- Cao, Jianjun ;
- , Asan ;
- Wu, Zhigang ;
- Zhang, Juanbin ;
- Cai, Qingle ;
- Bai, Yinqi ;
- Zhao, Bowen ;
- Han, Yonghua ;
- Li, Ying ;
- Li, Xuefeng ;
- Wang, Shenhao ;
- Shi, Qiuxiang ;
- Liu, Shiqiang ;
- Cho, Won, Kyong ;
- Kim, Jae-Yean ;
- Xu, Yong ;
- Heller-Uszynska, Katarzyna ;
- Miao, Han ;
- Cheng, Zhouchao ;
- Zhang, Shengping ;
- Wu, Jian ;
- Yang, Yuhong ;
- Kang, Houxiang ;
- Li, Man ;
- Liang, Huiqing ;
- Ren, Xiaoli ;
- Shi, Zhongbin ;
- Wen, Ming ;
- Jian, Min ;
- Yang, Hailong ;
- Zhang, Guojie ;
- Yang, Zhentao ;
- Chen, Rui ;
- Liu, Shifang ;
- Li, Jianwen ;
- Ma, Lijia ;
- Liu, Hui ;
- Zhou, Yan ;
- Zhao, Jing ;
- Fang, Xiaodong ;
- Li, Guoqing ;
- Fang, Lin ;
- Li, Yingrui ;
- Liu, Dongyuan ;
- Zheng, Hongkun ;
- Zhang, Yong ;
- Qin, Nan ;
- Li, Zhuo ;
- Yang, Guohua ;
- Yang, Shuang ;
- Bolund, Lars ;
- Kristiansen, Karsten ;
- Zheng, Hancheng ;
- Li, Shaochuan ;
- Zhang, Xiuqing ;
- Yang, Huanming ;
- Wang, Jian ;
- Sun, Rifei ;
- Zhang, Baoxi ;
- Jiang, Shuzhi ;
- Wang, Jun ;
- Du, Yongchen ;
- Li, Songgang