SNP detection for massively parallel whole-genome resequencing (2009)
Li, Ruiqiang, Li, Yingrui, Fang, Xiaodong, Yang, Huanming, Wang, Jian, Kristiansen, Karsten, ...
Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key...
The YH database: the first Asian diploid genome database (2009)
Li, Guoqing, Ma, Lijia, Song, Chao, Yang, Zhentao, Wang, Xiulan, Huang, Hui, ...
The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and...
SOAP2: an improved ultrafast tool for short read alignment (2009)
Li, Ruiqiang, Yu, Chang, Li, Yingrui, Lam, Tak-Wah, Yiu, Siu-Ming, Kristiansen, Karsten, ...
Summary: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We...
Gene conversion in the rice genome (2008)
Xu, Shuqing, Clark, Terry, Zheng, Hongkun, Vang, Søren, Li, Ruiqiang, Wong, Gane, ...
Abstract Background Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby...
Gene conversion in the rice genome Elektronische Daten (2008)
Xu, Shuqing, Clark, Terry, Zheng, Hongkun, Vang, Søren, Li, Ruiqiang, Wong, Gane Ka-Shu, ...
Weitere Autoren: Terry Clark, Hongkun Zheng, Søren Vang, Ruiqiang Li, Gane Ka-Shu Wong, Jun Wang and Xiaoguang Zheng
Ruan, Jue, Li, Heng, Chen, Zhongzhong, Coghlan, Avril, Coin, Lachlan James M., Guo, Yiran, ...
TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
Background Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs),...
2007 Gorodkin et Volume al. 8, Issue 4, Article R45 Open Access (2007)
Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, ...
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
WEGO: a web tool for plotting GO annotations (2006)
Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, ...
Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many...
WEGO: a web tool for plotting GO annotations (2006)
Ye, Jia, Fang, Lin, Zheng, Hongkun, Zhang, Yong, Chen, Jie, Zhang, Zengjin, ...
Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many...
TreeFam: a curated database of phylogenetic trees of animal gene families (2006)
Li, Heng, Coghlan, Avril, Ruan, Jue, Coin, Lachlan James, Hériché, Jean-Karim, Osmotherly, Lara, ...
TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as...
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, ...
We describe an algorithm ReAS to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
The Genomes of Oryza sativa: A History of Duplications (2005)
Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, ...
Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes.
The Genomes of Oryza sativa: A History of Duplications (2005)
Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
J: SilkDB: a knowledgebase for silkworm biology and genomics (2005)
Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, ...
The Silkworm Knowledgebase (SilkDB) is a webbased repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a 6X draft genome sequence...
SilkDB: a knowledgebase for silkworm biology and genomics (2005)
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
The analysis of large-scale gene expression correlated to the phase changes of the migratory locust
Kang, Le, Chen, XiangYong, Zhou, Yan, Liu, BoWan, Zheng, Wei, Li, RuiQiang, ...
The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the...
SilkDB: a knowledgebase for silkworm biology and genomics
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
The Genomes of Oryza sativa: A History of Duplications
Yu, Jun, Wang, Jun, Lin, Wei, Li, Songgang, Li, Heng, Zhou, Jun, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
TreeFam: a curated database of phylogenetic trees of animal gene families
Li, Heng, Coghlan, Avril, Ruan, Jue, Coin, Lachlan James, Hériché, Jean-Karim, Osmotherly, Lara, ...
TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as...
WEGO: a web tool for plotting GO annotations
Ye, Jia, Fang, Lin, Zheng, Hongkun, Zhang, Yong, Chen, Jie, Zhang, Zengjin, ...
Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many...
The analysis of large-scale gene expression correlated to the phase changes of the migratory locust
Kang, Le, Chen, XiangYong, Zhou, Yan, Liu, BoWan, Zheng, Wei, Li, RuiQiang, ...
The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the...
SilkDB: a knowledgebase for silkworm biology and genomics
Wang, Jing, Xia, Qingyou, He, Ximiao, Dai, Mingtao, Ruan, Jue, Chen, Jie, ...
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome...
The Genomes of Oryza sativa: A History of Duplications
Yu, Jun, Wang, Jun, Lin, Wei, Li, Songgang, Li, Heng, Zhou, Jun, ...
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested...
Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, ...
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist...
TreeFam: a curated database of phylogenetic trees of animal gene families
Li, Heng, Coghlan, Avril, Ruan, Jue, Coin, Lachlan James, Hériché, Jean-Karim, Osmotherly, Lara, ...
TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as...
WEGO: a web tool for plotting GO annotations
Ye, Jia, Fang, Lin, Zheng, Hongkun, Zhang, Yong, Chen, Jie, Zhang, Zengjin, ...
Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine...
Ruan, Jue, Li, Heng, Chen, Zhongzhong, Coghlan, Avril, Coin, Lachlan James M., Guo, Yiran, ...
TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains...
Gene conversion in the rice genome
Xu, Shuqing, Clark, Terry, Zheng, Hongkun, Vang, Søren, Li, Ruiqiang, Wong, Gane Ka-Shu, ...
The YH database: the first Asian diploid genome database
Li, Guoqing, Ma, Lijia, Song, Chao, Yang, Zhentao, Wang, Xiulan, Huang, Hui, ...
The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and...