Improving consensus contact prediction via server correlation reduction (2009)
Gao, Xin, Bu, Dongbo, Xu, Jinbo, Li, Ming
Abstract Background Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although...
Finding Compact Structural Motifs in Many Proteins (2009)
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
Abstract. Multiple structural alignment is a fundamental problem in computational biology. Compared with sequence alignment, structural alignment is more powerful in detecting the evolutionary...
FragQA: predicting local fragment quality of a sequence-structure alignment (2008)
Xin Gao, Dongbo Bu, Shuai Cheng, Li Jinbo, Xu Ming Li
Although protein structure prediction has made great progress in recent years, a protein model derived from automated prediction methods is subject to various errors. As methods for structure...
TREC-10 Experiments at CAS-ICT: Filtering, Web and QA (2008)
Bin Wang, Hongbo Xu, Zhifeng Yang, Yue Liu, Xueqi Cheng, Dongbo Bu, ...
CAS-ICT took part in the TREC conference for the first time this year. We have participated in three tracks of TREC-10. For adaptive filtering track, we paid more attention to feature selection and...
Fragment-HMM: A new approach to protein structure prediction (2008)
Li, Shuai Cheng, Bu, Dongbo, Xu, Jinbo, Li, Ming
We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly,...
Designing succinct structural alphabets (2008)
Li, Shuai Cheng, Bu, Dongbo, Gao, Xin, Xu, Jinbo, Li, Ming
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more...
Chen, Xiang, He, Si-Min, Bu, Dongbo, Zhang, Fa, Wang, Zhiyong, Chen, Runsheng, ...
Motivation: RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has...
Zhang, Zhuo, Sun, Shiwei, Zhu, Xiaopeng, Chang, Suhua, Liu, Xiaofei, Yu, Chungong, ...
Abstract Background Tandem mass spectrometry (MS/MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass spectra and an...
Deng, Wei, Zhu, Xiaopeng, Skogerbø, Geir, Zhao, Yi, Fu, Zhuo, Wang, Yudong, ...
Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created...
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...
R: Noncode: an integrated knowledge database of non-coding rnas (2005)
Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, ...
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered...
NONCODE: an integrated knowledge database of non-coding RNAs (2005)
Liu, Changning, Bai, Baoyan, Skogerbø, Geir, Cai, Lun, Deng, Wei, Zhang, Yong, ...
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered...
Deng, Wei, Zhu, Xiaopeng, Skogerbø, Geir, Zhao, Yi, Fu, Zhuo, Wang, Yudong, ...
Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created...
Date of origin of the SARS coronavirus strains (2004)
Lu, Hongchao, Zhao, Yi, Zhang, Jingfen, Wang, Yuelan, Li, Wei, Zhu, Xiaopeng, ...
Abstract Background A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been...
the protein–protein interaction network (2004)
Hongchao Lu, Xiaopeng Zhu, Haifeng Liu, Geir Skogerbø, Jingfen Zhang, Yong Zhang, ...
The interactome as a tree—an attempt to visualize
Lu, Hongchao, Zhu, Xiaopeng, Liu, Haifeng, Skogerbø, Geir, Zhang, Jingfen, Zhang, Yong, ...
The refinement and high-throughput of protein interaction detection methods offer us a protein–protein interaction network in yeast. The challenge coming along with the network is to find better...
Topological structure analysis of the protein-protein interaction network in budding yeast (2003)
Bu, Dongbo, Zhao, Yi, Cai, Lun, Xue, Hong, Zhu, Xiaopeng, Lu, Hongchao, ...
Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large‐scale data sets is important to present‐day...
Topological structure analysis of the protein–protein interaction network in budding yeast
Bu, Dongbo, Zhao, Yi, Cai, Lun, Xue, Hong, Zhu, Xiaopeng, Lu, Hongchao, ...
Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here,...
Date of origin of the SARS coronavirus strains
Lu, Hongchao, Zhao, Yi, Zhang, Jingfen, Wang, Yuelan, Li, Wei, Zhu, Xiaopeng, ...
The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast
Lu, Hongchao, Zhu, Xiaopeng, Liu, Haifeng, Skogerbø, Geir, Zhang, Jingfen, Zhang, Yong, ...
The refinement and high-throughput of protein interaction detection methods offer us a protein–protein interaction network in yeast. The challenge coming along with the network is to find better...
NONCODE: an integrated knowledge database of non-coding RNAs
Liu, Changning, Bai, Baoyan, Skogerbø, Geir, Cai, Lun, Deng, Wei, Zhang, Yong, ...
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered...
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...
Deng, Wei, Zhu, Xiaopeng, Skogerbø, Geir, Zhao, Yi, Fu, Zhuo, Wang, Yudong, ...
Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created...
Topological structure analysis of the protein–protein interaction network in budding yeast
Bu, Dongbo, Zhao, Yi, Cai, Lun, Xue, Hong, Zhu, Xiaopeng, Lu, Hongchao, ...
Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here,...
Date of origin of the SARS coronavirus strains
Lu, Hongchao, Zhao, Yi, Zhang, Jingfen, Wang, Yuelan, Li, Wei, Zhu, Xiaopeng, ...
The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast
Lu, Hongchao, Zhu, Xiaopeng, Liu, Haifeng, Skogerbø, Geir, Zhang, Jingfen, Zhang, Yong, ...
The refinement and high-throughput of protein interaction detection methods offer us a protein–protein interaction network in yeast. The challenge coming along with the network is to find better...
NONCODE: an integrated knowledge database of non-coding RNAs
Liu, Changning, Bai, Baoyan, Skogerbø, Geir, Cai, Lun, Deng, Wei, Zhang, Yong, ...
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered...
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...
Deng, Wei, Zhu, Xiaopeng, Skogerbø, Geir, Zhao, Yi, Fu, Zhuo, Wang, Yudong, ...
Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created...
Designing succinct structural alphabets
Li, Shuai Cheng, Bu, Dongbo, Gao, Xin, Xu, Jinbo, Li, Ming
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more...
Fragment-HMM: A new approach to protein structure prediction
Li, Shuai Cheng, Bu, Dongbo, Xu, Jinbo, Li, Ming
We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly,...