Shi, Baochen, Guo, Xiangqian, Wu, Tao, Sheng, Sitong, Wang, Jie, Skogerbø, Geir, ...
Abstract Background A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I...
Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells (2009)
Tan, Yuliang, Zhang, Bo, Wu, Tao, Skogerbø, Geir, Zhu, Xiaopeng, Guo, Xiangqian, ...
Abstract Background Small noncoding RNAs (ncRNAs), including short interfering RNAs (siRNAs) and microRNAs (miRNAs), can silence genes at the transcriptional, post-transcriptional or translational...
MicroRNA-encoding long non-coding RNAs (2008)
He, Shunmin, Su, Hua, Liu, Changning, Skogerbø, Geir, He, Housheng, He, Dandan, ...
Abstract Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these...
Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray (2007)
He, Housheng, Wang, Jie, Liu, Tao, Liu, X. Shirley, Li, Tiantian, Wang, Yunfei, ...
The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein-coding transcriptome remains unknown....
Model-based analysis of two-color arrays (MA2C) (2007)
Song, Jun S, Johnson, W Evan, Zhu, Xiaopeng, Zhang, Xinmin, Li, Wei, Manrai, Arjun K, ...
Abstract A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown...
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis (2006)
Zhang, Yong, Li, Shaojuan, Skogerbø, Geir, Zhang, Zhihua, Zhu, Xiaopeng, Zhang, Zefeng, ...
Abstract Background As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is...
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors (2006)
Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, ...
Transcription factors with a large number of target genes—transcription hub(s), or THub(s)—are usually crucial components of the regulatory system of a cell, and the different patterns through...
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...
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray (2006)
He, Housheng, Cai, Lun, Skogerbø, Geir, Deng, Wei, Liu, Tao, Zhu, Xiaopeng, ...
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small...
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database (2006)
Wu, Tao, Wang, Jie, Liu, Changning, Zhang, Yong, Shi, Baochen, Zhu, Xiaopeng, ...
The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents...
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...
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...
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database
Wu, Tao, Wang, Jie, Liu, Changning, Zhang, Yong, Shi, Baochen, Zhu, Xiaopeng, ...
The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; or ) is a database that documents experimentally determined functional interactions between noncoding RNAs...
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors
Zhang, Zhihua, Liu, Changning, Skogerbø, Geir, Zhu, Xiaopeng, Lu, Hongchao, Chen, Lan, ...
Transcription factors with a large number of target genes—transcription hub(s), or THub(s)—are usually crucial components of the regulatory system of a cell, and the different patterns through...
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...
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
He, Housheng, Cai, Lun, Skogerbø, Geir, Deng, Wei, Liu, Tao, Zhu, Xiaopeng, ...
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small...
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
Zhang, Yong, Li, Shaojuan, Skogerbø, Geir, Zhang, Zhihua, Zhu, Xiaopeng, Zhang, Zefeng, ...
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...
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database
Wu, Tao, Wang, Jie, Liu, Changning, Zhang, Yong, Shi, Baochen, Zhu, Xiaopeng, ...
The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; or ) is a database that documents experimentally determined functional interactions between noncoding RNAs...
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...
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors
Zhang, Zhihua, Liu, Changning, Skogerbø, Geir, Zhu, Xiaopeng, Lu, Hongchao, Chen, Lan, ...
Transcription factors with a large number of target genes—transcription hub(s), or THub(s)—are usually crucial components of the regulatory system of a cell, and the different patterns through...
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
He, Housheng, Cai, Lun, Skogerbø, Geir, Deng, Wei, Liu, Tao, Zhu, Xiaopeng, ...
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small...
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
Zhang, Yong, Li, Shaojuan, Skogerbø, Geir, Zhang, Zhihua, Zhu, Xiaopeng, Zhang, Zefeng, ...
Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
He, Housheng, Wang, Jie, Liu, Tao, Liu, X. Shirley, Li, Tiantian, Wang, Yunfei, ...
The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein-coding transcriptome remains unknown....
Model-based analysis of two-color arrays (MA2C)
Song, Jun S, Johnson, W Evan, Zhu, Xiaopeng, Zhang, Xinmin, Li, Wei, Manrai, Arjun K, ...
A normalization method based on probe GC content for two-color tiling arrays and an algorithm for detecting peak regions are presented. They are available in a stand-alone Java program.
MicroRNA-encoding long non-coding RNAs
He, Shunmin, Su, Hua, Liu, Changning, Skogerbø, Geir, He, Housheng, He, Dandan, ...
Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells
Tan, Yuliang, Zhang, Bo, Wu, Tao, Skogerbø, Geir, Zhu, Xiaopeng, Guo, Xiangqian, ...
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
Zhang, Yong, Wang, Jie, Huang, Shoujun, Zhu, Xiaopeng, Liu, Jun, Yang, Ning, ...
Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique...