Genomic regions with distinct genomic distance conservation in vertebrate genomes (2009)
Sun, Hong, Skogerbø, Geir, Zheng, Xiaohui, Liu, Wei, Li, Yixue
Abstract Background A number of vertebrate highly conserved elements (HCEs) have been detected and their genomic interval distances have been reported to be more conserved than protein coding genes...
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...
In vivoanalysis of Caenorhabditis elegansnoncoding RNA promoter motifs (2008)
Li, Tiantian, He, Housheng, Wang, Yunfei, Zheng, Haixia, Skogerbø, Geir, Chen, Runsheng
Abstract Background Noncoding RNAs (ncRNAs) play important roles in a variety of cellular processes. Characterizing the transcriptional activity of ncRNA promoters is therefore a critical step toward...
Aftab, Muhammad, He, Housheng, Skogerbø, Geir, Chen, Runsheng
Abstract Background Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs....
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...
NONCODE v2.0: decoding the non-coding (2008)
He, Shunmin, Liu, Changning, Skogerbø, Geir, Zhao, Haitao, Wang, Jie, Liu, Tao, ...
The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown...
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....
Jia, Dong, Cai, Lun, He, Housheng, Skogerbø, Geir, Li, Tiantian, Aftab, Muhammad, ...
Abstract Background The 2,2,7-trimethylguanosine (TMG) cap structure is an important functional characteristic of ncRNAs with critical cellular roles, such as some snRNAs. Here we used...
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...
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...
Conserved distances between vertebrate highly conserved elements (2006)
Sun, Hong, Skogerbø, Geir, Chen, Runsheng
High numbers of sequence element with very high (>95%) sequence conservation between the human and other vertebrate genomes have been reported and ascribed putative cis-regulatory functions. We have...
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...
Conserved distances between vertebrate highly conserved elements (2006)
Sun, Hong, Skogerbø, Geir, Chen, Runsheng
High numbers of sequence element with very high (>95 %) sequence conservation between the human and other vertebrate genomes have been reported and ascribed putative cis-regulatory functions. We have...
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...
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...
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...
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...
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, ...
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...
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, ...
NONCODE v2.0: decoding the non-coding
He, Shunmin, Liu, Changning, Skogerbø, Geir, Zhao, Haitao, Wang, Jie, Liu, Tao, ...
The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown...
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....
MicroRNA-encoding long non-coding RNAs
He, Shunmin, Su, Hua, Liu, Changning, Skogerbø, Geir, He, Housheng, He, Dandan, ...
In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs
Li, Tiantian, He, Housheng, Wang, Yunfei, Zheng, Haixia, Skogerbø, Geir, Chen, Runsheng
Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes
Sun, Hong, Skogerbø, Geir, Wang, Zhen, Liu, Wei, Li, Yixue
Large numbers of sequence elements have been identified to be highly conserved among vertebrate genomes. These highly conserved elements (HCEs) are often located in or around genes that are involved...
Genomic regions with distinct genomic distance conservation in vertebrate genomes
Sun, Hong, Skogerbø, Geir, Zheng, Xiaohui, Liu, Wei, Li, Yixue
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...