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...
Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen
Tandem mass spectrometry (MS/MS) is an essential and reliable tool for biologists to identify peptide and protein sequences. Many approaches have been designed for peptide sequencing. One important...
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...
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...
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...
antiCODE: a natural sense-antisense transcripts database (2007)
Yin, Yifei, Zhao, Yi, Wang, Jie, Liu, Changning, Chen, Shuguang, Chen, Runsheng, ...
Abstract Background Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of...
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...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, ...
© 2007 Yin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Nmpp: A usercustomized nimblegen microarray data processing pipeline (2006)
Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li
Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process selfdesigned NimbleGen microarray data. It features a command-linebased integrative...
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...
NMPP: a user-customized NimbleGen microarray data processing pipeline (2006)
Wang, Xiangfeng, He, Hang, Li, Lei, Chen, Runsheng, Deng, Xing Wang, Li, Songgang
Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative...
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...
Guo, Peng, Zhang, Liqiang, Qi, Zhen, Chen, Runsheng, Jing, Guozhong
A very promising approach to understanding the mechanism of protein thermostability is to investigate the structure–function relationship of homologous proteins with different thermostabilities....
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
Conservation analysis of small RNA genes in Escherichia coli (2004)
Zhang, Yong, Zhang, Zhihua, Ling, Lunjiang, Shi, Baochen, Chen, Runsheng
Motivation: Small RNA (sRNA) genes in Escherichia coli have been in focus recently, as 44 out of 55 experimentally confirmed sRNA genes have been precisely located in the genome. The object of this...
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...
Conservation analysis of small RNA genes in Escherichia coli (2004)
Zhang, Yong, Zhang, Zhihua, Ling, Lunjiang, Shi, Baochen, Chen, Runsheng
Motivation: Small RNA (sRNA) genes in Escherichia coli have been in focus recently, as 44 out of 55 experimentally confirmed sRNA genes have been precisely located in the genome. The object of this...
Reversibly switchable DNA nanocompartment on surfaces (2004)
Mao, Youdong, Luo, Chunxiong, Deng, Wei, Jin, Guangyin, Yu, Xiaomei, Zhang, Zhaohui, ...
Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery...
Conservation analysis of small RNA genes in Escherichia coli (2004)
Zhang, Yong, Zhang, Zhihua, Ling, Lunjiang, Shi, Baochen, Chen, Runsheng
Motivation: Small RNA (sRNA) genes in Escherichia coli have been in focus recently, as 44 out of 55 experimentally confirmed sRNA genes have been precisely located in the genome. The object of this...
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...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
A Complete Sequence of the T. tengcongensis Genome (2002)
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
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,...
A Complete Sequence of the T. tengcongensis Genome
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
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...
Reversibly switchable DNA nanocompartment on surfaces
Mao, Youdong, Luo, Chunxiong, Deng, Wei, Jin, Guangyin, Yu, Xiaomei, Zhang, Zhaohui, ...
Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery...
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, ...
Jin, Qi, Yuan, Zhenghong, Xu, Jianguo, Wang, Yu, Shen, Yan, Lu, Weichuan, ...
We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a...
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,...
A Complete Sequence of the T. tengcongensis Genome
Bao, Qiyu, Tian, Yuqing, Li, Wei, Xu, Zuyuan, Xuan, Zhenyu, Hu, Songnian, ...
Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
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...
Reversibly switchable DNA nanocompartment on surfaces
Mao, Youdong, Luo, Chunxiong, Deng, Wei, Jin, Guangyin, Yu, Xiaomei, Zhang, Zhaohui, ...
Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery...
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, ...
Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome
Li, Lei, Wang, Xiangfeng, Sasidharan, Rajkumar, Stolc, Viktor, Deng, Wei, He, Hang, ...
Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the...
antiCODE: a natural sense-antisense transcripts database
Yin, Yifei, Zhao, Yi, Wang, Jie, Liu, Changning, Chen, Shuguang, Chen, Runsheng, ...
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....
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, ...
In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs
Li, Tiantian, He, Housheng, Wang, Yunfei, Zheng, Haixia, Skogerbø, Geir, Chen, Runsheng
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...