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Topological structure analysis of the protein–protein interaction network in budding yeast

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 spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi‐cliques and quasi‐bipartites) of complicated protein–protein...

HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma

Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1 in the immunotherapy of melanoma and other cancers. However, identification of TAAs has often been hampered by the complicated and laborsome laboratory procedures. In order to...

The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast

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 ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of...

Date of origin of the SARS coronavirus strains

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 identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS...

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database

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 experimentally determined functional interactions between noncoding RNAs (ncRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs). NPInter intends to provide the...

NONCODE: an integrated knowledge database of non-coding RNAs

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 automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of...

NONCODE v2.0: decoding the non-coding

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 rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs...

MicroRNA-encoding long non-coding RNAs

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 ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that...

antiCODE: a natural sense-antisense transcripts database

at its websites http://bioinfo.ibp.ac.cn/ ANTICODE or http://www.anticode.org Authors' contributions Yifei Yin and Yi Zhao carried out the design and the collection of data. Jie Wang carried for

NONCODE v3.0: integrative annotation of long noncoding RNAs

Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and...

Effects of Aliskiren on Stroke in Rats Expressing Human Renin and Angiotensinogen Genes

Objective Pre-treatment with angiotensin receptor blockers is known to improve neurological outcome after stroke. This study investigated for the first time, whether the renin inhibitor aliskiren has similar neuroprotective effects. Methods Since aliskiren specifically blocks human renin, double transgenic rats expressing human renin and angiotensinogen genes were used. To...

dbDEMC: a database of differentially expressed miRNAs in human cancers

(InCoB2010): Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S4. Authors contributions Haitao Zhao, Yi Zhao and Yang Zhong

LRRK2 A419V Is Not Associated with Parkinson's Disease in Different Chinese Populations

It has been suggested that a common LRRK2 polymorphic variant (A419V (rs34594498 C >T)) may be a risk factor among Asians (especially in Taiwan). In this study, we examined this variant in a larger and independent Taiwan cohort. We found the frequency of the variant (A419V) to be very rare in our Taiwan PD and controls (?0.6%). Further studies were conducted in two other Chinese...

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

Qi Liao Changning Liu Xiongying Yuan Shuli Kang Ruoyu Miao Hui Xiao Guoguang Zhao Haitao Luo Dechao Bu Haitao Zhao Geir Skogerb Zhongdao Wu Yi Zhao Although accumulating evidence has provided

ncFANs: a web server for functional annotation of long non-coding RNAs

Recent interest in the non-coding transcriptome has resulted in the identification of large numbers of long non-coding RNAs (lncRNAs) in mammalian genomes, most of which have not been functionally characterized. Computational exploration of the potential functions of these lncRNAs will therefore facilitate further work in this field of research. We have developed a practical and...

Transient filament occlusion of the middle cerebral artery in rats: does the reperfusion method matter 24 hours after perfusion?

Background There are two widely used transient middle cerebral artery occlusion (MCAO) methods, which differ in the use of unilateral or bilateral carotid artery reperfusion (UNICAR and BICAR). Of the two methods, UNICAR is easier to perform. This study was designed to comprehensively compare the two reperfusion methods to determine if there are any differences in outcomes...

Clustered microRNAs' coordination in regulating protein-protein interaction network

Background MicroRNAs (miRNAs), a growing class of small RNAs with crucial regulatory roles at the post-transcriptional level, are usually found to be clustered on chromosomes. However, with the exception of a few individual cases, so far little is known about the functional consequence of this conserved clustering of miRNA loci. In animal genomes such clusters often contain non...

Optimal STBC Precoding with Channel Covariance Feedback for Minimum Error Probability

,” IEEE Journal on Selected Areas in Communications , vol. 21 , no. 3 , pp. 406 - 417 , 2003 . Yi Zhao received his B .S. degree from Tsinghua University, Beijing, China, in 2001 and the M.S. degree from

Alu-directed transcriptional regulation of some novel miRNAs

Background Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression pattern of human miRNA gene loci. Several lines of experimental results have indicated that both polymerase II (Pol-II) and polymerase III (Pol-III) may be involved...

Global transcriptome profiles of Camellia sinensis during cold acclimation

Background Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold...