The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
Surface Enhanced Raman spectroscopy (SERS) is an enhanced technique of Raman spectroscopy. It produces Raman spectra with higher intensity peak than the conventional Raman spectroscopy. Using SERS, detection of low concentration of NS1 in saliva seems promising. NS1 protein is an early biomarker for viral diseases caused by flavivirus such as Dengue fever, Yellow fever, Japanese Encephalitis etc....
A large number of long non-coding RNAs (lncRNAs) have been identified over the past decades. Accumulating evidence proves that lncRNAs play key roles in various biological processes. However, the majority of the lncRNAs have not been functionally characterized. The annotation of lncRNA functions has become an area of focus in the fields of biology and bioinformatics. In this paper, we develop a global...
Many pathogenic mutations percolate to protein dysfunction by altering dynamics. Reconstructing protein energy landscapes promises to relate dynamics to function but is generally infeasible due to the disparate spatio-temporal scales involved. Recent algorithmic innovation allows reconstructing energy landscapes of medium-size proteins in the presence of sufficient prior wet-laboratory structure data...
The presence of heterogeneity in the data representation of the commercial protein screen makes the analysis of experimental results and the protein crystallization screening process difficult and time-consuming. In order to reduce the human effort required to deal with this problem, we present our application based on schema matching and data integration to automatically find the matching elements...
The collaborations of the diseases might be the key to understand the mechanism of the diseases since it is difficult to detect the role of complex genes and micro RNA in diseases. With the rapid development of technology, several metabolites of many kinds of diseases could be obtained by the advanced machines. Some diseases are related to several metabolites, and some metabolites have strong relationship...
This paper presents a new method of segmenting and classifying protein crystallization trial images that were collected using trace fluorescent labeling. Trace fluorescent labeling typically involves fluorescence dye that can re-emit the illumination light at other wavelengths around the principal wavelength. The captured image has a primary color channel with respect to illumination light and fluorescence...
Biological network alignment benefits the evolutionary and comparative biology by providing regions of topological and functional similarity between different species. However, most existing network aligners follow heuristic methods and only capture the static information that based purely on the original isolated networks, while there also exists valuable interactive information hidden in the resulted...
Ligand binding site prediction from protein structure plays an important role in various complex rational drug design efforts. Its applications include drug side effects prediction, docking prioritization in inverse virtual screening and elucidation of protein function in genome wide structural studies. Currently available tools have limitations that disqualify them from many possible use cases. In...
It is a grand challenge to reveal the causal effects of DNA variants in complex phenotypes. Although statistical techniques can establish correlations between genotypes and phenotypes in Genome-Wide Association Studies (GWAS), they often fail when the variant is rare. The emerging Network-based Association Studies aim to address this shortcoming in statistical analysis, but are mainly applied to coding...
Protein-protein interaction extraction research can be widely applied to the field of life science research. However, most of the machine learning based methods focus on binary PPI relation extraction, which loses rich relationship type information that is critical to the PPIs study. The rule based open information extraction methods can extract the PPI triple (i.e. “protein1, interaction word, protein2”),...
Pairwise protein structure comparison has taken significant scientific research effort in last two decades. Even though it all started with alignment-based comparison methods, recently there are several non-alignment based methods that have shown good potential. One such approach is based on shape descriptors. These methods use histograms or vectors to represent the molecular shapes. They have shown...
The complexity of biological data is a difficult challenge for data integration. Thus, this study develops a localized web service platform for the specific bioinformatics study needs of Southwest University of China. Our platform includes the following three innovation features, (1) Graphical Survival time analysis kit; (2) Codon Deviation Coefficient (CDC) computing kit and (3) Long non-coding RNA...
Various problems in biomedicine can be formulated as a ranking problem, where a set of candidate components is ranked relatively based on a set of known components. The most popular problem in biomedicine is identification of disease-associated cellular components, where cellular components can be genes, proteins, microRNAs or other molecules. Besides that, a number of problems in pharmacology is...
Soybean tissue-specific network helps identify and visualize the gene-gene relationships in various tissues [1]. We have built SoyTSN, a web-based tool for tissue-specific network prediction in soybean using 14 tissues RNA-Seq datasets including flower, root, nodule, leaf, stem, seed, etc. SoyTSN first combines multiple tissue specific RNA-Seq studies, and later Cross-Conditions Cluster Detection...
Protein crystallization is the process of formation of protein crystals. Many combinations of chemicals need to be tried to obtain a crystal for some difficult proteins. This paper discusses a novel way of identifying the various conditions necessary for a successful crystal growth by using a variation of genetic algorithm which explores unexplored territories of the chemical search space, thereby...
With the increasing number of ontologies being designed to represent and manage knowledge in all sorts of sectors, ontology alignment and integration become more and more important in aggregating intelligent efforts on homogenous and heterogeneous data. From the computational perspective, it is challenging due to the ubiquitous existence of diverse classifications of same data. In this paper, we propose...
Protein Docking is an important task in computational chemistry and computational biology and yet is very computationally expensive. This paper presents a study on implementing molecular docking program in the Hadoop-based system. The molecular docking platform based on Hadoop provides the preprocessing of ligand datasets and the analysis function of the docking results, it also implements the parallel...
Disease processes are usually driven by several genes interacting in molecular modules or pathways leading to the disease. The identification of such modules in gene or protein networks is at the core of several analysis methods in biomedical research. However, there is still a need to develop a generic framework to uncover biologically relevant modules for different types of networks. With this pretext...
Ginger is a well-known traditional Chinese medicine which has been identified with positive digestive function regulations e.g. vomit prevention and warming interior. 6-shogaol is one of ginger's major bioactive constituents. In this study, digestive functions regulated by 6-shogaol towards stomach and small intestine were investigated. Started with biomarkers regulated by 6-shogaol reported in PubMed...
Ginger is widely used as a spice and traditional Chinese medicine achieving warming interior for dispelling cold during its long time clinical observations and practices. However, its mechanism is still obscure. In this study, interior is restricted to stomach and small intestine. 6-gingerol, ginger's quality control and main bio-active chemical compound, is chosen to represent ginger. Started with...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.