scholarly journals SNPRanker: a tool for identification and scoring of SNPs associated to target genes

2010 ◽  
Vol 7 (3) ◽  
pp. 331-345 ◽  
Author(s):  
Andrea Calabria ◽  
Ettore Mosca ◽  
Federica Viti ◽  
Ivan Merelli ◽  
Luciano Milanesi
Keyword(s):  
Target Genes ◽  
A Priori ◽  
Significant Snps ◽  
Biological Data ◽  
Biological Knowledge ◽  
Web Based ◽  
Specific Biological Process ◽  
Public Resources ◽  
Ranked List ◽  
Selection Of

Summary The identification of genes and SNPs involved in human diseases remains a challenge. Many public resources, databases and applications, collect biological data and perform annotations, increasing the global biological knowledge. The need of SNPs prioritization is emerging with the development of new high-throughput genotyping technologies, which allow to develop customized disease-oriented chips. Therefore, given a list of genes related to a specific biological process or disease as input, a crucial issue is finding the most relevant SNPs to analyse. The selection of these SNPs may rely on the relevant a-priori knowledge of biomolecular features characterising all the annotated SNPs and genes of the provided list. The bioinformatics approach described here allows to retrieve a ranked list of significant SNPs from a set of input genes, such as candidate genes associated with a specific disease. The system enriches the genes set by including other genes, associated to the original ones by ontological similarity evaluation. The proposed method relies on the integration of data from public resources in a vertical perspective (from genomics to systems biology data), the evaluation of features from biomolecular knowledge, the computation of partial scores for SNPs and finally their ranking, relying on their global score. Our approach has been implemented into a web based tool called SNPRanker, which is accessible through at the URL http://www.itb.cnr.it/snpranker. An interesting application of the presented system is the prioritisation of SNPs related to genes involved in specific pathologies, in order to produce custom arrays.

Innovative Approach to Information Search by Example of a Patent Analysis of an Important Substitution Plan

2020 ◽  
pp. 143-157
Author(s):  
Maria A. Milkova
Keyword(s):  
Information Search ◽  
Topic Modeling ◽  
Cognitive Biases ◽  
A Priori ◽  
Import Substitution ◽  
Innovative Approach ◽  
Iterative Search ◽  
Comprehensive Picture ◽  
Priori Information ◽  
Selection Of

Nowadays the process of information accumulation is so rapid that the concept of the usual iterative search requires revision. Being in the world of oversaturated information in order to comprehensively cover and analyze the problem under study, it is necessary to make high demands on the search methods. An innovative approach to search should flexibly take into account the large amount of already accumulated knowledge and a priori requirements for results. The results, in turn, should immediately provide a roadmap of the direction being studied with the possibility of as much detail as possible. The approach to search based on topic modeling, the so-called topic search, allows you to take into account all these requirements and thereby streamline the nature of working with information, increase the efficiency of knowledge production, avoid cognitive biases in the perception of information, which is important both on micro and macro level. In order to demonstrate an example of applying topic search, the article considers the task of analyzing an import substitution program based on patent data. The program includes plans for 22 industries and contains more than 1,500 products and technologies for the proposed import substitution. The use of patent search based on topic modeling allows to search immediately by the blocks of a priori information – terms of industrial plans for import substitution and at the output get a selection of relevant documents for each of the industries. This approach allows not only to provide a comprehensive picture of the effectiveness of the program as a whole, but also to visually obtain more detailed information about which groups of products and technologies have been patented.

Web-based Tools for Drug Repurposing: Successful Examples of Collaborative Research

2020 ◽  
Vol 28 (1) ◽  
pp. 181-195
Author(s):  
Quentin Vanhaelen
Keyword(s):  
User Interfaces ◽  
Collaborative Research ◽  
Meta Analysis ◽  
A Priori ◽  
Drug Repurposing ◽  
Data Access ◽  
Estimation Methods ◽  
Large Set ◽  
Computational Tools ◽  
Web Based

: Computational approaches have been proven to be complementary tools of interest in identifying potential candidates for drug repurposing. However, although the methods developed so far offer interesting opportunities and could contribute to solving issues faced by the pharmaceutical sector, they also come with their constraints. Indeed, specific challenges ranging from data access, standardization and integration to the implementation of reliable and coherent validation methods must be addressed to allow systematic use at a larger scale. In this mini-review, we cover computational tools recently developed for addressing some of these challenges. This includes specific databases providing accessibility to a large set of curated data with standardized annotations, web-based tools integrating flexible user interfaces to perform fast computational repurposing experiments and standardized datasets specifically annotated and balanced for validating new computational drug repurposing methods. Interestingly, these new databases combined with the increasing number of information about the outcomes of drug repurposing studies can be used to perform a meta-analysis to identify key properties associated with successful drug repurposing cases. This information could further be used to design estimation methods to compute a priori assessment of the repurposing possibilities.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Incorporating radiomics into clinical trials: expert consensus on considerations for data-driven compared to biologically driven quantitative biomarkers

2021 ◽  
Author(s):  
Laure Fournier ◽  
Lena Costaridou ◽  
Luc Bidaut ◽  
Nicolas Michoux ◽  
Frederic E. Lecouvet ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Quantitative Imaging ◽  
A Priori ◽  
External Validation ◽  
Data Driven ◽  
Imaging Biomarkers ◽  
Clinical Validation ◽  
Biological Processes ◽  
Imaging Data ◽  
Selection Of

Abstract Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. Key Points • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

scholarly journals Towards Developing a Framework to Analyze the Qualities of the University Websites

Computers ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 57
Author(s):  
Maliha Rashida ◽  
Kawsarul Islam ◽  
A. S. M. Kayes ◽  
Mohammad Hammoudeh ◽  
Mohammad Shamsul Arefin ◽  
...  
Keyword(s):  
University Ranking ◽  
Web Based ◽  
Ranking Systems ◽  
Notice Board ◽  
Academic Websites ◽  
Multi Method Approach ◽  
The University ◽  
University Ranking Systems ◽  
Ranked List

The website of a university is considered to be a virtual gateway to provide primary resources to its stakeholders. It can play an indispensable role in disseminating information about a university to a variety of audience at a time. Thus, the quality of an academic website requires special attention to fulfil the users’ need. This paper presents a multi-method approach of quality assessment of the academic websites, in the context of universities of Bangladesh. We developed an automated web-based tool that can evaluate any academic website based on three criteria, which are as follows: content of information, loading time and overall performance. Content of information contains many sub criteria, such as university vision and mission, faculty information, notice board and so on. This tool can also perform comparative analysis among several academic websites and generate a ranked list of these. To the best of our knowledge, this is the very first initiative to develop an automated tool for accessing academic website quality in context of Bangladesh. Beside this, we have conducted a questionnaire-based statistical evaluation among several universities to obtain the respective users’ feedback about their academic websites. Then, a ranked list is generated based on the survey result that is almost similar to the ranked list got from the University ranking systems. This validates the effectiveness of our developed tool in accessing academic website.

scholarly journals A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network

2016 ◽  
Vol 2016 ◽  
pp. 1-17 ◽  
Author(s):  
Erkhembayar Jadamba ◽  
Miyoung Shin
Keyword(s):  
Breast Cancer ◽  
Drug Repositioning ◽  
Expression Profiles ◽  
A Priori ◽  
Gene Expression Profiles ◽  
Biological Data ◽  
Genomic Knowledge ◽  
High Level ◽  
Systematic Framework ◽  
Phenotype Expression

Drug repositioning offers new clinical indications for old drugs. Recently, many computational approaches have been developed to repurpose marketed drugs in human diseases by mining various of biological data including disease expression profiles, pathways, drug phenotype expression profiles, and chemical structure data. However, despite encouraging results, a comprehensive and efficient computational drug repositioning approach is needed that includes the high-level integration of available resources. In this study, we propose a systematic framework employing experimental genomic knowledge and pharmaceutical knowledge to reposition drugs for a specific disease. Specifically, we first obtain experimental genomic knowledge from disease gene expression profiles and pharmaceutical knowledge from drug phenotype expression profiles and construct a pathway-drug network representing a priori known associations between drugs and pathways. To discover promising candidates for drug repositioning, we initialize node labels for the pathway-drug network using identified disease pathways and known drugs associated with the phenotype of interest and perform network propagation in a semisupervised manner. To evaluate our method, we conducted some experiments to reposition 1309 drugs based on four different breast cancer datasets and verified the results of promising candidate drugs for breast cancer by a two-step validation procedure. Consequently, our experimental results showed that the proposed framework is quite useful approach to discover promising candidates for breast cancer treatment.

scholarly journals Assessment of brain reference genes for RT-qPCR studies in neurodegenerative diseases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Rasmus Rydbirk ◽  
Jonas Folke ◽  
Kristian Winge ◽  
Susana Aznar ◽  
Bente Pakkenberg ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Reference Genes ◽  
Target Gene ◽  
Structural Changes ◽  
A Priori ◽  
Brain Regions ◽  
Quantitative Real Time Pcr ◽  
Human Brain Tissue ◽  
Web Based ◽  
Gene Expression Levels

Abstract Evaluation of gene expression levels by reverse transcription quantitative real-time PCR (RT-qPCR) has for many years been the favourite approach for discovering disease-associated alterations. Normalization of results to stably expressed reference genes (RGs) is pivotal to obtain reliable results. This is especially important in relation to neurodegenerative diseases where disease-related structural changes may affect the most commonly used RGs. We analysed 15 candidate RGs in 98 brain samples from two brain regions from Alzheimer’s disease (AD), Parkinson’s disease (PD), Multiple System Atrophy, and Progressive Supranuclear Palsy patients. Using RefFinder, a web-based tool for evaluating RG stability, we identified the most stable RGs to be UBE2D2, CYC1, and RPL13 which we recommend for future RT-qPCR studies on human brain tissue from these patients. None of the investigated genes were affected by experimental variables such as RIN, PMI, or age. Findings were further validated by expression analyses of a target gene GSK3B, known to be affected by AD and PD. We obtained high variations in GSK3B levels when contrasting the results using different sets of common RG underlining the importance of a priori validation of RGs for RT-qPCR studies.

Sistem Informasi Geografis (Sig) Properti Di Kota Tanjungpinang Berbasis Website

2019 ◽  
Vol 8 (1) ◽  
pp. 39-47
Author(s):  
Zulfachmi ◽  
Angger Andrea Amanda ◽  
Dedy Jauhari
Keyword(s):  
Information System ◽  
Geographic Information System ◽  
Unified Modeling Language ◽  
Geographic Information ◽  
Web Based ◽  
Unified Modeling ◽  
The Public ◽  
Property Specification ◽  
System Requirements ◽  
Selection Of

The increasing need for property in Tanjungpinang City is very growing, especially in the housing sector. Selection of property based on location and facilities and infrastructure is always a consideration for the community in making decisions to buy a property. Difficulty finding property location information in a certain area often occurs, resulting in people not getting references about the properties offered in Tanjungpinang City. The purpose of this research is to create a web-based geographic information system (GIS) regarding the distribution of the number of properties on offer, especially in Tanjungpinang City using a web-based mapping approach. In the development of Property GIS the author uses the Waterfall method and in the analysis of system requirements it is modeled with UML (Unified Modeling Language) and implemented with the PHP programming language and MySQLI database. It is hoped that the results of making this property's geographic information system can help the public to find out information about the distribution of properties offered, such as the location of property coordinates, addresses, prices, property photos, property specification data and property developer data.

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