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Application of Articifial Intelligence or machine learning in risk sharing agreements for pharmacotherapy risk management
J Integr Bioinform. 2023 Dec 12. doi: 10.1515/jib-2023-0014. Online ahead of print.ABSTRACTApplications of Artificial Intelligence in medical informatics solutions risk sharing have social value. At a time of ever-increasing cost for the provision of medicines to citizens, there is a need to restrain the growth of health care costs. The search for computer technologies to stop or slow down the growth of costs acquires a new very important and significant meaning. We discussed the two information technologies in pharmacotherapy and the possibility of combining and sharing them, namely the combination of risk-sharing agreeme...
Source: Journal of integrative bioinformatics - December 11, 2023 Category: Bioinformatics Authors: Grigory A Oborotov Konstantin A Koshechkin Yuriy L Orlov Source Type: research

Data literacy in genome research
J Integr Bioinform. 2023 Dec 5. doi: 10.1515/jib-2023-0033. Online ahead of print.ABSTRACTWith an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes....
Source: Journal of integrative bioinformatics - December 4, 2023 Category: Bioinformatics Authors: Katharina Wolff Ronja Friedhoff Friderieke Schwarzer Boas Pucker Source Type: research

TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus
J Integr Bioinform. 2023 Dec 5. doi: 10.1515/jib-2023-0021. Online ahead of print.ABSTRACTTidyGEO is a Web-based tool for downloading, tidying, and reformatting data series from Gene Expression Omnibus (GEO). As a freely accessible repository with data from over 6 million biological samples across more than 4000 organisms, GEO provides diverse opportunities for secondary research. Although scientists may find assay data relevant to a given research question, most analyses require sample-level annotations. In GEO, such annotations are stored alongside assay data in delimited, text-based files. However, the structure and sem...
Source: Journal of integrative bioinformatics - December 4, 2023 Category: Bioinformatics Authors: Avery Mecham Ashlie Stephenson Badi I Quinteros Grace S Brown Stephen R Piccolo Source Type: research

Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection
J Integr Bioinform. 2023 Nov 20. doi: 10.1515/jib-2023-0013. Online ahead of print.ABSTRACTHepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogenesis, remain unclear. We hypothesized that HCV proteins might modulate the activity of aberrantly methylated HCC genes through regulatory pathways. Virus-host regulatory pathways, interactions between proteins, gene expression, transport, and stability regulation, were reconstructed using the ANDSyst...
Source: Journal of integrative bioinformatics - November 18, 2023 Category: Bioinformatics Authors: Evgeniya A Antropova Tamara M Khlebodarova Pavel S Demenkov Anastasiia R Volianskaia Artur S Venzel Nikita V Ivanisenko Alexandr D Gavrilenko Timofey V Ivanisenko Anna V Adamovskaya Polina M Revva Nikolay A Kolchanov Inna N Lavrik Vladimir A Ivanisenko Source Type: research

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder
In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI...
Source: Journal of integrative bioinformatics - November 18, 2023 Category: Bioinformatics Authors: Yulia E Uvarova Pavel S Demenkov Irina N Kuzmicheva Artur S Venzel Elena L Mischenko Timofey V Ivanisenko Vadim M Efimov Svetlana V Bannikova Asya R Vasilieva Vladimir A Ivanisenko Sergey E Peltek Source Type: research