Ústav informačních systémů

Browse

Now showing 1 - 5 of 11

Comparative Analysis of DNS over HTTPS Detectors
(Elsevier, 2024-04-20) Jeřábek, Kamil; Hynek, Karel; Ryšavý, Ondřej
DNS over HTTPS (DoH) is a protocol that encrypts DNS traffic to improve user privacy and security. However, its use also poses challenges for network operators and security analysts who need to detect and monitor network traffic for security purposes. Therefore, there are multiple DoH detection proposals that leverage machine learning to identify DoH connections; however, these proposals were often tested on different datasets, and their evaluation methodologies were not consistent enough to allow direct performance comparison. In this study, seven DoH detection proposals were recreated and evaluated with six different experiments to answer research questions that targeted specific deployment scenarios concerning ML-model transferability, usability, and longevity. For thorough testing, a large Collection of DoH datasets along with a novel 5-week dataset was used, which enabled the evaluation of models’ longevity. This study provides insights into the current state of DoH detection techniques and evaluates the models in scenarios that have not been previously tested. Therefore, this paper goes beyond classical replication studies and shows previously unknown properties of seven published DoH detectors.
A computational workflow for analysis of missense mutations in precision oncology
(BMC, 2024-07-24) Khan, Rayyan; Pokorná, Petra; Štourač, Jan; Borko, Simeon; Arefiev, Ihor; Planas-Iglesias, Joan; Dobiáš, Adam; Pinto, Gaspar P.; Szotkowská, Veronika; Štěrba, Jaroslav; Slabý, Ondřej; Damborský, Jiří; Mazurenko, Stanislav; Bednář, David
Every year, more than 19 million cancer cases are diagnosed, and this number continues to increase annually. Since standard treatment options have varying success rates for different types of cancer, understanding the biology of an individual's tumour becomes crucial, especially for cases that are difficult to treat. Personalised high-throughput profiling, using next-generation sequencing, allows for a comprehensive examination of biopsy specimens. Furthermore, the widespread use of this technology has generated a wealth of information on cancer-specific gene alterations. However, there exists a significant gap between identified alterations and their proven impact on protein function. Here, we present a bioinformatics pipeline that enables fast analysis of a missense mutation's effect on stability and function in known oncogenic proteins. This pipeline is coupled with a predictor that summarises the outputs of different tools used throughout the pipeline, providing a single probability score, achieving a balanced accuracy above 86%. The pipeline incorporates a virtual screening method to suggest potential FDA/EMA-approved drugs to be considered for treatment. We showcase three case studies to demonstrate the timely utility of this pipeline. To facilitate access and analysis of cancer-related mutations, we have packaged the pipeline as a web server, which is freely available at https://loschmidt.chemi.muni.cz/predictonco/.Scientific contributionThis work presents a novel bioinformatics pipeline that integrates multiple computational tools to predict the effects of missense mutations on proteins of oncological interest. The pipeline uniquely combines fast protein modelling, stability prediction, and evolutionary analysis with virtual drug screening, while offering actionable insights for precision oncology. This comprehensive approach surpasses existing tools by automating the interpretation of mutations and suggesting potential treatments, thereby striving to bridge the gap between sequencing data and clinical application.
BenchStab: A tool for automated querying of web-based stability predictors
(Oxford University Press, 2024-09-15) Velecký, Jan; Berezný, Matej; Musil, Miloš; Damborský, Jiří; Bednář, David; Mazurenko, Stanislav
Protein design requires information about how mutations affect protein stability. Many web-based predictors are available for this purpose, yet comparing them or using them en masse is difficult. Here, we present BenchStab, a console tool/Python package for easy and quick execution of 19 predictors and result collection on a list of mutants. Moreover, the tool is easily extensible with additional predictors. We created an independent dataset derived from the FireProtDB and evaluated 24 different prediction methods.
Uncovering associations between users' behaviour and their flow experience
(TAYLOR & FRANCIS LTD, 2024-10-25) Oliveira, Wilk; Hamari, Juho; Ferreira, William; Pastushenko, Olena; Toda, Armando; Toledo Palomino, Paula; Isotani, Seiji
Flow experience is one of the most ambitious targets of any user interface designer. However, it has remained elusive to evaluate how well user interfaces give rise to flow experience outside conducting invasive self-reporting-based questionnaires, which remove the users from the flow experience and can't be massively applied. At the same time, otherwise, well-built systems do track the behaviour of users on the interface, and therefore, user behaviour data could act as a reliable proxy for assessing the experience of users. Currently, there is little empirical research or data about which indices of user behaviours might correspond with having a flow experience as well as the different psychological constituents of the flow experience. Therefore, facing the challenge of using users' behaviour data to model users' experience, we investigated the associations between users' behaviour data (e.g. mouse clicks, activity time in the system, and average response time) and their self-reported flow experience by using data mining (i.e. associations rules) analysing data from 204 subjects. Results demonstrate that the speed of users' actions negatively affects the flow experience antecedents while also positively affecting the loss of self-consciousness. Our study advances the literature, providing insights to identify users' flow experience through behaviour data.
Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO
(Elsevier, 2024-12-01) Khan, Rayyan; Pokorná, Petra; Štourač, Jan; Borko, Simeon; Dobiáš, Adam; Planas-Iglesias, Joan; Mazurenko, Stanislav; Arefiev, Ihor; Pinto, Gaspar P.; Szotkowská, Veronika; Štěrba, Jaroslav; Damborský, Jiří; Slabý, Ondřej; Bednář, David
Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of missense variants that influence oncogenic drivers. However, computational pipelines that handle biological data must integrate multiple software tools, which can add complexity and hinder nonspecialist users from accessing the pipeline. Here, we have developed an online user-friendly web server tool PredictONCO that is fully automated and has a low barrier to access. The tool models the structure of the mutant protein in the first step. Next, it calculates the protein stability change, pocket level information, evolutionary conservation, and changes in ionisation of catalytic amino acid residues, and uses them as the features in the machine-learning predictor. The XGBoost-based predictor was validated on an independent subset of held-out data, demonstrating areas under the receiver operating characteristic curve (ROC) of 0.97 and 0.94, and the average precision from the precision-recall curve of 0.99 and 0.94 for structure-based and sequence-based predictions, respectively. Finally, PredictONCO calculates the docking results of small molecules approved by regulatory authorities. We demonstrate the applicability of the tool by presenting its usage for variants in two cancer-associated proteins, cellular tumour antigen p53 and fibroblast growth factor receptor FGFR1. Our free web tool will assist with the interpretation of data from next-generation sequencing and navigate treatment strategies in clinical oncology: https://loschmidt.chemi.muni.cz/predictonco/.

Browse

Recent Submissions