Bertalan Takács

DeltaMut: An Integrative Database of AlphaFold2-Derived Missense Variant Structures

Erda Qorri, Krisztián Ádám, Bertalan Takács, Sára Shemesh et autres

Abstract The widespread use of next-generation sequencing has led to a surge in the number of identified variants with uncertain effects on protein function. These variants pose a significant challenge in diagnostics and hinder patient treatment strategies. Numerous variant effect predictors (VEPs) …

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Development of a novel metagenomic classification method

Bertalan Takács

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Assessing the impact of parental linear gene normalization on the performance of statistical models for circular RNA differential expression analysis

Erda Qorri, V Varga, Katalin Priskin, Dóra Latinovics et autres

Abstract Background Circular RNAs (circRNAs) emerged as promising non-invasive cancer biomarkers due to their stability, abundance in body fluids, and regulatory potential. However, circRNA differential expression analysis (DEA) remains challenging, largely owing to lack of consensus on important preprocessing strategies such as …

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Advancing metagenomic classification with NABAS+: a novel alignment-based approach

Bertalan Takács, Gábor Jaksa, Erda Qorri, Zoltán Gyuris et autres

Abstract Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify …

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Distinct Gut Microbiota Profiles in Unruptured and Ruptured Intracranial Aneurysms: Focus on Butyrate-Producing Bacteria

Péter Csécsei, Bertalan Takács, Lídia Pasitka, Réka Várnai et autres

Background: Gut microbiome composition may influence the risk of intracranial aneurysm rupture. Methods: This study analyzed the gut microbiota of 48 patients—24 with ruptured aneurysms (RA) and 24 with unruptured intracranial aneurysms (UIA)—using next-generation sequencing. Results: While alpha diversity was similar between …

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Abstract 6244: Comparative diversity analysis of microbial composition across tissue and fecal samples in multi-cohort, multi-study cancer analyses

Tiffany Zhang, K. M. Chan, Caitlin Guccione, Bertalan Takács et autres

Abstract The microbial ecosystems in tumors, surrounding tissues, and the gut (which influences processes throughout the body) offer new opportunities for oncology diagnostics and treatment, but inconsistencies in metadata quality and parameters across abundant public data hinder generalizable conclusions. To address these …

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Shotgun Analysis of Gut Microbiota with Body Composition and Lipid Characteristics in Crohn’s Disease

Péter Bacsúr, T Resál, B Farkas, Boldizsár Jójárt et autres

Alterations to intestinal microbiota are assumed to occur in the pathogenesis of inflammatory bowel disease (IBD). This study aims to analyze the association of fecal microbiota composition, body composition, and lipid characteristics in patients with Crohn’s disease (CD). In our cross-sectional study, …

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Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy

Gergely Imre, Bertalan Takács, Erik Czipa, Andrea Bakné Drubi et autres

DNA transposon-based gene delivery vectors represent a promising new branch of randomly integrating vector development for gene therapy. For the side-by-side evaluation of the piggyBa c and Sleeping Beauty systems—the only DNA transposons currently employed in clinical trials—during therapeutic intervention, we treated …

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Concordant or not? Performance and concordance rate analysis of ten prediction algorithms on clinically relevant variants from the BRCA1 and BRCA2 genes

Erda Qorri, Bertalan Takács, Márton Zsolt Enyedi, Alexandra B. Graf et autres

The widespread use of next-generation sequencing (NGS) technologies in clinical diagnostics has resulted in the identification of thousands of novel genomic variants whose clinical significance is uncertain. To address this issue, a variety of computational tools have been developed that facilitate the …

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A Comprehensive Evaluation of the Performance of Prediction Algorithms on Clinically Relevant Missense Variants

Erda Qorri, Bertalan Takács, Alexandra B. Graf, Márton Zsolt Enyedi et autres

The rapid integration of genomic technologies in clinical diagnostics has resulted in the detection of a multitude of missense variants whose clinical significance is often unknown. As a result, a plethora of computational tools have been developed to facilitate variant interpretation. However, …

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A Comprehensive Evaluation of the Performance of Prediction Algorithms on Clinically Relevant Missense Variants

Erda Qorri, Bertalan Takács, Alexandra B. Graf, Márton Zsolt Enyedi et autres

Benchmarking Datasets.

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