Journal of integrative bioinformatics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.SnakeLines: integrated set of computational pipelines for sequencing reads
J Integr Bioinform. 2023 Aug 21. doi: 10.1515/jib-2022-0059. Online ahead of print.ABSTRACTWith the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We pro...
Source: Journal of integrative bioinformatics - August 21, 2023 Category: Bioinformatics Authors: Jaroslav Budi š Werner Krampl Marcel Kuchar ík Rastislav Hekel Adri án Goga Jozef Sitar čík Michal Lichv ár D ávid Smol'ak Miroslav B öhmer Andrej Bal áž Franti šek Ďuriš Juraj Gazdarica Katar ína Šoltys J án Turňa J án Radvánszky Tom Source Type: research
Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks
In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respe...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Hamed Ghazikhani Gregory Butler Source Type: research
