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Michał Aleksander Ciach, Elissavet Zacharopoulou, Michał Piotr Startek, Błażej Miasojedow et autres
Discriminative learning framework for parameters of alignment of biological sequences
mt, pl (code pays fourni par la source)
Elissavet Zacharopoulou, Vasiliki Kotsira, Dimosthenis Tzimotoudis, Stephanie Sammut et autres
fun-miRBench is a benchmarking framework for evaluating functional microRNA (miRNA) target prediction methods using experimentally derived differential expression (DE) datasets. The benchmark compares predicted miRNA–target interactions against transcriptomic responses observed after miRNA overexpression (OE) or knockout (KO) experiments, enabling systematic assessment of …
gr, mt, es (code pays fourni par la source)
Elissavet Zacharopoulou, Vasiliki Kotsira, Dimosthenis Tzimotoudis, Stephanie Sammut et autres
fun-miRBench is a benchmarking framework for evaluating functional microRNA (miRNA) target prediction methods using experimentally derived differential expression (DE) datasets. The benchmark compares predicted miRNA–target interactions against transcriptomic responses observed after miRNA overexpression (OE) or knockout (KO) experiments, enabling systematic assessment of …
gr, mt, es (code pays fourni par la source)
Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Mark Galea et autres
MOTIVATION: Extracting knowledge from biomedical data is crucial for advancing our understanding of biological systems and developing novel therapeutics. The quantity, quality, and resolution of biomedical data constantly evolves, requiring the automation of biomedical machine learning (ML). Existing Automated ML tools lack …
mt, cz, at (code pays fourni par la source)
Elissavet Zacharopoulou, Stephanie Sammut, Dimosthenis Tzimotoudis, Vasiliki Kotsira et autres
FuNmiRBench is a benchmarking framework for evaluating functional microRNA (miRNA) target prediction methods using experimentally derived differential expression (DE) datasets. The benchmark compares predicted miRNA–target interactions against transcriptomic responses observed after miRNA overexpression (OE) or knockout (KO) experiments, enabling systematic assessment of …
gr, mt, es (code pays fourni par la source)
Michał Aleksander Ciach, Elissavet Zacharopoulou, Michał Piotr Startek, Błażej Miasojedow et autres
Abstract Pairwise alignment scores are used to classify pairs of sequences in many areas of bioinformatics, including homology search, predicting interactions, or read mapping. The relative scores of different pairs strongly depend on the choice of a substitution matrix and gap penalties, …
mt, pl (code pays fourni par la source)
Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Mark Galea et autres
Abstract Motivation Extracting knowledge from biomedical data is crucial for advancing our understanding of biological systems and developing novel therapeutics. The quantity, quality, and resolution of biomedical data constantly evolves, requiring the automation of biomedical machine learning (ML). Existing Automated ML tools …
mt, cz (code pays fourni par la source)
Elissavet Zacharopoulou, Maria D. Paraskevopoulou, Spyros Tastsoglou, Athanasios Alexiou et autres
microRNAs (miRNAs) are central post-transcriptional gene expression regulators in healthy and diseased states. Despite decades of effort, deciphering miRNA targets remains challenging, leading to an incomplete miRNA interactome and partially elucidated miRNA functions. Here, we introduce microT-CNN, an avant-garde deep convolutional neural …
gr, fr, us (code pays fourni par la source)
Steve Stavropoulos, Elissavet Zacharopoulou, Spiros V. Georgakopoulos, Sotiris K. Tasoulis et autres
The rapid growth of biomedical literature necessitates efficient Information Extraction systems able to identify relevant knowledge for various biological applications, such as understanding gene regulation by microRNA (miRNA). In this study, we employed a Large Language Model, specifically GPT-3.5 (version 0301), in …
gr (code pays fourni par la source)
Giorgos Skoufos, Panos Kakoulidis, Spyros Tastsoglou, Elissavet Zacharopoulou et autres
TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.e-ce.uth.gr/tarbasev9), it pushes the envelope by introducing virally-encoded miRNAs, interactions leading to target-directed miRNA degradation (TDMD) events …
gr, dk (code pays fourni par la source)
Spyros Tastsoglou, Athanasios Alexiou, Dimitra Karagkouni, Giorgos Skoufos et autres
DIANA-microT-CDS is a state-of-the-art miRNA target prediction algorithm catering the scientific community since 2009. It is one of the first algorithms to predict miRNA binding sites in both the 3' Untranslated Region (3'-UTR) and the coding sequence (CDS) of transcripts, with increased …
gr, us (code pays fourni par la source)
Dimitra Karagkouni, Maria D. Paraskevopoulou, Spyros Tastsoglou, Giorgos Skoufos et autres
DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to ∼240 000 unique tissue and cell type specific miRNA-lncRNA pairs. This compilation of interactions is derived …
gr (code pays fourni par la source)
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