Related papers: RACS: Rapid Analysis of ChIP-Seq data for contig b…
Molecular subtypes of colorectal cancer (CRC) significantly influence treatment decisions. While convolutional neural networks (CNNs) have recently been introduced for automated CRC subtype identification using H&E stained histopathological…
Purpose: As interest in CEST-MRI grows, particularly in the preclinical setting, the necessity for standardized and easy-to-use acquisition and data analysis pipelines has become apparent. While vendors have increasingly introduced support…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
Most genetic algorithms (GAs) used in literature to solve control problems are time consuming and involve important storage memory requirements. In fact, the search in GAs is iteratively performed on a population of chromosomes (control…
It has been shown that for automated PAP-smear image classification, nucleus features can be very informative. Therefore, the primary step for automated screening can be cell-nuclei detection followed by segmentation of nuclei in the…
Accurate diagnosis of spitzoid tumors (ST) is critical to ensure a favorable prognosis and to avoid both under- and over-treatment. Epigenetic data, particularly DNA methylation, provide a valuable source of information for this task.…
High-throughput cDNA sequencing (RNA-seq) is a very powerful technique to quantify gene expression in an unbiased way. The Crustacean family is among the groups of organisms sparsely represented in current genomic databases. Here we present…
Retrieval-augmented generation (RAG) has become a common strategy for updating large language model (LLM) responses with current, external information. However, models may still rely on memorized training data, bypass the retrieved…
Insertion Sequences (ISs) are small DNA segments that have the ability of moving themselves into genomes. These types of mobile genetic elements (MGEs) seem to play an essential role in genomes rearrangements and evolution of prokaryotic…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
High annotation costs are a substantial bottleneck in applying modern deep learning architectures to clinically relevant medical use cases, substantiating the need for novel algorithms to learn from unlabeled data. In this work, we propose…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
Spatial transcriptomics aims to connect high-resolution histology images with spatially resolved gene expression. To achieve better performance on downstream tasks such as gene expression prediction, large-scale pre-training is required to…
Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…
Root cause analysis (RCA) is crucial for enhancing the reliability and performance of complex systems. However, progress in this field has been hindered by the lack of large-scale, open-source datasets tailored for RCA. To bridge this gap,…
The biological processes involved in a drug's mechanisms of action are oftentimes dynamic, complex and difficult to discern. Time-course gene expression data is a rich source of information that can be used to unravel these complex…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
The deployment of reconfigurable intelligent surfaces (RISs) in a communication system provides control over the propagation environment, which facilitates the augmentation of a multitude of communication objectives. As these performance…
Classification algorithms using RNA-Sequencing (RNA-Seq) data as input are used in a variety of biological applications. By nature, RNA-Seq data is subject to uncontrolled fluctuations both within and especially across datasets, which…