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Bone marrow cytology is required to make a hematological diagnosis, influencing critical clinical decision points in hematology. However, bone marrow cytology is tedious, limited to experienced reference centers and associated with high…
Gene Regulatory Networks (GRNs) are intricate biological systems that control gene expression and regulation in response to environmental and developmental cues. Advances in computational biology, coupled with high throughput sequencing…
DNA methylation is a crucial regulator of gene transcription and has been linked to various diseases, including autoimmune diseases and cancers. However, diagnostics based on DNA methylation face challenges due to large feature sets and…
The identification of reproducible biological patterns from high-dimensional data is a bottleneck for understanding the biology of complex illnesses such as schizophrenia. To address this, we developed a biologically informed, multi-stage…
In many real-world scientific problems, generating ground truth (GT) for supervised learning is almost impossible. The causes include limitations imposed by scientific instrument, physical phenomenon itself, or the complexity of modeling.…
We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules…
MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
The scientific study of the Solar System's minor bodies ultimately starts with a search for those bodies. This chapter presents a review of the use of machine learning techniques to find moving objects, both natural and artificial, in…
Knowing the type (i.e., the biochemical composition) of kidney stones is crucial to prevent relapses with an appropriate treatment. During ureteroscopies, kidney stones are fragmented, extracted from the urinary tract, and their composition…
To test the effectiveness of process discovery algorithms, a Process Discovery Contest (PDC) has been set up. This PDC uses a classification approach to measure this effectiveness: The better the discovered model can classify whether or not…
Quantitative computed tomography (QCT) is a widely used tool for osteoporosis diagnosis and monitoring. The assessment of cortical markers like cortical bone mineral density (BMD) and thickness is a demanding task, mainly because of the…
Vertebrae identification in arbitrary fields-of-view plays a crucial role in diagnosing spine disease. Most spine CT contain only local regions, such as the neck, chest, and abdomen. Therefore, identification should not depend on specific…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning…
We introduce a machine learning-based method for fully automated diagnosis of sickle cell disease of poor-quality unstained images of a mobile microscope. Our method is capable of distinguishing between diseased, trait (carrier), and normal…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Diagnosing knee osteoarthritis (OA) early is crucial for managing symptoms and preventing further joint damage, ultimately improving patient outcomes and quality of life. In this paper, a bioimpedance-based diagnostic tool that combines…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…