Related papers: Methylator: A Modular Framework for DNA Methylatio…
Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms.…
Glioblastomas, constituting over 50% of malignant brain tumors, are highly aggressive brain tumors that pose substantial treatment challenges due to their rapid progression and resistance to standard therapies. The methylation status of the…
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…
DNA methylation datasets in cancer studies are comprised of measurements on a large number of genomic locations called cytosine-phosphate-guanine (CpG) sites with complex correlation structures. A fundamental goal of these studies is the…
evortran is a modern Fortran library designed for high-performance genetic algorithms and evolutionary optimization. evortran can be used to tackle a wide range of problems in high-energy physics and beyond, such as derivative-free…
Repetitive DNA sequences underpin genome architecture and evolutionary processes, yet they remain challenging to classify accurately. Terrier is a deep learning model designed to overcome these challenges by classifying repetitive DNA…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide…
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA…
Methane is a potent greenhouse gas and a major driver of climate change, making its timely detection critical for effective mitigation. Machine learning (ML) deployed onboard satellites can enable rapid detection while reducing downlink…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…
Virtual high throughput screening (VHTS) and machine learning (ML) have greatly accelerated the design of single-site transition-metal catalysts. VHTS of catalysts, however, is often accompanied with high calculation failure rate and wasted…
The number of studies on deep learning for medical diagnosis is expanding, and these systems are often claimed to outperform clinicians. However, only a few systems have shown medical efficacy. From this perspective, we examine a wide range…
We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of…
Hematology analyzers are essential diagnostic and monitoring tools for detecting blood diseases. Although contemporary analyzers produce only basic insights, they are often not as detailed as required under the personalized medicine…
Glioblastoma (GBM) is a highly aggressive primary brain tumor with limited therapeutic options and poor prognosis. The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a critical molecular biomarker…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
The integration of command-line tools into the Galaxy platform is crucial for making complex computational methods accessible to a broader audience and ensuring reproducible research. However, the manual development of tool wrappers is a…