Related papers: MitoFREQ: A Novel Approach for Mitogenome Frequenc…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
Advances in next-generation metagenome sequencing have the potential to revolutionize the point-of-care diagnosis of novel pathogen infections, which could help prevent potential widespread transmission of diseases. Given the high volume of…
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
Automatic subphenotyping from electronic health records (EHRs)provides numerous opportunities to understand diseases with unique subgroups and enhance personalized medicine for patients. However, existing machine learning algorithms either…
Previous statistical approaches to hierarchical clustering for social network analysis all construct an "ultrametric" hierarchy. While the assumption of ultrametricity has been discussed and studied in the phylogenetics literature, it has…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
The widespread application of machine learning techniques to biomedical data has produced many new insights into disease progression and improving clinical care. Inspired by the flexibility and interpretability of graphs (networks), as well…
Counting of mitotic figures is a fundamental step in grading and prognostication of several cancers. However, manual mitosis counting is tedious and time-consuming. In addition, variation in the appearance of mitotic figures causes a high…
The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
This study investigates the feasibility of using electrocardiogram (ECG) data combined with basic patient metadata to estimate and monitor prompt laboratory abnormalities. We use the MIMIC-IV dataset to train multimodal deep learning models…
Mitosis detection is one of the challenging problems in computational pathology, and mitotic count is an important index of cancer grading for pathologists. However, current counts of mitotic nuclei rely on pathologists looking…
Mitosis nuclei count is one of the important indicators for the pathological diagnosis of breast cancer. The manual annotation needs experienced pathologists, which is very time-consuming and inefficient. With the development of deep…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
The rapid growth of high-dimensional datasets across various scientific domains has created a pressing need for new statistical methods to compare distributions supported on their underlying structures. Assessing similarity between datasets…
Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of…
High-frequency oscillations (HFOs) in intracranial Electroencephalography (iEEG) are critical biomarkers for localizing the epileptogenic zone in epilepsy treatment. However, traditional rule-based detectors for HFOs suffer from…