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Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges.…
Researchers have shown significant correlations among segmented objects in various medical imaging modalities and disease related pathologies. Several studies showed that using hand crafted features for disease prediction neglects the…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
This paper describes a Bayesian statistical method for determining the genetic basis of a complex genetic trait. The method uses a sample of unrelated individuals classified into two groups, for example cases and controls. Each group is…
Detecting copy number alterations (CNAs) from next-generation sequencing data remains challenging, particularly for short segments under noisy conditions. Existing segmentation methods often suffer from high false positive rates or fail to…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions.…
Diagnosing diseases such as leukemia or anemia requires reliable counts of blood cells. Hematologists usually label and count microscopy images of blood cells manually. In many cases, however, cells in different maturity states are…
Practical application of genomic-based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-mediated illness,…
Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing…
Although melanoma occurs more rarely than several other skin cancers, patients' long term survival rate is extremely low if the diagnosis is missed. Diagnosis is complicated by a high discordance rate among pathologists when distinguishing…
Identifying genes that display spatial patterns is critical to investigating expression interactions within a spatial context and further dissecting biological understanding of complex mechanistic functionality. Despite the increase in…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the…
In our study, we introduce a novel hybrid ensemble model that synergistically combines LSTM, BiLSTM, CNN, GRU, and GloVe embeddings for the classification of gene mutations in cancer. This model was rigorously tested using Kaggle's…