Related papers: Classifying Copy Number Variations Using State Spa…
Thalassemia is a group of inherited blood disorders that happen when hemoglobin, the protein in red blood cells that carries oxygen, is not made enough. It is found all over the body and is needed for survival. If both parents have…
Thalassemia is a heritable blood disorder which is the outcome of a genetic defect causing lack of production of hemoglobin polypeptide chains. However, there is less understanding of the precise frequency as well as sharing in these areas.…
Identifying disease-indicative genes is critical for deciphering disease mechanisms and has attracted significant interest in biomedical research. Spatial transcriptomics offers unprecedented insights for the detection of disease-specific…
Tumor heterogeneity is a challenge to designing effective and targeted therapies. Glioma-type identification depends on specific molecular and histological features, which are defined by the official WHO classification CNS. These guidelines…
Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…
Thalassaemia, triggered by defects in the globin genes, is one of the most common monogenic diseases. The beta-thalassaemia carrier state is clinically asymptomatic, thus, making it onerous to diagnose. The current gold standard technique…
Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples…
Next-generation sequencing (NGS) is a key technique for studying the DNA and RNA of organisms. However, identifying quality problems in NGS data across different experimental settings remains challenging. To develop automated…
Epilepsy affects 50 million people worldwide and is one of the most common serious neurological disorders. Seizure detection and classification is a valuable tool for diagnosing and maintaining the condition. An automated classification…
Thalamic nuclei have been implicated in several neurological diseases. WMn-MPRAGE images have been shown to provide better intra-thalamic nuclear contrast compared to conventional MPRAGE images but the additional acquisition results in…
Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…
A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…
The Constrained Minimal Supersymmetric Standard Model (CMSSM) is one of the simplest and most widely-studied supersymmetric extensions to the standard model of particle physics. Nevertheless, current data do not sufficiently constrain the…
A mutation in the DNA of a single cell that compromises its function initiates leukemia,leading to the overproduction of immature white blood cells that encroach upon the space required for the generation of healthy blood cells.Leukemia is…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, inferential algorithms do not scale to available data sets. A…
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder (NDD) that is caused by genetic, epigenetic, and environmental factors. Recent advances in genomic analysis have uncovered numerous candidate genes with common…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Batch effects represent a major confounder in genomic diagnostics. In copy number variant (CNV) detection from NGS, many algorithms compare read depth between test samples and a reference sample, assuming they are process-matched. When this…
We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and…