Related papers: High-Throughput SNP Genotyping by SBE/SBH
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…
One way of investigating how genes affect human traits would be with a genome-wide association study (GWAS). Genetic markers, known as single-nucleotide polymorphism (SNP), are used in GWAS. This raises privacy and security concerns as…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Genome wide association studies directly assay 10^6 single nucleotide polymorphisms (SNPs) across a study cohort. Probabilistic estimation of additional sites by genotype imputation can increase this set of variants by 10- to 40-fold. Even…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
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…
Single nucleotide polymorphisms (SNPs) are variations at specific locations in DNA. Sequence responsible for marking genes associated with diseases or tracking inherited diseases within The family. These variations in the Rb1 gene can cause…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not…
Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Spiking Neural Networks (SNNs) operate with asynchronous discrete events (or spikes) which can potentially lead to higher energy-efficiency in neuromorphic hardware implementations. Many works have shown that an SNN for inference can be…
In cancer research, profiling studies have been extensively conducted, searching for genes/SNPs associated with prognosis. Cancer is a heterogeneous disease. Examining similarity and difference in the genetic basis of multiple subtypes of…
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To…
Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…
We introduce a multiple testing procedure (TreeBH) which addresses the challenge of controlling error rates at multiple levels of resolution. Conceptually, we frame this problem as the selection of hypotheses which are organized…
Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the…
We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. The pipeline involves training deep convolutional neural networks…