相关论文: High-Throughput SNP Genotyping by SBE/SBH
Next-generation sequencing technology enables routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens.…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide…
Biometric data is often highly sensitive, and a leak of this data can lead to serious privacy breaches. Some of the most sensitive of this type of data relates to the usage of DNA data on individuals. A leak of this type of data without…
Polygenic risk scores and other genomic analyses require large individual-level genotype datasets, yet strict data access restrictions impede sharing. Synthetic genotype generation offers a privacy-preserving alternative, but most existing…
The job sequencing and tool switching problem (SSP) has been extensively studied in the field of operations research, due to its practical relevance and methodological interest. Given a machine that can load a limited amount of tools…
Studying the effects of groups of Single Nucleotide Polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases, above that which can be gleaned from studying SNPs individually. Common…
Single nucleotide polymorphism (SNP) datasets are fundamental to genetic studies but pose significant privacy risks when shared. The correlation of SNPs with each other makes strong adversarial attacks such as masked-value reconstruction,…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
Searchable symmetric encryption (SSE) has been used to protect the confidentiality of genomic data while providing substring search and range queries on a sequence of genomic data, but it has not been studied for protecting single…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
Concurrent advances across fields such as organoid technology, Microelectrode Arrays (MEAs), neuromorphic computing, and machine learning have given rise to a groundbreaking research paradigm: Synthetic Biological Intelligence (SBI). SBI…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…