Genomics
A structural genetic model incorporating a modern understanding of the genome and common practice in genome-wide association studies is derived mathematically. The model shows the Haldane map distance as a direct consequence of the…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…
Genome-wide association studies (GWAS) have successfully identified a large number of genetic variants associated with traits and diseases. However, it still remains challenging to fully understand functional mechanisms underlying many…
With the advancements in Artificial intelligence (AI) and the accumulation of healthrelated big data, it has become increasingly feasible and commonplace to leverage machine learning technologies to analyze clinical and omics metadata to…
A large number of inorganic and organic compounds are able to bind DNA and form complexes, among which drug-related molecules are important. Chromatin accessibility changes not only directly affects drug-DNA interactions, but also promote…
Imaging genetic studies aim to find associations between genetic variants and imaging quantitative traits. Traditional genome-wide association studies (GWAS) are based on univariate statistical tests, but when multiple traits are analyzed…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…
Antigen-specific T cells play an essential role in immunoregulation and diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of…
The accurate prediction of biological features from genomic data is paramount for precision medicine and sustainable agriculture. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and…
We revisit the topic of human genome guanine-cytosine content under neutral evolution. For this study, the de novo mutation data within human is used to estimate mutational rate instead of using base substitution data between related…
We were interested to read the recent update on recommendations for reporting of secondary findings in clinical sequencing1, and the accompanying updated list of genes in which secondary findings should be sought (ACMG SF v3.0)2. Though the…
Metagenomic datasets from pangolin tissue specimens have previously yielded SARS-related coronaviruses which show high homology in their receptor binding domain to SARS-CoV-2, suggesting a potential zoonotic source for this feature of the…
CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to…
Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological…
Multi-trait genome-wide association studies (GWAS) use multi-variate statistical methods to identify associations between genetic variants and multiple correlated traits simultaneously, and have higher statistical power than independent…