Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.

Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification.

Inference of mutability landscapes of tumors from single cell sequencing data.

One of the hallmarks of cancer is the extremely high mutability and genetic instability of tumor cells. Inherent heterogeneity of intra-tumor populations manifests itself in high variability of clone instability rates. Analogously to fitness landscapes, the instability rates of clonal populations form their mutability landscapes.

Inference of clonal selection in cancer populations using single-cell sequencing data.

Summary: Intra-tumor heterogeneity is one of the major factors influencing cancer progression and treatment outcome. However, evolutionary dynamics of cancer clone populations remain poorly understood. Quantification of clonal selection and inference of fitness landscapes of tumors is a key step to understanding evolutionary mechanisms driving cancer.

Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits.

Lyme disease (LD), the most prevalent vector-borne illness in the United States and Europe, is caused by No vaccine is available for humans. Dogmatically, can establish a persistent infection in the mammalian host (e.g.

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.

Background: Many biological analysis tasks require extraction of families of genetically similar sequences from large datasets produced by Next-generation Sequencing (NGS). Such tasks include detection of viral transmissions by analysis of all genetically close pairs of sequences from viral datasets sampled from infected individuals or studying of evolution of viruses or immune repertoires by analysis of network of intra-host viral variants or antibody clonotypes formed by genetically close sequences. The most obvious naïeve algorithms to extract such sequence families are impractical in light of the massive size of modern NGS datasets.