Gintaras Y. Deikus

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The paper assesses low-biomass microbiome detection in tissues using long-read sequencing, finding that genuine microbiome signals are limited to tissues with natural microbial exposure.

Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

The paper introduces HIV SMRTcap, a method for characterizing HIV-1 reservoirs by identifying integration sites and proviral integrity using long-read sequencing, and validates its performance across subtypes and tissue samples.

The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations

The paper identifies structural variants and coding polymorphisms in the human IGHC locus, revealing population-specific diversity and potential functional impacts.

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

The paper characterizes the immunoglobulin lambda chain locus in diverse populations, identifying novel alleles and highlighting limitations of short-read sequencing.

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus

The paper introduces a framework combining long-read sequencing and a new tool to fully characterize haplotype diversity in the human immunoglobulin heavy chain locus, demonstrating high accuracy and scalability.

The genome of a subterrestrial nematode reveals an evolutionary strategy for adaptation to heat

This paper reports the genome and transcriptome of the subterrestrial nematode Halicephalobus mephisto, identifying adaptations to heat stress including expanded Hsp70 genes and horizontally transferred AIG1 genes.

High-coverage, long-read sequencing of Han Chinese trio reference samples.

The paper presents high-coverage long-read sequencing data from a Han Chinese trio for developing and evaluating long-read bioinformatics methods.