Shamoni Maheshwari

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Unequal contribution of two paralogous centromeric histones to function the cowpea centromere

The paper investigates the functional roles of two paralogous CENH3 variants in cowpea centromeres, finding that CENH3.1 is essential for plant development and reproduction while CENH3.2 shows reduced functionality.

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression

The paper combines single cell DNA-Seq and RNA-Seq in gastric cancer to reveal subclonal genomic instability and gene expression patterns, showing evidence of tumor evolution.

Resolving sub-clonal heterogeneity within cell-line growths by single cell sequencing genomic DNA

The paper uses single-cell sequencing of genomic DNA to resolve sub-clonal heterogeneity in the COLO829 cell line, identifying four major sub-clones and explaining conflicting bulk sequencing results.

Resolving the Full Spectrum of Human Genome Variation using Linked-Reads

This paper introduces Linked-Reads as a method to comprehensively analyze genome variation, showing it can detect both small and large variants and reconstruct haplotypes more effectively than short-read sequencing.

Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

This study uses Linked-Read sequencing to assemble a high-quality, contiguous reference genome for Capsicum annuum, demonstrating its utility for complex plant genomes.