Vijay Kumar

Erythrocytic plasma membrane calcium ATPase (PMCA4b) variations mediate redox imbalance to determine artemisinin sensitivity in malaria

This study shows that host PMCA4b variations affect intraerythrocytic calcium and ROS levels, reducing artemisinin sensitivity in malaria parasites.

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.

Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders

The paper shows that rare secondary mutations in functionally intolerant genes affect the expressivity of neurodevelopmental disorders in individuals with primary mutations.

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.

Mutational sequencing for accurate count and long-range assembly

The paper introduces muSeq, a protocol that uses mutational sequencing to improve count accuracy and long-range assembly from short-read data.

Direct determination of diploid genome sequences

This paper introduces a low-cost method to generate true diploid de novo genome assemblies using 10x Genomics and a new algorithm, Supernova, achieving contigs, phase blocks, and scaffolds longer than 100 kb, 2.5 Mb, and 15 Mb respectively.