Gautam S. Shirsekar

Efficient and Robust Genomic DNA Isolation and Next-Generation Sequencing Library Preparation from Recalcitrant Wild Grape Species

This paper describes a protocol for isolating high-quality genomic DNA and preparing sequencing libraries from wild grape species, overcoming challenges from polyphenols and secondary metabolites.

Pangenomic context reveals the extent of intraspecific plant NLR evolution

The paper analyzes NLR gene diversity in Arabidopsis thaliana using pangenomic methods to show that multiple mutational processes contribute to NLR variation without a single metric capturing all diversity.

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

Atlas of telomeric repeat diversity in Arabidopsis thaliana

The paper characterizes telomeric repeat diversity in 49 Arabidopsis thaliana accessions, revealing repeat unit types, evolutionary processes, and haplotype patterns.

vcf2gwas - Python API for comprehensive GWAS analysis using GEMMA

vcf2gwas streamlines GWAS analysis by integrating GEMMA, bcftools, and PLINK into a Python API, reducing workflow complexity and effort.

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

The paper combines shotgun sequencing and rDNA amplicon data to improve detection of microbe-microbe interaction networks in plant leaves by addressing compositionality issues in amplicon data.