Singh Decodes Omics

Dr. Nikhil Kumar Singh, PhD

DST-INSPIRE Faculty | Genomics, Bioinformatics & Fungal Evolution
ICAR-Indian Institute of Agricultural Biotechnology, Ranchi
niksingh29@gmail.com

I am a computational biologist. I have over 7 years of international research experience. My expertise lies in genome biology, population genetics, and multi-omics integration. I’ve worked in Switzerland, Germany, and India. The projects ranged from genome assembly to transcriptome profiling. I also worked on GWAS and variant interpretation.

Present Research Areas

1. Population Genomics and Pathogen Evolution

My research explores how fungal plant pathogens evolve across time and space by applying population genomics. I focus on mapping genetic diversity, identifying adaptive mutations, and understanding the reproduction modes (clonal vs. sexual) that shape pathogen populations. Using large-scale field sampling and genome resequencing, I trace the evolutionary trajectory of pathogens like Ustilaginoidea virens, linking genotype to phenotype—such as virulence and fungicide resistance. This helps reveal how rapidly evolving fungal pathogens adapt to different agroecological conditions and host genotypes.

2. Comparative Genomics and Genome Architecture

I investigate the structural and functional variation in fungal genomes with a particular focus on transposable elements (TEs), chromosomal rearrangements, and gene family expansions. By comparing high-quality genomes across isolates and species, I identify lineage-specific adaptations and evolutionary signatures, including genome compartmentalisation and the presence of “two-speed genomes” My work reveals how TEs not only shape genome plasticity but also contribute to virulence by influencing effector gene dynamics and regulatory networks.

3. Functional Genomics for Crop Disease Management

Combining experimental assays with computational pipelines, I connect genomic data to phenotypic traits through genome-wide association studies (GWAS) and transcriptomics. I phenotype fungal isolates for key traits like virulence and fungicide tolerance, and link them to genomic loci under selection. This integrative approach facilitates the discovery of molecular markers and candidate genes associated with pathogenicity. Ultimately, these insights support the development of disease-resistant crop varieties and help inform sustainable plant protection strategies.