Nivesh Jain

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

This study investigates speciation in boobies through genomic analysis, finding introgression, divergence patterns, and a neo-sex chromosome linked to coloration diversity.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

The paper identifies genomic and transcriptomic changes associated with chromosomal instability and seasonal brain size plasticity in the Eurasian common shrew.

The paper presents the first chromosome-level genome assembly of the Brazilian merganser, revealing genomic features and population history insights.

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

The paper presents haplotype-resolved genomes for five sea turtle species, revealing conserved synteny and divergence hotspots linked to immune and sensory genes, and population expansion during the Pleistocene.

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.