Srividya Ramakrishnan

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Indirect genomic effects shape cancer risk across species

This study identifies genes linked to cancer risk variation across species, showing indirect effects on body size dominate cancer suppression, while direct effects increase tumour prevalence.

A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation

The paper shows a neofunctionalized gene in Solanaceae plants became a flowering antagonist, influencing adaptation across species and environments.

Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop

This paper uses CRISPR/Cas9 to engineer compact Physalis peruviana plants to improve yield and scalability for agricultural production.

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time

The paper investigates convergent evolution of plant prickles, finding that mutations in a cytokinin gene repeatedly cause prickle loss across species.

The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.

The paper presents the genome of the Wollemi pine, revealing ancient transposon activity and insights into its conservation and evolutionary history.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Minos integrates variant calls from multiple tools to adjudicate discrepancies and jointly genotype bacterial cohorts, improving accuracy in detecting SNPs and indels.

Fast and accurate reference-guided scaffolding of draft genomes

RaGOO rapidly and accurately scaffolds draft genomes using a reference genome, achieving chromosome-scale assemblies and identifying structural variants in tomato and Arabidopsis thaliana.

The DOE Systems Biology Knowledgebase (KBase)

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

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.