Sanjit Singh Batra

The paper trains machine learning models to predict gene expression from histone PTMs using ENCODE data and validates predictions with CRISPR-Cas9-based epigenome editing experiments.

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

The paper presents high-quality genomes and chromatin structure analyses of frogs, revealing conserved ancestral chromosomes and stable genome evolution.

The paper develops HiDENSEC to analyze Hi-C data in heterogeneous cancer samples, identifying chromosomal rearrangements and their impact on melanoma progression.

This paper introduces GPN, a DNA language model that predicts genome-wide variant effects and outperforms conservation-based predictors in Arabidopsis thaliana.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

This paper presents a de novo genome assembly of the olive baboon using long-read and Hi-C data, significantly improving contig size and chromosome scaffolding compared to the previous reference genome.

The paper uses Hi-C data to improve the genome assembly of Trifolium subterraneum, resulting in chromosome-length scaffolds covering 95% of the genome.

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

Point-and-click correction of misassemblies on Hi-C heatmaps, paired with the automated 3D-DNA pipeline, gave chromosome-length wombat, opossum and raccoon scaffolds from just short-insert DNA-Seq and in situ Hi-C reads.