Vishnu Dileep

This study compares the effects of TREM2 R47H/+ and T66M mutations on iPSC-derived microglia, finding distinct gene expression and functional changes linked to neurodegeneration.

The paper identifies that DNA double strand breaks in neurons activate immune pathways, leading to microglia activation in neurodegeneration.

This paper introduces TIP-seq, a high-throughput single-cell method for mapping DNA binding sites, achieving higher coverage and signal-to-noise than existing methods.

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

The paper measures single-cell replication timing variation using DNA copy number and finds stochastic variation is widespread and independent of known regulatory factors.