Vishnu Dileep

Distinct effects of disease-associated TREM2 R47H/+ and T66M mutations on iPSC-derived microglia.

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.

Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.

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

High throughput genome-wide single cell protein:DNA binding site mapping by targeted insertion of promoters (TIP-seq)

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.

An integrative ENCODE resource for cancer genomics

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.

Identification of cis elements for spatio-temporal control of DNA replication

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

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

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.

Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program.

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